diff --git a/LICENSE.md b/LICENSE.md new file mode 100644 index 00000000..75596a51 --- /dev/null +++ b/LICENSE.md @@ -0,0 +1,63 @@ +# Licenses + +## Instructional Material + +All Common Workflow Language project instructional material and changes +to the structure are also made available under the [Creative Commons Attribution +license][cc-by-human]. The following is a human-readable summary of +(and not a substitute for) the [full legal text of the CC BY 4.0 +license][cc-by-legal]. + +You are free: + +* to **Share**---copy and redistribute the material in any medium or format +* to **Adapt**---remix, transform, and build upon the material + +for any purpose, even commercially. + +The licensor cannot revoke these freedoms as long as you follow the +license terms: + + + +* **Attribution**---You must give appropriate credit (mentioning that + your work is derived from work that is Copyright © the Common Workflow + Language project, and, where practical, linking to + https://www.commonwl.org/ ), provide a [link to the + license][cc-by-human], and indicate if changes were made. You may do + so in any reasonable manner, but not in any way that suggests the + licensor endorses you or your use. + +* **No additional restrictions**---You may not apply legal terms or +technological measures that legally restrict others from doing +anything the license permits. With the understanding that: + + * You do not have to comply with the license for elements of the + material in the public domain or where your use is permitted by an + applicable exception or limitation. + * No warranties are given. The license may not give you all of the + permissions necessary for your intended use. For example, other + rights such as publicity, privacy, or moral rights may limit how you + use the material. + +## Software + +Except where otherwise noted, the example programs and other software +provided by Common Workflow Language project are made available under the +[OSI][osi]-approved +[Apache 2.0 license][apache-2.0-license]. + +Unless required by applicable law or agreed to in writing, software +distributed under the License is distributed on an "AS IS" BASIS, +WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +See the License for the specific language governing permissions and +limitations under the License. + + + + +[cc-by-human]: https://creativecommons.org/licenses/by/4.0/ +[cc-by-legal]: https://creativecommons.org/licenses/by/4.0/legalcode +[apache-2.0-license]: https://opensource.org/licenses/Apache-2.0 +[mit-license]: https://opensource.org/licenses/mit-license.html +[osi]: https://opensource.org diff --git a/LICENSE.rst b/LICENSE.rst deleted file mode 100644 index cc6a19b0..00000000 --- a/LICENSE.rst +++ /dev/null @@ -1,59 +0,0 @@ -Licenses -======== - -Instructional Material ----------------------- - -All Common Workflow Language project instructional material and changes -to the structure are also made available under the `Creative Commons -Attribution license `_. The following is a human-readable summary of (and -not a substitute for) the `full legal text of the CC BY 4.0 license `_. - -You are free: - -- to **Share**—copy and redistribute the material in any medium or - format -- to **Adapt**—remix, transform, and build upon the material - -for any purpose, even commercially. - -The licensor cannot revoke these freedoms as long as you follow the -license terms: - -- **Attribution**—You must give appropriate credit (mentioning that - your work is derived from work that is Copyright © the Common - Workflow Language project, and, where practical, linking to - https://www.commonwl.org/ ), provide a `link to the license `_, and - indicate if changes were made. You may do so in any reasonable - manner, but not in any way that suggests the licensor endorses you or - your use. - -- **No additional restrictions**—You may not apply legal terms or - technological measures that legally restrict others from doing - anything the license permits. With the understanding that: - - - You do not have to comply with the license for elements of the - material in the public domain or where your use is permitted by an - applicable exception or limitation. - - No warranties are given. The license may not give you all of the - permissions necessary for your intended use. For example, other - rights such as publicity, privacy, or moral rights may limit how - you use the material. - -Software --------- - -Except where otherwise noted, the example programs and other software -provided by Common Workflow Language project are made available under -the `OSI`_-approved `Apache 2.0 license `_. - -Unless required by applicable law or agreed to in writing, software -distributed under the License is distributed on an “AS IS” BASIS, -WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. -See the License for the specific language governing permissions and -limitations under the License. - -.. _cc-by-human: https://creativecommons.org/licenses/by/4.0/ -.. _cc-by-legal: https://creativecommons.org/licenses/by/4.0/legalcode -.. _OSI: https://opensource.org -.. _Apache-2.0: https://opensource.org/licenses/Apache-2.0 diff --git a/Makefile b/Makefile index 81bc3c77..83ba9e13 100644 --- a/Makefile +++ b/Makefile @@ -3,7 +3,7 @@ # You can set these variables from the command line, and also # from the environment for the first two. -SPHINXOPTS = "-W" +SPHINXOPTS = "" # was "-W" (turn warnings into errors) SPHINXBUILD = sphinx-build SOURCEDIR = src BUILDDIR = _build diff --git a/locales/es/LC_MESSAGES/user_guide.po b/locales/es/LC_MESSAGES/user_guide.po index 523946d0..ba080ed4 100644 --- a/locales/es/LC_MESSAGES/user_guide.po +++ b/locales/es/LC_MESSAGES/user_guide.po @@ -9,124 +9,149 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 17:03+0100\n" +"POT-Creation-Date: 2023-01-24 19:53+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" +"Language-Team: Spanish \n" "Language: es\n" -"Language-Team: Spanish \n" -"Plural-Forms: nplurals=2; plural=n != 1;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=2; plural=n != 1;\n" +"X-Generator: Weblate 4.16-dev\n" "Generated-By: Babel 2.10.3\n" -#: ../../LICENSE.rst:2 dcdc2e8da0ec4d9e9453601fdd83bac5 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "Licencias" -#: ../../LICENSE.rst:5 3e165520ca56481b8f8d494a8d471de3 +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "Material didáctico" -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d msgid "" "All Common Workflow Language project instructional material and changes " -"to the structure are also made available under the `Creative Commons " -"Attribution license `_. The following is a human-readable " -"summary of (and not a substitute for) the `full legal text of the CC BY " -"4.0 license `_." +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo el material instructivo del proyecto Common Workflow Language y los " -"cambios en la estructura también están disponibles bajo la `licencia " -"Creative Commons Attribution `_. Lo que sigue es un resumen" -" legible por humanos (y no un sustituto) del `texto legal completo de la " -"licencia CC BY 4.0 `_." +"cambios en la estructura también están disponibles bajo la [licencia " +"Creative Commons Attribution][cc-by-human]. Lo que sigue es un resumen " +"legible por humanos (y no un sustituto) del [texto legal completo de la " +"licencia CC BY 4.0][cc-by-legal]." -#: ../../LICENSE.rst:12 b7a7a0fb40344fe087c1cc3ec19308aa +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "Usted es libre de:" -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -"**Compartir**—copiar y redistribuir el material en cualquier medio o " +"**Compartir**---copiar y redistribuir el material en cualquier medio o " "formato" -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remezclar, transformar y construir a partir del material" +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remezclar, transformar y construir a partir del material" -#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "para cualquier propósito, incluso comercialmente." -#: ../../LICENSE.rst:20 8bc6672f4a33428296226112a1be6fbe -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "La licenciante no puede revocar estas libertades en tanto usted siga los " "términos de la licencia." -#: ../../LICENSE.rst:23 be38276e7b374f57b9997391bf898a62 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" -"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su" -" trabajo se deriva de un trabajo que tiene «Copyright © The Common " -"Workflow Language Project» y, cuando sea práctico, con un enlace a " -"https://www.commonwl.org/ ), brindar un `enlace a la licencia `_, e indicar si se han realizado cambios. Puede hacerlo en " -"cualquier forma razonable, pero no de forma tal que sugiera que usted o " -"su uso tienen el apoyo de la licenciante." +"Atribución — Usted debe dar crédito de manera adecuada(mencionando que su " +"trabajo se deriva de un trabajo que tiene «Copyright © The Common Workflow " +"Language Project» y, cuando sea práctico, con un enlace a https://www." +"commonwl.org/ ), brindar un [enlace a la licencia][cc-by-human], e indicar " +"si se han realizado cambios. Puede hacerlo en cualquier forma razonable, " +"pero no de forma tal que sugiera que usted o su uso tienen el apoyo de la " +"licenciante." -#: ../../LICENSE.rst:31 f00d5c3846034c2ea116c2f74786d9fc -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**No hay restricciones adicionales**---No puede aplicar términos legales " -"ni medidas tecnológicas que restrinjan legalmente a otras a hacer " -"cualquier uso permitido por la licencia. Con el entendimiento de que:" +"**No hay restricciones adicionales**---No puede aplicar términos legales ni " +"medidas tecnológicas que restrinjan legalmente a otras a hacer cualquier uso " +"permitido por la licencia. Con el entendimiento de que:" -#: ../../LICENSE.rst:35 1798d65c10104040923c2fea2199bab2 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "No tiene que cumplir con la licencia para elementos del materiale en el " "dominio público o cuando su uso esté permitido por una excepción o " "limitación aplicable." -#: ../../LICENSE.rst:38 c65198b804f8436ba783643d51bc72d9 -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "No se dan garantías. La licencia podría no darle todos los permisos que " -"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como" -" publicidad, privacidad, o derechos morales pueden limitar la forma en " -"que utilice el material." +"necesita para el uso que tenga previsto. Por ejemplo, otros derechos como " +"publicidad, privacidad, o derechos morales pueden limitar la forma en que " +"utilice el material." -#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "Software" -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 msgid "" "Except where otherwise noted, the example programs and other software " "provided by Common Workflow Language project are made available under the" -" `OSI`_-approved `Apache 2.0 license `_." +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Excepto cuando se indique lo contrario, los programas de ejemplo y otro " "software proporcionado por el proyecto Common Workflow Language están " -"disponibles bajo la `licencia Apache 2.0 `_ aprobada por la " -"`OSI`_." +"disponibles bajo la [licencia Apache 2.0][apache-2.0-license] aprobada por " +"la [OSI][Osi]." -#: ../../LICENSE.rst:50 4ee4d68b90fe422880da856cd539b982 +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" -" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" -" License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" +"Unless required by applicable law or agreed to in writing, software " +"distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT " +"WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the " +"License for the specific language governing permissions and limitations " +"under the License." #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 271049c39d294b11b9bd94cb6be2857f 61af90891e2d4542b5f45fb3ec6480af -#: bf309fa01bed4355bf052ae4afbf9a67 +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -135,30 +160,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 055f0e960450410585b59760ef3ad284 6294af2e32e04207a87399c7f0780011 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 6428125fc43c43bba8518ece2f5d150f +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 ce8fade1e88e4b03ac0d3fc71d16f844 +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 9e7483b53a984b689964c69afcaa7123 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 8c5a89257ef248cd99cba303713e5082 +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 9e80d8eeefcf4a9d95fd5fe9d9fa124a +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -166,94 +191,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 c2e5f62490f940aab19166403a840597 +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 ffcffabdf25a4c398e8e53bc817ea769 +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 c8a6b85cfca542ccb042a0269294e5e3 +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 98f583e5e36941c1856d719a16e58e4a +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fb9cac0954474b5284793330b7424949 +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 cc45d609de1f423db86d58eea933e132 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 27ee63895cb14321a1814f4372d3180f +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 f1c841980f3d4364a2158a4eb2f0d257 +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 6d53d38ddcf244fb997db37eae7fcf90 +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 b6d60d66f3744ab3aea1b175ecb23d4a +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 cf4fa3ae602841d393b4143e9f6f5e82 +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 41a3c9aa55c5406f9b52af2243c79ccc +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 3b8eb247425a4a708f51c08cf258e30a +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 388a6e091a054dc48afc928f46dac7b7 +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 28c59d12156e44ea833822fd3ecaf824 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 8267843ff5c940c590b10047455f2102 +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 6e6f55bc915e4cceb8e360544d6b4ae5 +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 1bc80953bd60405082a10a7798c1413d +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -261,22 +286,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 a6cd4bf4dc314e66a951f7f1227c7bb7 +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 7ab2440a92aa44b09e8a324cd67ca728 +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 152a529dfa2c42c1b6f0083589fa5aeb +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 b278c137167d4b958c099c0509edb79c +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -285,25 +310,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 f0b38723838f479d9db8eb5142d28a1e +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 fc1e4a808e85422cbb4d128c5a1f4d0c +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 d74964c9d19241848f4dd92a201e201f +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 859b8e18e05a4c3285fb20bbb44c1ed4 +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 eb6e932924a54afd9114c629b2d0e93b +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -311,26 +336,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 31d70b41ddf042f6aa530b7bd6daae73 +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 9aa3ff8c957b42c8a30f37167a8177fd +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 777ac7f6bde2470b981efc91feb01c81 +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 8647071efc0548a1807c03fe8a4ee54c +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 4404233183124085990c44793a6b25f6 +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -339,77 +364,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 c5eecacfa07f47649f07ef9d888f4c5e +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 1efef04061fd48f1ab39a99508b5bc0b +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 57e8ace8e8d64e7a90510e1ccea69612 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 138606e8d7be40bb960f278977f9107f +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 d0f668dc78464469a9f2bfc61a90aa76 +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 f2a49a7663e1456cac6b2eac0c46c662 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 eefe4adebdba4063af0cac3ab5d46442 +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 526f2816123a43ecbcf09c46904b4b5f +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 0ecf267c5f4d4557ad0d7ddef2f4b5e6 +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 935a253376854d12928f00c2870ed4c0 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 bc6c0bf679ae48e7822add7ab2cda220 +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 a63643806a2a4eee8ebd3502fd6ce2b5 +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 fc54964adcd648948d7baff02f47598e +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 aabc495306a149fdb15835ae1df93c42 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 2930faead8be45a6b9adbf51dcdfef6e +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 f885e4716a8d4de0b25d2d3356789672 +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 6487ff3c19c944eb8257b2cf60d0aac7 +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -418,11 +443,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 4cbacce539ce4f6cb5bb8ccf1574640c +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 27321576de714cd5b82c67f59b2e3e6f +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -433,22 +458,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 6afded7ba21247099c9bfcedf40c9171 +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 17c386e7cd25496784207140f9876b90 +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 3bfd9bcf826a4400935dfad338612b12 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 4b38f1439da44ebb967b5b1e3df8f78a +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -457,11 +482,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 a4a60a8d010448b0b8ad1e05cbc78f2b +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 e23e00e89c81410ba8381fd81bc73b3c +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -469,7 +494,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 7274d92e678a440eb0d3ae3109f4157a +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -477,15 +502,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 6ad5f2d254a24ac1b3faf382d08b58aa +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 7208cbccb84d45d58c7d5becec74b7d3 +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 8b9809abb49840b195a89943ba15f78a +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -496,18 +521,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 9a934bf0848b438aaef7c4f00e0f2901 +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 5a299600dc304fd886b7153de1a706f7 +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 55f7696f07d64277ad1b39d283175b37 +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -517,18 +542,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 b854ca0af98347d2b66e74754eb92a50 +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d9785269c51e4902bf3a70e917d33238 +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 b57a31b8d26545d1823fcd1fa2c83316 +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -537,24 +562,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 4e264b1a40bd4935abb5bdeb75fa5c64 +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 791b02bb1ee6459d8d8332fc2dee353c +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 17300bbe695044e7b8917d23bd0aa597 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: 526614f195614818a614fc9a576e7cb5 +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -563,39 +588,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 7b47991653054f2d9f49a91720754abf +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: aa8838c0ee0a4b4285cb1b5dc6eb5d31 +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: 457c73a37cb143d98005ebf6e67f5bf1 +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c28057f3b7814f8395dbc3ad54d5f6f9 +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 83afed0785cd4b0bb86863c2841ce982 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: f332864bcc1e49d582a82f3d721ff3cf +#: cf2922f645904ac7955428ecddc37b8a msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: 3005c6d669de412ab7f8e30d00752a20 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -604,7 +629,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: 2e4041cb402e4054a53ea5890b938ac1 +#: f6f589481d0c4891beaccb63160619ef msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -613,7 +638,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: 972f9a1e64394a63be3258d3af0b1d79 +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -623,7 +648,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: a572f0789084402fb2d216ac845bbfdb +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -632,24 +657,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: c7c5c9a1e98e47c0a5a6dfa69e96f921 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: 357d42768e794286bf5463ca5850a7ed +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 61966aab989744c1b9b93f7751f35ebc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: e14a2082d2c44f3690a07d3cee5b13d1 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -659,7 +684,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: c128a76992e04d20bcc3edae8b6c0bc0 +#: e4643938445b48cc80eb8973ceeb126e msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -668,12 +693,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 42953a3d591c48c6b4e80e9ea4b97bb3 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: e3762a763ba24571a9627efafe172441 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -687,7 +712,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: be8e01a012ed45d6b7e4e6aab1afcc32 +#: 074af9633627470485e5225326d5f20a msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -696,7 +721,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: cf31aca4294d486cb0e25c6436996d17 +#: 847951c055b94a83b1e081594cef22ee msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -705,71 +730,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: cc7adbdc66df4aeaad1429f7268c90c0 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 71beb059c9e54a9ab5430f0dc44e07ea -#: 84679c5b03a3469294de849d9abe0a82 fd690fdd46344e0e8d9fc546f6d4013b +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 89ddaddb64f64b0c86c7e89da0edfaae +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: e920a824207746ffae63242d33137ac7 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 51d619152aa44651889ff2006c8f5800 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 88f3f5dd8aa6401793b89e8de3b8c7a7 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: f1f9ee90d07c4381a8bb0851bdac231e +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: e3b710dabec2482d8ec1072d64d4e1f8 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 418699fcb6c241dcbeeed81d82e9f84f +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 28b6521a55aa4ab190ca998a59c52609 +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 0e4969399eda48b98d883a3fc1540633 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 6d59f082157b494ebcfff2f649abc524 +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -779,11 +804,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 2b83beccbc1b43969b705156b9c29482 +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 594fe5e0aaf0499ebfa9218aaad4d08d +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -791,29 +816,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 f69c7c75a36048f5af0ed1b56df9320d +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 f28638ffb8394ccead4ac52f30adc627 +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 8993d7d5c8d24fc5a9c7005800c0a1f1 +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 2073109799e748d68304f5558c82b105 +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 9fb2c31bd36d495786397c7a7d6b3417 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 43e1957537034c5886574118fc2533da +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -823,11 +848,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 e3a3d9b94b1e44c48f298dfcdcd27104 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 8a385803ed3945ff81d38a3543a69d94 +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -835,7 +860,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 bf56727d93994d3995b0af0c68c2c583 +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -843,26 +868,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 9a959bd914d543b78f9625f03df95765 +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 198ce7d893a04fcb806ec1671838d588 +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 cc2be8feeab54a22a0b64a2a72991003 +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 749c672e8c234c1c9a5eb2cc9b77c4e3 +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 29c64936318a4a2ba882e1eae8f03f57 +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -873,23 +898,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 44106744147f45bab675eb66148531c7 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 6d84c6890f564b4baf7b34f6a52cbfc4 +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 7eb67993e8ca48dc929e1a992f78cb39 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 52886c54c3c54b83896c52ebd7d53fad +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 097945c33f7542e2bae2e9f7ba1cf84d +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -900,32 +925,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 3853bfc6a85747019c615a50c7ca6b40 +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 662230f538504f44941c6f4801f6251c +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 1c9eb9e2bb9e40a9985ada16c34eea2d +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 7f53ba159979461393c0f278fe97fb30 +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 7e8077c2dd584eda89ead60ecc5eabf3 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 1787a3c749ee48218b87c8401f6255d7 +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -933,30 +958,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 a52ca4ce9a184e938c3a5cac9cb882ca +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 41d3287a9a774a73aefd49bd709764bf +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 3b9d30094611400b85b55db163cb303e +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 b6ea77357b4f45528ed1379f8fe67cfd +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 8797ce327d7443fdb3d4617d3fc2cf7f +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 896b6896b1e44d0cab5f35e7d0dd88e3 +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -966,47 +991,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 4b839d23d72f4d3fbe4f1ce7e568b20b +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 a42b9ab315b5402493e4ce0067d0a18e +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 2f63483960634a7782f95e9e2feaa5a6 +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 3471105073204d7998aaf790b73f785d +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 0b8b47511b5e4296b7438be0ad2604ed +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 3e3eec00f23f4f21873ddb005204a875 +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 2ceb25f2668442839e3e9f4512772a03 +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 20c753c5371b43ed834fa741b0ce7692 +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1014,7 +1039,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 a19c4fc9fa404912a0389337536d9c25 +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1022,57 +1047,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 a0f38c1e28ca4850b3986617625acbf2 +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 37e1162f30894a1ca7dada9870ffa3da +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 1c25a51edf6f47c5979c721b19cf11b5 +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 ace930cf878d45a99f12b71bf0987a87 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 46587a5e0d534af5867ae4f70a116bee +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 a0774d4e779e46f7a983922425203066 +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 1658ee6f3cac4d04afc732aa758b1f48 +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 d8e2bc671b894f3fa8a091261754c728 +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 683a469bf4824c64a8ea32e048d5df73 +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 b7c50413f7864a86815f3b581561cdb5 +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1080,11 +1105,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 d2ed66bdfcab4f7dad95b00c95d4a3d6 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 4dcbe776a70645e5a6c7513348fa6bee +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1092,11 +1117,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 bae5b03fb74541e6ad79277a576e0516 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 8ff0d7a8d37b48488e4504ff8e3adcc5 +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1104,32 +1129,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 6255b499b9b144128afaeed64fabe8e5 +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e861db9c43ed4b8ba262af8e435a350a +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 c6318f06bcd74cda8c1f0caef9452b51 +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 c862e745217244d28cd4c2f0842e203f +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 eba007736b92434a9711f683e64bb153 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 aebc2caf5d1b47f1b7cc0aa53e5a684e +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1137,21 +1162,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 1242171f8b854562bb7848b06d2d065d +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 24e82ecf7926428386a89f18a34eb00c +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 00e75efe03554835bc33ebaed0652626 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 4ba34ec455704844a9cfcbac3522ea0c +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1159,46 +1184,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 c0e9673440db454bb51af04432aeddbb +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 39a23a9d02ab4bccb36d6a714639509b +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 23a878e0166b40d78984a2263f63b760 +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 5d9c435820674bf4b1c5d3fef5df736d +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 e724ee53db1940b9b09a909f4db531a4 +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 7820eb801a8145feb603145f153263b9 +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 e8db3f10be294f13abe3a4418bbae4b6 +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 95211ea6924148a6a1fa5ae8facc2c7b +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1206,19 +1231,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: b742a74d586e42e6b0480b7af3e49c9e +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: cd3da03d43044ec9843e476a54e704be +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: 0d48e2f07d784504a17cad0ae20262c2 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1229,37 +1254,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 4d372b89f0ce451db2a505b1754b8356 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 573e903ef3d34514ab7b20e79c446567 -#: cfb40fbe52174d3799a6bec175db60a5 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 95841b1c75c84f01bd5fcb7cf3afe78d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: c8bca3654ebb4b29bf3f028b4c65fa35 +#: 9643449da1da46d7861866dce490cbcb msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: 1432105e38014a6d9d0cf80007141007 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: bcad473b34ec43f7906253123a1661fa +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1270,11 +1295,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 e1c8949e663b4debaf87735f1d62a2fc +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 dcc991b647d34ffc8ea3bf9c3a38258d +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1282,13 +1307,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 f26c222638e54187b8bb62fe30b66bc3 +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 23720e4ab3d1407597f1d1c2a4d4d90c +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1304,7 +1329,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 b3638183c59744c897246af7dab5d10e +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1314,43 +1339,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 2c0291133b964ad8b751f8a8ed2338fc +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 325c8c4058f045aa8fbd705238122798 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 05333866485b43479352f7ee9326c7fd +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 f8140ec6e9cc41ee88ec4bde61a44d47 +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 1d68f50dafaf4cc1851e2d67b3e78603 +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 b283942434c54456a3f29fbb0960b6c4 +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 0b4477c5b0184e59aa0c07161008a7bf +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1358,13 +1383,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 9741651d51f249ffba1820694ab78e92 +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 5e76d4a9708244ff91f2587350d684a4 +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1376,44 +1401,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 89e7028e55b54f968e87b9c1c3caeecf +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 88e2338fb2614ef29dc497d8c01a2f2f +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 0f3aad35924344659eb5a6719ab2b8f0 +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 877cbb1d537b46d3b6d05b2d8c025e70 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 5c0debbc1c1b428ebb32b589b99fe17d +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 1ff97183191240edb98f0cc365cc028b +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 22f7725deb07422fa0a7bc2e6f01e4d0 +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1421,31 +1446,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 982313839ccc4f5a8527fe9a854c78eb +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 267c9d10ab5e4b6c8a6104952deb1690 +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 2eff0eec58c94f4d8986a4cb91b14b8e +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 f38db701740b442c89ce58e937bd35c5 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 034aac9e186645e384c28bb2a739cfff +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1453,52 +1478,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 5f835cdfc0ae4f378d8dad6ae7ab1855 +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 02900cb8ae4c4da89d264b76a984d6cd +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 753e48d6dfd54a88a12773b996f182d7 +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 c7ed6d1654c54bf390e933ef0f847b99 +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 0a0f855ce34449a0a37c036105c65839 +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 c4300454f49548f49e4bd186192515a1 +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 f985d58070de4c0fb5f5a491fd4dc31c +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 2f4e2c85677a4e56a35b6bef36d67334 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 13c6d5600a30406c81ffa25ce42eb0c8 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1507,17 +1532,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: 3bf773b8560e44a3a37c68b6fcdc6a23 +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 68b8578d2f6442929941ed2522b218ad +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 755149ed46c348c2b723b49c3b3152a8 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1525,7 +1550,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: 54b7ff590d52454eb87d9f23fca44501 +#: 9454a330b9324744b89448f2694b1b03 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1535,7 +1560,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a7c74a4a74c9414e9f29fa20bab7e295 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1543,13 +1568,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 0cbf233379024800bcebb963e0a3eb6f ae3bc02e4f3b404c89f3c461a62c5bc4 -#: dc32a2bacf2d4c8cb841be6eb8b839ad +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 34a56bc23af44353a003ee295fb2c609 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1557,7 +1582,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: c7855ec1f09d4945afcb0aec22567b31 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1569,7 +1594,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: 5c60492e27014735bb9a86307ee654d6 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1579,19 +1604,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 80a9c04358e64ca28ef4879ad74ef733 a2b470f06ad94871970b7d95339fd369 -#: dc65b4b5e48e48a6ada03da0fac18a51 ea2360c5286b43ccabac202dfa97fbe7 -#: ee4ca94dadf64ab69a70b6cd4eaf451a +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 285d23ef9bbc46c9890ae7957d487c12 +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 3edd322daad940d8957f88a2637876b5 +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1600,21 +1625,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 a1bd9b0dfa234e6caa6a684e981d89b5 +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 0aeacb6ac20f4ebca3600425ca32f5f4 +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 1c813ebce2904f008b5b33656f673ebc +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 cc36359e94c841d3aa5cbb26a094e1d5 +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1623,13 +1648,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 dc79668b05e8439591a0beb4b57acc66 +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 08aba4f77aa442d4a34aa1535f78c49e +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1640,15 +1665,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 63431a972f994bccacf55d5fac0d614e +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 55e7695aca4f4319b1cf7551105a8782 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 0c5ab34ebbf54ff6940b8ce3f080d744 +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1656,7 +1681,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 f97e18d2d3b946468c4fac227920e011 +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1666,26 +1691,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 62644031403548898ff36addbc0b1f6f +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 595630b0687c4467aa65bfed289281f4 +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 34e005c135864a89a00e817d79118e2e +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 b624f9f99c294e6996f212c8b62f20b0 +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 14df63ab847e4efca820f712548cd076 +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1693,32 +1718,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 91d4224b41c6473f936c03bd0ab9d370 +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 519989399dab493ea41941ed85cb9670 +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 28dd1cf24309404eaf717d417272e094 +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 3f536ad8c86d442c8bbe61777dbb1a54 +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 b9e9894c6d024e60929d020dbaa553f0 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 482debe1a40f490b90d4ece1b3f9d732 +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1726,7 +1751,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 708346038be745d097685970cc462f4a +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1735,67 +1760,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 99347b6b2c404a4b9bbcc96e0b4bd925 +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 e6629f0914324c76a08fe179575b73d5 +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 2287002a87184fb9b95d775a368f0e46 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 c23d4543d9f949a9a7015fdcbb40dcd0 +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 c04a9dcc84b84f37bcf32c3790672038 +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 9f27c79365db455d9d31053576ebe05e +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 a2b3ad1e2c884e24948a915c3305aee1 +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 dd7665bbc5e9449588c9539e3c1910de +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 0972c757f7c74ea9beabf6b9ef9dbf4c +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 175de3b9854546568f60a20cc19887de +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 0c286e5ba1714a059a95b566fe49be31 +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 3029c1dfe5424c2b812597b03ea76178 -#: a5503b6c524e4848aa308b0f4c26d774 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 msgid "`arguments`" msgstr "" @@ -1803,32 +1828,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 0e03befa46c74dc2b09420e1eb2a6fbd -#: 50f81e7ab73a4713bbc60f6f5609b906 718dc3def33c462786174fb42097981f -#: 9c2acd930553458eb105f96213b5d7b0 d4bf86a995d546c0a9159b3f29a84125 -#: e98424244f554c7399e9e7ad560849a6 +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2be930b5da674874a0b634eca3ad9346 -#: ce445ad0f00f403985eed1328103a500 +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 2fe48d6404864ea39ef0634169f67be1 -#: 43453d90db244c558a815ca872dc716c +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 78eaa318ba81407e9ca9c2c1702ead11 -#: f5da7058f7f146d584314a5bf4de5498 +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 7189f4415d204fb388c4a7e927e15b71 +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1839,11 +1864,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 17a83cc91963434e89822a3e46df8401 -#: 194d3e48d38c476fa8f731e3bc2d8c7f 3a3000a6446b4ef4ac66a28acb13b136 -#: 5cc35210e95e4f2ba6a1a6f118926fdd 68b3d1481a4e4375b1b0c4fca8285374 -#: 94f2bc195bc0487da014bc3f4d2dc8fa b92b4eff2429437d9da911ca68cef954 -#: fc0a1353e87e479d8c8b6c973d547465 +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1852,51 +1877,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 5478cbeadc64412bbb32619fae9b9958 -#: 6950cbe52d334fe58bf4fa20e5f1f8ca 6b5bda581d0047819c6d92edd8ac9045 -#: 8248329fbe504b3a96bcd890908b070f 978c0fea8ed1481a9f06b6abb31ebd21 -#: a24ba514d66d49cea281fd4c9c7a2b8d b6e2c8e7abf74d64b2915063dda8479b -#: bc184adfad0e4642bc864d367b8779b7 +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 5bba2d465e0a4c5d9575406d1294a225 +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 da385d3cde614749887e195ea6d95291 +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 487c95417f8e48be8391163578ca9519 +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 48437402c00147d4b4ca8bd6b38a5823 -#: bdcb3920048f4e578a4005fc2e30233b +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 121556d49d584cc491a15ef8404ce462 -#: 183ba52666744f7ca5772939db2efd6c +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 08ad064936d8406f8c3852526f4f863d -#: 30c927925c6b483b80b583ca7c735437 +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 32a26dd9c5f84e88995f093cda953ac9 +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1905,32 +1930,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 05ee6df2f9b247629d148fd59c293660 -#: e7b7d782b6ac49b3aa0c8d8ce7ff04d1 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 b0cccc07e5bb4effb60424623351499e +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 4e5281c8663c4b6e8851be10f50143f1 -#: b5c22c66397e4268b4b3d53b9a253a3a +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 98a28fec818e42af9e177e17fa12aa7a -#: c37d0b1fd75e44a28b3b6409f912e865 +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 dcc42c6c49964a4ca7bcf2124e26ebfd +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1938,61 +1963,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 d2ba352ac5fe427ea7ceb0bde01458ba +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 235cfd6e9baf48698102447fcb83e0e1 -#: 8aad01df8d8d4ab7905a5da7ce7f6bbf +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 058ba8c9c2da4ebf8b2291600dafd611 -#: cea47d3e10f641a2b64f08ee100ea6bf +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 3b039de5ad144207ae337aa88b3b1a1f -#: e0ecfe44b34e45dea513459b6b3e44a6 +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 1cfc6cb0be4e4ddd90f546adb796b805 -#: b62f6eaa7c394792929dda83a187c632 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 8b13b0e4071444179b26401929de8a10 -#: 8ffb471129c04fc6bb52b782fbd09f9b +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 331f58b998cd4d309940ebfcc60a44f8 -#: 5041700e6ccc48989e395a6dcb1be3c4 +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 14402b41c64548f8a9691c3b7ccaf3ac -#: cb4837a2b25343d2880a07143f85f40e +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 1d1c2894600544b686a8ec3c36cdf767 eaa30e987ec543ef8d6f7171de5525f0 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 065c97a553904db6ba61c20cf9d9939c +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -2000,33 +2025,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 36be05289972455ea4a60aa1f0b9cbdf 49e1ab5bc5734debb83060759d5c3236 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 f8e37cd35aea4bbb92d28e8d7e803ebb +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: de816d1dc9f24c0cbef86fd6a09eff6b e265df9d1cfe439bb798ab6cd32485af +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 0363e32e12604eb896f4bdf6bbefd550 8b5289393b7f477699d007ded45a4df1 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 2c704cae43d64ecbbed33d18eb3f66f3 89acc8f8387d4643a844ac3efb186000 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 0597c6c214924e75ba2f212cd6b0c9f2 +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2034,22 +2059,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 1eb1c2432dd943f6a27a1f8b92e3981b 5b9ba9380f10425b809c6157a1f0b052 +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 b4cc7cc55cf04449b291a27514fc99ae +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 cdb48eff43e7459fbf3ed21eb7791d66 +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 67a4dc675c0e444585d579954b99614e +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2057,7 +2082,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 ea3238db48494ab7b044bab9f96590af +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2067,54 +2092,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 baf2f6ac8d514705a1f7bf7ea8c71d2e +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 ef45f4e14fb943cd9fbf179f5d3680e5 +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 030261615c38485d83ed986c9c98ce15 +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 1728e2370cbb49ab97bee4c2f74fff2d +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 4514fc0c99ac4688a37bf30bffe139e8 +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 33804649720143e5a70e890af9ad9119 +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 c114496be4c243d6834776e17bf15010 +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 c784e86f14f54e4982db206741fbd96e +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 f9de69aad9b44afabded71221c84adc2 +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 b853c964611e45c2b37a8ac3c34a4133 +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2123,15 +2148,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 a10d143210b94f83857f62e972d69134 +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 b07734b172664040aff04f83bd4395a5 +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 1f9a5377a1f04ee3b8a9ae22390e0cae +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2140,11 +2165,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 359bb6448aa140f8b940baf769c13db6 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 c4aba730bee14931b051d6aead7c2dae +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2152,7 +2177,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 c4dfcff573424bccb97580fdd1ef27a1 +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2161,34 +2186,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 1457fa489c894f1bae8a3949ef200527 +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 cc4fa87d57b344ed8961c31bc4397e71 +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 091815ab1d824787a1460ce11ffb834d +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 414b68dac4654163b3dc13e140ffdbf8 96fad38b4aea461493bf0827476163bd +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 4f71de1140974e73ab033fe7dd9dc165 +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 b84e3294c8f648aab634e59b6f58441e +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2196,11 +2221,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 6d9ae44900d64532906532432881d29d +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 5b99384b3a854832bcca2fb02bdfc1b6 +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2209,80 +2234,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 3141fc6828024c3e8201e88ca10e19ee +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 5f8c8ea68d7f46fead000315226ec164 +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 86c18e5105b1400d86d413e28ad72f48 +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 fa15037f9b0b4a2c9a1f4cff9b8fde43 +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 fba6d2b7843e466abee33183103cf47d +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 09f5a55611d14e39b2266245b79ed763 +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 bdfb39c2656040858616afe731111d1a +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 c306335ff07e4c03955fe87cad16efd1 +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 50bd3db6bfb348eea13ba4714ecb2a20 +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 5d32cfb6f6ed4dd8b11ed316830edba8 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 b90fb1b2d38b42c1bad2d9667aaa22fd +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 6029a96abf9c4d7295eb86d435a1f58d +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 902e9df74f78431ca9cf1421a26e097a +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 9760d15bad144e70a86dc0a8da72363a +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 75bf3fae131049308441bc496f543f6e +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2290,7 +2315,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 38d8a9c157404bb496bc49f1e427bf99 +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2298,7 +2323,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 502994ee84234f048e545633bb04cd3c +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2306,14 +2331,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 551b06b8a3064bcd8d0f1693a4c0ee94 +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 1838e7438be5449c91c6406a7e40d8cb +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2321,7 +2346,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 098bb02c941a4bf2a8d4dd9ab3bf052e +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2329,7 +2354,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 b43194d2b3ef4fc6a8c4b58741317b29 +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2339,13 +2364,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 e17c55c9ed034dd68f4d24272a61d2f1 +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 c97a6945e4bc49888d280bbc43c3c069 +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2356,17 +2381,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 503666cda07b4d7397c65561714d8034 +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 e5463be0a00d42e386aa6fd3dfacaeaf +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 14b98bd0ef4a4065a24e66443458d607 +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2376,23 +2401,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 98fa5dab117e41d4a42da8d78c533c64 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 116c212444da4488b32abdbd725db98a +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 065e556e01b34c35b6be4b54b7cc0203 -#: 4745f370dcbd4ee8bbf4b3a20ac5b9fe d11761f2d576464f8a2c63bdec02d410 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 b3bf1d7e95704682b1bae17472eaa4bc +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2402,7 +2427,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 04bc655130234786b06b2d5b9e693635 +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2413,11 +2438,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 e2c18a43b2794448b45c489dd2fa951e +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 38968ed627514ef38e43b3d1e4a5e25f +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2425,46 +2450,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 06aab84eceeb41d087b7e295ffa21586 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 a0317edb8b964cd2a36c59eaa6df302a +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 5a3d1b82c79c4ccdb7d06381f4d0acda +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 e1fc6c3a324a46ee84b0eb59f8396552 +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 f22e7d9e23b541ef88f3254095147519 +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 d473d2fa11f64e8fa86554b5777c98e4 +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 290461c321d14d23b39003b93008a7cb +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 add43f7531bb4c6988053ae799c366f0 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 b12b6f5e34c14dbc9b40458d92e6797f +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2472,18 +2497,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 4d8f38679952486095a77692387db2d3 +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 47ec49759e274e59834192b794ec2d9b +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 0657044c742348fe9e63f662692570a1 +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2491,7 +2516,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 30c21cafda144f848bfe79d8e232296e +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2499,7 +2524,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 1cc8ea6abb684470b7790808acea2be1 +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2509,12 +2534,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: c3b84742343449f9b3866285d98b53bb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: 0a1b08fe707c41089ad3d4895960ba17 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2529,7 +2554,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 5bc4ef6584c74b948ffd5c0bddf8e569 +#: 80af387fe3ff4e2da999903385bd602b msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2537,17 +2562,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 47ee25d60a4a4faa80476797954ec7a9 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 195d4a8d5aad41159beffafd198d4640 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: b0c5946fbf79415aa74c8e72fa88cf85 +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2557,15 +2582,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: a98236fc1be745a69271855e1b5eecdb +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5f0da8d7e06a47fda38053dbadcbec18 +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 23d41792b0524742878a6ab8f3ff0fe1 +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2573,56 +2598,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 c0f723242f11464392dfc32f67a3b67b +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 c9f3a48a3a064cb3b1759effe724301d +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 fbad0b0144984ae78b84307ea68d0a03 +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 59e9ff3276454ff19eb351ff33737f12 +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 ba74f2ab7f6d4c178f3c4c43c461afbd +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 93c8b61a12134991ae9bb78223e2017e +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 cbbdba36dc3841f2b1d820f369a8c680 +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 4649c8d743f448ab94ee589a1b3a342a +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 1a9d6e2e33244d01b820cf11fe2beaff +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 233c8865faac4d6c8ec7704e9a997719 +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2630,7 +2655,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 5aab1c0db3d5449cbb4a0f0dad615d87 +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2639,17 +2664,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 46b4eeb3ce8946dca0f8a94c399b4c96 +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8d322609948a4d6e87d7962b3d29df2f +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 9fdcb55e965444ee8b5d74a2a9870d27 +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2657,71 +2682,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 e4c490f599a0469a821aa8e74f4ef0ef +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 b8ed6ebe6928455cb094ea430e21e5d4 +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 3e65c52d218946fc83b8c3e6adcb21fe +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 03751b45cdf647b689a3a69156989db5 +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 1b6f59623f5d4cd984426da21b8438bf +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 095902cca30944d19a0d5f17f582e3b0 +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 6d95fbfa321144a9932f26ab5f9ddc74 +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 8be7ef160e8b421a89124a639dc7fd84 +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 fcf4490c351d4cd6a208345308168ef7 +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 00f1bb92a38b4f3a8c0065ac75530689 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 1477d0fc5c4c4f82bcc1c8e6ba8eed4d +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 dee904cb678d4eb49dc829d6590b267a +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 a21c1fd3194a49ae992a743023653dc5 +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 e72c526da47a455da4b10e33938d1600 +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2730,11 +2755,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 6447f4b8bb5f4f93bd8ec2c7b1fb09cb +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 1faea30495a440a68dbd1647dacc404c +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2747,40 +2772,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 0c0a3f58a93f492dbfca14523809aacc +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 460842f202db493dbb901be73a02797f +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 2591c2cf9e5f402281031ea8dd41a251 +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 b093abbff3614b2ba0141f07376a5220 +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 fda3718113354215bd2ac212553fb2d4 +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 271e78089c274154a0233289d705e628 +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 29ab4fa0876b4c11a0c7482cca56ed80 +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2788,45 +2813,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 78e1857c5bd54af1b7ca4728879e6219 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 dae7873015254aa7874379164c90a8d0 +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 7a45deb4682b49fd86d62fae41831db8 +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 442f77a69b314cba8e8857470263c706 +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 d4455241f14549b791e59fc1f942c8cb +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 ff4b1c05c5804ec7846043ae8814ad21 +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 119e026b595f49c090d62aa7b7c77de4 +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 5449d9c5687544a3bfbf8b2b25640a83 +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2834,13 +2859,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 b3191a7bd03d4ff18802ae0f5d419676 +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 ea9cfbbd4cbd4f26ba4b0cb50d58635b +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2848,43 +2873,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 7d39ed2a3a724dc1a75e6b2cdf87d91d +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: a1306ee650344278ae39d6086b1ed7d9 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: 21d76d22f3044460b925fee68ac74454 +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 6b8a5c59217c4928874710ead1456622 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a9f6d09055c24029a5f85c3a663c4202 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: d3948618f9274ad0a333722567efeea5 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: 44623c81141345a0b0080e719e1418ab +#: 574d93d1d592458a985f259519c036cb msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2894,14 +2919,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 6e80d82ed57b441b8292961ec3163213 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: fc61f369e720463f8a5cd6c751d1d5e6 +#: 02e40154eac74ecc98d0447d03475b44 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2910,7 +2935,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: f20aadbfc13243498ad199376c314e72 +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2926,11 +2951,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 e66956313b8f4f02bb96cfb256e2a7d4 +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 f18c5a8fcbe84135a6e06cbf8008cd63 +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2940,26 +2965,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 87fe14c9a0594602aa56a7706e089458 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 6e10063f55b747e1b07d6109ab7b046b +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 e8831832b32449f4a8a3dde3c1b479cd +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 9c86467137864626a2079cb6cecb71c0 +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 24b66a3e2e464ec6a85b5dfbaad1cbf4 +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2968,7 +2993,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 6d28f1cd40c045f384313c4d74073ed2 +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2978,18 +3003,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 5235ff0c35c54396aceb799a65f6158e +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 fc49344510594559b4f888bc45093b51 +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 6e62be8d7d1344e8917904278b508518 +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2997,7 +3022,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 c91b3a2818b143f58bd37da63479c560 +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -3005,7 +3030,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 86f283bc522c4be2adfac16256f01b0e +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3015,7 +3040,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 5362aa1d28344968953ab9cb389ccd8e +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3025,15 +3050,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4bb1aafde4f745a083d3a276497523dc +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 b00987baf6974ff9b7e3b8cdfd7abd9a +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 9ac51c5a2a0a45859e14d9e388edd5f0 +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3046,35 +3071,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 5494ccdb1a354b2386c82bd9a6f0b6a9 +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 4cfa8fc2bb224883946d5f63b372de82 +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 e16c1922527a46e28bb5d933614cdaf7 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 7498a71704be462abef71c42e6b83d1b +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 ac0689bff9db46ea8bff8cd35cde86f3 +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 c4b7da5575674ca3ae734424022ef090 +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3087,23 +3112,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 d24fcecc17d0461cbd8689067f770c0d +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 833d4d3b3f0e4c7cb8b1d35cb9a78a7e +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 50fc0573276e4dd4a47208ed81109991 +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 f72e10e746604421904057ddf7078d3e +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3111,44 +3136,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 ee126833f6014e378c7841c4048dae85 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 0325bd610aa747b0b657afa0c978a1eb +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 7c901105cf6949909d87be5681331368 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 74138d0c2ded4311bf688df4a28387b5 +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 1ec4773e7319414b997d746d1965ff56 +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 5f860dd70e3b435188c61a538e5de0ef +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 a9c56df6dca441dfabda7fa54fbe56c6 +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 586d561ddf724319b3da9ae857828648 +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3156,33 +3181,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f3e80b1903534065a30323611c267e9b +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 6ed53c6f9fb94d4ab3d10532c605c46b +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 3fcfdf43b0a049388634625c45e0b1bb +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 49415efafae64f94b66cb46ca2bbd40a +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 4806a2ef982944e8b073fafd416d3d74 d45701eeaa6e42feb4ef79d2fc4af756 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 155cd684ff304258ae374b2e13090e5f +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3195,34 +3220,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 d8bdb44011274f94b606277799a6fa6f +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 9e1d9bc2f83743ea9964ec418d225200 +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 a1240eab3ef746cf82a2c5451042b888 +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 a73cdc43a8e44973808027c29903afa3 +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 4277837a9fd443378d5ca3d9252993c9 +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 09b714af60ee4ecc8ab1b95eac8284dd +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3230,7 +3255,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 3e99a3be9265463daf74b00a21d89cff +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3239,7 +3264,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 1c4a959d43b74686ab801a26ef412b3d +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3250,7 +3275,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 55daf180336d4045ac0cc4c14af98cfc +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3258,7 +3283,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 5ae40eb04d5440d5ba882a74aa5b9708 +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3268,13 +3293,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 f93e9b776a4544018877b7a13399609b +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 0e587435e3884334bc51a4abf4b4d785 +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3284,11 +3309,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 81b98764289245c79f18fcff478f4a9b +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 9baddec4015f40ad82ea2dee30305654 +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3296,17 +3321,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 986c3dd9460b42b3b20e2d01ba1fbe51 +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 4558f174fea445fd97b80d963fc74f43 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 532823a13154401090e9fee3e018fda9 +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3314,7 +3339,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 7b6f46b70bac4f848a956ea160243621 +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 3861b4a31f71471b97bf9dc18cc80594 +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3336,7 +3361,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 a10c37f65ac14ef2a5971872bc9b8f9a +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3345,7 +3370,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 34175f932716406f836840732618caee +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3355,7 +3380,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 0d132dc39cdf4818bc8e20132073f669 +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3363,14 +3388,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 9f8c45f077974cf79612ee83df3d152b +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 435f80d0599b4d93ae1339e8c7bc020a +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3379,7 +3404,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 d39b024a1a8d4eae8d7fd3c929a782e9 +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3388,7 +3413,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 3cbbe074843d4306b762d2fbc6fe9850 +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3396,11 +3421,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 7118b6e09b9f44129c7d98d90570f2c2 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 70f3e73ee3714f22ad6ee43dd5ece703 +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3411,7 +3436,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 279495257ead4a4fa725c7d68c504162 +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3419,23 +3444,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 86d1d742bb5c4a9898aa573ce648f0ec +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 f4987847f46e4a2db54127ec7ebcadf7 +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 80e7c22dfe4d40749f2e9c3bf02bf8bc +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 e930bb5d430a41d9b5bf49e473dd2ed1 +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3443,7 +3468,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 4076e9eb67ed4bd5942f089e394bad26 +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3451,59 +3476,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 1b44092e87b840de8f1d022676d0990d +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 a8afac626f5d4240a57267085b9bef26 +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 0896efc674bc402495c6e73c6c352523 +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 91a53d918d4b47bdbe0b0a6d4adfc0dc +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 8325682d51d8421b9ea507f424f71e73 +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 503d068602d8477a820b91d835fa3f28 +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 4e768b91eb274a5cb157f1e3fe2f85cd +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 18ec5231b7bf4c9ea59361b325fcdd01 +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 87fd118dc2774cf08db0a3ba56520da5 +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 8168ffcb23124b3f839a9862a7ec0958 +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 37c222ea14904fd4a8fa93a1e0103239 +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3521,7 +3546,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 d392813fc6d14851a294a391426d41f6 +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3529,38 +3554,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 652155460eaa42b6856c16cffdb845c0 +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 6313cb377dc249e0b2262a3fe732fe32 +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 11f73cf24fb044e3a3afb3adb6137708 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 def9e62bf73f49eebce09677954e2a92 +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 200dfe47d09d4b0b9e4acf29b7e038da +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 858bda7fb6524e9dbfb35596ce6a6d07 +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 28897819504247a3a6cf9a9d9476b63b +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3569,7 +3594,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 4f8fd11e29b048e1851299002c3a48c4 +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3577,62 +3602,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 ed33196347d949eda752a081c7af4657 +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 738c67568dbb4f2bbb5756fc5e727c01 +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 19b016a1fec14056a9812c1c195c7c90 +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 a513367d60a74f559339c05d8ef10eb7 +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 5e30680941164047a47f98417e916188 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 ca02f2bf1d754d5190f296674245b936 +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 466615194bb541fdbe2e6515b50531b3 +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 33e664d59a30407891336db290a8a5b2 +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 3e52ab079dcf4fc6a3f052a517f4d31b +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 abcad6b7d37a4342a90c2d5952ea1232 +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 500a489e4fae4d1abaa8883f632d1a24 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 546c1ef51a63487c91c98059dd46b0cb +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 72b4262833054edd9efe6078381de654 +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3642,7 +3667,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 7b7e8242660744b791ba3868e4ed7e37 +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3651,7 +3676,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 492d994a541c4c948fb5da9041153bcf +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3662,28 +3687,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 e2209269db394f3988f18b147a57677c +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 e15c39c65aca47f690264d8008463bec +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 afa546fcb7fb447d939d4a167f206f79 +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 7dd375e0fd964413af4957396d2a0474 +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 af8ef039a64a4c0783d7229dbdac65ef +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3694,7 +3719,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 3ce968cb39a443059f6a828b3c8c2f33 +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3707,11 +3732,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 3c2f48a8e616400b9a8ffb4b6f7efc9b +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 c432b1656e0e49ef87aa3d6e42acad84 +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3722,26 +3747,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 cac5e52767f74ce98693e2a19ee1eb0d +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 101666907f8b4fb994e25ceffcf04a13 +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 5461960a469042a487b89e440f856aea +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 e31349c164c84a9da46e2fb1861793df +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 49a0b3dfdc9e4d58b6bc966db979ace8 +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3751,52 +3776,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 e08ec8c473e847f98e8a18b9ca0f2670 +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 6ee7bfb4a9e04dd19b5180bca5b02705 +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 42614ab7ba1546f89abeb8f48991271c +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 b8df5b8393ed4d869c066640fe83ec7b +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5b9aee5af41f438b9f4208294bf97f4a +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 a71d3022dcfc44979cca4655ea51ad42 +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 42b5a982e86f46dfbfcd7bfcc99d72a5 +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 12dc402d053044b78d69927dd391fe9d +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 687c20e2e4bc4f869c7ee9390e61476a +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 a975fbb3ea7d467881ce0245de538295 +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/locales/pt/LC_MESSAGES/user_guide.po b/locales/pt/LC_MESSAGES/user_guide.po index 3ed0733d..3584ce39 100644 --- a/locales/pt/LC_MESSAGES/user_guide.po +++ b/locales/pt/LC_MESSAGES/user_guide.po @@ -9,115 +9,142 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-24 17:23+0100\n" "PO-Revision-Date: 2023-01-25 13:37+0000\n" "Last-Translator: Michael Crusoe \n" +"Language-Team: Portuguese \n" "Language: pt\n" -"Language-Team: Portuguese \n" -"Plural-Forms: nplurals=2; plural=n > 1;\n" "MIME-Version: 1.0\n" -"Content-Type: text/plain; charset=utf-8\n" +"Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -"Generated-By: Babel 2.10.3\n" +"Plural-Forms: nplurals=2; plural=n > 1;\n" +"X-Generator: Weblate 4.16-dev\n" -#: ../../LICENSE.rst:2 75de2be8809847b8bf1ccd42aa694a24 +#: ../../LICENSE.md:2 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "Licenças" -#: ../../LICENSE.rst:5 2edd71801f6245ef821887a74f21b94c +#: ../../LICENSE.md:4 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.rst:7 f2219cfc916b407fb5b97e7d39a891ee -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +#: ../../LICENSE.md:6 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "" +"All Common Workflow Language project instructional material and changes " +"to the structure are also made available under the [Creative Commons " +"Attribution license][cc-by-human]. The following is a human-readable " +"summary of (and not a substitute for) the [full legal text of the CC BY " +"4.0 license][cc-by-legal]." msgstr "" "Todo o material instrucional do projeto Common Workflow Language e " -"alterações na estrutura também são disponibilizados sob a `licença " -"Creative Commons Attribution `_. O seguinte é um resumo " -"legível por humanos de (e não um substituto para) o `texto legal completo" -" da licença CC BY 4.0 `_." +"alterações na estrutura também são disponibilizados sob a [licença Creative " +"Commons Attribution][cc-by-human]. O seguinte é um resumo legível por " +"humanos de (e não um substituto para) o [texto legal completo da licença CC " +"BY 4.0][cc-by-legal]." -#: ../../LICENSE.rst:12 90cc755d172e4c82b882b4ee620fe652 +#: ../../LICENSE.md:12 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "Você tem o direito de:" -#: ../../LICENSE.rst:14 02fe5f2d7df143c69637b2908baf0715 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -"**Compartilhar**—copiar e redistribuir o material em qualquer suporte " -"ou formato" +"**Compartilhar**---copiar e redistribuir o material em qualquer suporte ou " +"formato" -#: ../../LICENSE.rst:16 bd323b7141664c86a5bae059c81554b4 -msgid "to **Adapt**—remix, transform, and build upon the material" -msgstr "**Adaptar**—remixar, transformar, e criar a partir do material" +#: ../../LICENSE.md:15 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "**Adaptar**---remixar, transformar, e criar a partir do material" -#: ../../LICENSE.rst:18 430ff4de74924bc3a3b2c7e809ea4456 +#: ../../LICENSE.md:17 b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "para qualquer fim, mesmo que comercial." -#: ../../LICENSE.rst:20 2173e2af49be41ee97a74c4e879faf25 -msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +#: ../../LICENSE.md:19 6021e65292a149d5b15e14491f3eb05e +msgid "" +"The licensor cannot revoke these freedoms as long as you follow the " +"license terms:" msgstr "" "O licenciante não pode revogar estes direitos desde que você respeite os " "termos da licença." -#: ../../LICENSE.rst:23 42184243a01f4469943adff1ad982c74 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 8fb7a2946c384364814c6ec3910997d3 +msgid "" +"**Attribution**---You must give appropriate credit (mentioning that your " +"work is derived from work that is Copyright © the Common Workflow " +"Language project, and, where practical, linking to " +"https://www.commonwl.org/ ), provide a [link to the license][cc-by-" +"human], and indicate if changes were made. You may do so in any " +"reasonable manner, but not in any way that suggests the licensor endorses" +" you or your use." msgstr "" "Atribuição — Você deve atribuir o devido crédito (mencionando que o seu " "trabalho deriva de um trabalho que é «Copyright © The Common Workflow " -"Language project», e, quando prático, criar uma ligação para " -"https://www.commonwl.org/ ), fornecer um `link para a licença `_, e indicar se foram feitas alterações. Você pode fazê-lo de " -"qualquer forma razoável, mas não de uma forma que sugira que o " -"licenciante o apoia ou aprova o seu uso." +"Language project», e, quando prático, criar uma ligação para https://www." +"commonwl.org/ ), fornecer um [link para a licença][cc-by-human], e indicar " +"se foram feitas alterações. Você pode fazê-lo de qualquer forma razoável, " +"mas não de uma forma que sugira que o licenciante o apoia ou aprova o seu " +"uso." -#: ../../LICENSE.rst:31 5410799d7abc41e396e9a12e528fcc37 -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 8161753b7526445db319210044566200 +msgid "" +"**No additional restrictions**---You may not apply legal terms or " +"technological measures that legally restrict others from doing anything " +"the license permits. With the understanding that:" msgstr "" -"**Sem restrições adicionais**—Você não pode aplicar termos jurídicos ou" -" medidas de caráter tecnológico que restrinjam legalmente outros de " -"fazerem algo que a licença permita. Com o entendimento de que:" +"**Sem restrições adicionais**---Você não pode aplicar termos jurídicos ou " +"medidas de caráter tecnológico que restrinjam legalmente outros de fazerem " +"algo que a licença permita. Com o entendimento de que:" -#: ../../LICENSE.rst:35 f6aae4a5cd0547118c8a3240ca2b4be6 -msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." +#: ../../LICENSE.md:36 15314ba527864eaa834cf1185cfcc4e3 +msgid "" +"You do not have to comply with the license for elements of the material " +"in the public domain or where your use is permitted by an applicable " +"exception or limitation." msgstr "" "Não tem de cumprir com os termos da licença relativamente a elementos do " -"material que estejam no domínio público ou cuja utilização seja permitida" -" por uma exceção ou limitação que seja aplicável." +"material que estejam no domínio público ou cuja utilização seja permitida " +"por uma exceção ou limitação que seja aplicável." -#: ../../LICENSE.rst:38 a40c173be35b4c1b92e83f42bfe2382c -msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." +#: ../../LICENSE.md:39 b351ddf9847d48b1a2a87fc78eaba4d2 +msgid "" +"No warranties are given. The license may not give you all of the " +"permissions necessary for your intended use. For example, other rights " +"such as publicity, privacy, or moral rights may limit how you use the " +"material." msgstr "" "Não são dadas quaisquer garantias. A licença pode não lhe dar todas as " "autorizações necessárias para o uso pretendido. Por exemplo, outros " -"direitos, tais como direitos de imagem, de privacidade ou direitos " -"morais, podem limitar o uso do material." +"direitos, tais como direitos de imagem, de privacidade ou direitos morais, " +"podem limitar o uso do material." -#: ../../LICENSE.rst:44 3d7ca3f2cede4d5f998bf014bd970748 +#: ../../LICENSE.md:44 a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "Software" -#: ../../LICENSE.rst:46 72e0760cc40942c7957ec6dadd5d4ed2 -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +#: ../../LICENSE.md:46 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "" +"Except where otherwise noted, the example programs and other software " +"provided by Common Workflow Language project are made available under the" +" [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" "Salvo indicação em contrário, os programas de exemplo e outro software " -"fornecido pelo projecto Common Workflow Language são disponibilizados sob" -" a `licença Apache 2.0 `_ aprovada pela `OSI`_." +"fornecido pelo projecto Common Workflow Language são disponibilizados sob a [" +"licença Apache 2.0][apache-2.0-license] aprovada pela [OSI][osi]." -#: ../../LICENSE.rst:50 9c4d58a1129a4d4eb4db1bfabbeddb6e +#: ../../LICENSE.md:51 0f68eafafaef4b54accba7e13bfaa702 msgid "" "Unless required by applicable law or agreed to in writing, software " -"distributed under the License is distributed on an “AS IS” BASIS, WITHOUT" -" WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the" -" License for the specific language governing permissions and limitations " -"under the License." +"distributed under the License is distributed on an \"AS IS\" BASIS, " +"WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. " +"See the License for the specific language governing permissions and " +"limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 ../../src/_includes/what-is-cwl.md:2 -#: 5ad4be9b62d54c95a913795b514676fd bdd540403a5746ff99edf2dcad0e3122 -#: dfc7702e073140c985cf47272a20214d +#: d4f35995b0f6494d9771a4be0a82538f d6ccd4b546254f56a597d67dd4fdc5d6 +#: eab02dc13915490bb3c9ba744d78b6a7 msgid "" "CWL is a way to describe command-line tools and connect them together to " "create workflows. Because CWL is a specification and not a specific piece" @@ -126,30 +153,30 @@ msgid "" msgstr "" #: ../../src/episodes.md:5 ../../src/setup.md:5 -#: 810c4e8dd79247d6a6fd51a8f65d3975 f1b89ae4325343f783bce8b7c9971047 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" -#: ../../src/episodes.md:9 3060770b3bef41d7bcfcdfb413d7689c +#: ../../src/episodes.md:9 cc11f5d29206492d9f2f0922882b6159 msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. Please use the new [Table of Contents](index.md#table-of-" "contents) to browse the User Guide." msgstr "" -#: ../../src/faq.md:1 48bb9f628b344ba1a3b67ae1cb264e3c +#: ../../src/faq.md:1 e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" -#: ../../src/faq.md:11 7e3684e9672643738846756e1ebafd18 +#: ../../src/faq.md:11 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" -#: ../../src/faq.md:41 187ceabb7fd9480bb8cf0f2da47f65ef +#: ../../src/faq.md:41 d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" -#: ../../src/faq.md:43 b548b76bcc85420a9b30792386105139 +#: ../../src/faq.md:43 fc62427c0a004810b055dee90ec5e2d9 msgid "" "This example demonstrates how to change the name of an input file as part" " of a tool description. This could be useful when you are taking files " @@ -157,94 +184,94 @@ msgid "" " default names that these files were given when they were created." msgstr "" -#: ../../src/faq.md:59 9ce692b78ead47e4b0f8cdae8837d35b +#: ../../src/faq.md:59 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" -#: ../../src/faq.md:61 6df1201c159343da9e7515379980d6a0 +#: ../../src/faq.md:61 bc7ad10c929848a3a9a240a3c501d299 msgid "" "This example demonstrates how to change the name of an output file from " "the default name given to it by a tool:" msgstr "" -#: ../../src/faq.md:82 f9ab1d0dc1c842b6abb5385268c1d3bd +#: ../../src/faq.md:82 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" -#: ../../src/faq.md:84 9f6a84ab6a9343b6ad7db826f8964362 +#: ../../src/faq.md:84 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" -#: ../../src/faq.md:86 fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: ../../src/faq.md:86 450edf800a18423195bea4fe8793a2cb msgid "" "The first method involves adding the folder containing your scripts to " "the `PATH` environment variable. This allows you to run the shell script " "directly without using `sh` or `bash` commands." msgstr "" -#: ../../src/faq.md:89 3a871012fcfd4f3ebeca0cb86ec93435 +#: ../../src/faq.md:89 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" -#: ../../src/faq.md:95 d954edfff2584288ac8c600733070d2e +#: ../../src/faq.md:95 a7d84f740a714ec588503ee084fbbc34 msgid "" "After that, make the script executable with the command `chmod +x " "scriptname.sh`" msgstr "" -#: ../../src/faq.md:97 af6b1e37d6be4450a761854480ec9aab +#: ../../src/faq.md:97 569d553abe85450c9d1c37456bf412f4 msgid "" "Finally, modify your `PATH` to add the directory where your script is " "located. (It is good practice to use `$HOME/bin` for storing your own " "scripts)." msgstr "" -#: ../../src/faq.md:104 31f4a2d43062493ca64c648f80afc8e9 +#: ../../src/faq.md:104 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" -#: ../../src/faq.md:113 41c54e71b6cd4f63b2a619a515240d34 +#: ../../src/faq.md:113 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "" "When you wish to share your work later, you can place your script in a " "software container in the Docker format." msgstr "" -#: ../../src/faq.md:115 8edc3541ad134ab5a1d23c724f1f0a4e +#: ../../src/faq.md:115 8d86baa239364f799d4f9d5ea2b0e314 msgid "" "The second method involves including an input of `type: File` in the " "script itself:" msgstr "" -#: ../../src/faq.md:135 ac0ea81eba8842a18801ab03cbf80a57 +#: ../../src/faq.md:135 f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" -#: ../../src/faq.md:138 52be1a5640234feabe958ff7ade33653 +#: ../../src/faq.md:138 c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" -#: ../../src/faq.md:140 c6db734d5aef4f4f99676bdebf9c83c9 +#: ../../src/faq.md:140 2c38cc58cbb340bc935a5f00e96ba95c msgid "" "Currently, `cwltool` can't cope with missing optional inputs if their " "input binding makes use of `self`. Below is an example workaround for " "this, pending a more sophisticated fix." msgstr "" -#: ../../src/faq.md:165 a9f7b47c0dd741739795da39bf114879 +#: ../../src/faq.md:165 ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" -#: ../../src/faq.md:167 e3fdd9228b924905a4a1f4b2b7ad7159 +#: ../../src/faq.md:167 d06cbf89028b4638ad54c2529bcbfa25 msgid "" "Below is an example showing how to specify different strings to be added " "to a command line, based on the value given to a Boolean parameter." msgstr "" -#: ../../src/faq.md:188 3f7cda1437cc48f18745a827ebb74582 +#: ../../src/faq.md:188 d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" -#: ../../src/faq.md:190 5aeaba2cae64442e816bbd458aee833a +#: ../../src/faq.md:190 d9e30e11533b4d53a144f5df7041268d msgid "" "Using " "[`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement)" @@ -252,22 +279,22 @@ msgid "" "merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/faq.md:194 5af827a402834978addd82c70be6b5ab +#: ../../src/faq.md:194 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" -#: ../../src/faq.md:196 6d69e42bd8e443c4b19d80807c7efd6b +#: ../../src/faq.md:196 937cb94a370640c788fbc3fe0b19f2e5 msgid "" "The input must be an array consisting of exactly one entry for each input" " link. If \"merge_nested\" is specified with a single link, the value " "from the link must be wrapped in a single-item list." msgstr "" -#: ../../src/faq.md:199 404640397b6e40c2a2cd5cf85ab3b1c0 +#: ../../src/faq.md:199 a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" -#: ../../src/faq.md:201 1682c2486e224770b62269709a8663cf +#: ../../src/faq.md:201 c8c235a9bf6240628f0b5493ffebf7e0 msgid "" "Or in other words: if the destination is of type `File[]` (an array of " "`File`s) and the source is a single `File` then add " @@ -276,25 +303,25 @@ msgid "" " destination step." msgstr "" -#: ../../src/faq.md:229 9078fc009bc145808813c9cc2b734b58 +#: ../../src/faq.md:229 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" -#: ../../src/faq.md:231 d4b5a54a400c409cb7984428f6a03ec8 +#: ../../src/faq.md:231 89b90d3bf1ea4ebd88482d435241fac5 msgid "" "To make an input parameter optional, add a question mark to the type " "declaration." msgstr "" -#: ../../src/faq.md:247 9e8dbee6e8f84d08b1a54fffa06394ef +#: ../../src/faq.md:247 a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" -#: ../../src/faq.md:248 1d846bfb5f054d09a4afad1da8e4b642 +#: ../../src/faq.md:248 f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" -#: ../../src/faq.md:250 2d0e95fec8084787b734388d60188574 +#: ../../src/faq.md:250 10af80fa13af4158aec7060550485350 msgid "" "For command line flags that require a specific input as the argument an " "enum type can be declared in CWL. **Specifying null here is known as long" @@ -302,26 +329,26 @@ msgid "" "inputs.**" msgstr "" -#: ../../src/faq.md:267 eccc4a364330470fa474dcaaa3433390 +#: ../../src/faq.md:267 ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" -#: ../../src/faq.md:268 e945f6a337af4e4686bed482a4fe6c39 +#: ../../src/faq.md:268 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" -#: ../../src/faq.md:270 8a3efaa0ad1548428bcfd6e01d135cdc +#: ../../src/faq.md:270 52b8538177c64090af51f5f6a696c28c msgid "" "For commandline flags that are either **mutually exclusive** or " "**dependent** a special record type can be defined. You can also specify " "null here to create optional inputs." msgstr "" -#: ../../src/faq.md:322 cdab644adc5643708870fb08c06cbfca +#: ../../src/faq.md:322 f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" -#: ../../src/faq.md:324 089a5a0b076b44aeaab4d69ee3c79f97 +#: ../../src/faq.md:324 7dc0540508084a3495ff3b2ac90fd323 msgid "" "To properly set fields in a record input type, you need to pass a " "dictionary to the input to properly set the parameters. This is done by " @@ -330,77 +357,77 @@ msgid "" " the workflow to be used as the value." msgstr "" -#: ../../src/faq.md:342 561172559c6f41a68819608fd9e58bb0 +#: ../../src/faq.md:342 b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" -#: ../../src/faq.md:344 c5ee4946d2e840abaa3dc796a62652c7 +#: ../../src/faq.md:344 cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" -#: ../../src/faq.md:349 4f2069a2113c414db18eca95550e9e09 +#: ../../src/faq.md:349 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" -#: ../../src/faq.md:351 31f3390e6771414ba7bf57c044c4b0c4 +#: ../../src/faq.md:351 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" -#: ../../src/faq.md:359 3b77ce4930ae46d5be9f6965e8c54727 +#: ../../src/faq.md:359 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" -#: ../../src/faq.md:361 06f36bbe4d3840229b7374f27b86ae80 +#: ../../src/faq.md:361 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" -#: ../../src/faq.md:363 3cb2f70d00274a4dafd972ccd8c519c2 +#: ../../src/faq.md:363 fdaec25650ab4b0fb1c527610e24ae5a msgid "" "For example, the filename `a space is here.txt` includes 3 space " "characters." msgstr "" -#: ../../src/faq.md:371 093a1529262043ef84a99675054938e0 +#: ../../src/faq.md:371 182959fc9f4746d082994e07d05c8cde msgid "" "If you can not avoid these dangerous characters, then pass `--relax-path-" "checks` to `cwltool`." msgstr "" -#: ../../src/faq.md:373 45b6d9acbfaa47e5984184f7da554d0a +#: ../../src/faq.md:373 cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" -#: ../../src/faq.md:375 5705c9bacca5405ca6f14315a5575db8 +#: ../../src/faq.md:375 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" -#: ../../src/faq.md:384 82bfc285b59a439ca97d3278997f0fce +#: ../../src/faq.md:384 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" -#: ../../src/faq.md:396 181d5130101d45ccb22aebae3d154c2f +#: ../../src/faq.md:396 ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" -#: ../../src/faq.md:410 e864390b5ddb423aaa10e9d33d257dc1 +#: ../../src/faq.md:410 e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" -#: ../../src/faq.md:423 fe637c32fb15427a9045679b5da42ec5 +#: ../../src/faq.md:423 f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" -#: ../../src/faq.md:436 1f8004b9df8547029d82e57f9abdc979 +#: ../../src/faq.md:436 190099a242a645c9b9f8bc3ce89d920d msgid "" "If it is not possible to change the input identifier, then you can use an" " alternative CWL Parameter Reference syntax:" msgstr "" -#: ../../src/faq.md:442 70990dc5a0034099921ceb89c89e2dcc +#: ../../src/faq.md:442 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" -#: ../../src/faq.md:445 f679e26f18d9455f945fd13361a9c906 +#: ../../src/faq.md:445 1901c34201054a9cae199b0dbb8b945e msgid "" "The CWL standards are built around (optional) Docker format containers. " "The reference runner and several other CWL implementations support " @@ -409,11 +436,11 @@ msgid "" " standards." msgstr "" -#: ../../src/faq.md:450 fcd0273dbdd84e728cfd8fbe239f2a01 +#: ../../src/faq.md:450 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" -#: ../../src/faq.md:452 173ddbd1e7c64927a8dcb12a2a2140f8 +#: ../../src/faq.md:452 d7b044f5224a48eda09bc949cf645193 msgid "" "You can use the --js-console option of cwltool," " or you can try creating a JavaScript or TypeScript project for your " @@ -424,22 +451,22 @@ msgid "" "language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" -#: ../../src/index.md:1 662fe273e2fb4042b688512955e450a1 +#: ../../src/index.md:1 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" -#: ../../src/index.md:3 a15b52205f0145feaac298510e4d678a +#: ../../src/index.md:3 f8d6e4cd54cb42c88182a43171d97bab msgid "" "This guide will introduce you to writing workflows using the [Common " "Workflow Language](https://www.commonwl.org/) (CWL) open standards. This " "guide describes the latest specification {{ cwl_version }}." msgstr "" -#: ../../src/index.md:7 512aa0c7166b429e8116f71eef007f79 +#: ../../src/index.md:7 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" -#: ../../src/index.md:9 b1b19e17a18540939cb3bb7f8a700cab +#: ../../src/index.md:9 0f47157605a34ea58770ea898deebae4 msgid "" "If you find that something is missing from this guide, or if you would " "like to provide other feedback, file an Issue on the [project repository " @@ -448,11 +475,11 @@ msgid "" " each page." msgstr "" -#: ../../src/index.md:16 d58b36ac43ac44139897be752fbb1f87 +#: ../../src/index.md:16 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" -#: ../../src/index.md:18 6726cf3585a646a8b4cbeb543cf84a38 +#: ../../src/index.md:18 ed74c9a4b623464480e2c184668fcec0 msgid "" "If you are a beginner user get started with the " "[Introduction](/introduction/index.md) section. For advanced users the " @@ -460,7 +487,7 @@ msgid "" "about the most common topics for CWL." msgstr "" -#: ../../src/index.md:23 2e504aa7c46a426fa959e7254e9a84a5 +#: ../../src/index.md:23 cfa67cf5521b414da6f7d34cbed283f7 msgid "" "The Table of Contents is displayed at the top menu and also on the left " "sidebar. It also appears further down this page but with links to " @@ -468,15 +495,15 @@ msgid "" "page, and the Search form is on the left sidebar." msgstr "" -#: ../../src/index.md:28 e7be0df0838b432d9c7f296d777f120b +#: ../../src/index.md:28 ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" -#: ../../src/introduction/basic-concepts.md:1 173e0816db20432c8d9dba1de5393dee +#: ../../src/introduction/basic-concepts.md:1 e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" -#: ../../src/introduction/basic-concepts.md:3 30eacc583f6841719e2142d283811d97 +#: ../../src/introduction/basic-concepts.md:3 ac62d326a68145b695e46b714d4e8156 msgid "" "This section describes the basic concepts for users to get started on " "working with Common Workflow Language (CWL) workflows. Readers are " @@ -487,18 +514,18 @@ msgid "" "you may want to skip this section." msgstr "" -#: ../../src/introduction/basic-concepts.md:10 791b8f38a14147bbaa174c7eb595f17e +#: ../../src/introduction/basic-concepts.md:10 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" -#: ../../src/introduction/basic-concepts.md:21 1a3989dcbb9844b39d84bf6df6b352ed +#: ../../src/introduction/basic-concepts.md:21 cbe1d761da5b403d9605fa1fb8e62fdf msgid "" "The CWL specification is a document written and maintained by the CWL " "community. The specification has different versions. The version covered " "in this user guide is the {{ cwl_version }}." msgstr "" -#: ../../src/introduction/basic-concepts.md:25 db1bbc6e980f404f9f3fcd08e92ee9a3 +#: ../../src/introduction/basic-concepts.md:25 3a71b269bd3c49eb913cf69b60373c24 msgid "" "The specification version can have up to three numbers separated by `.`s " "(dots). The first number is the major release, used for backward-" @@ -508,18 +535,18 @@ msgid "" " typos and other corrections to the specification." msgstr "" -#: ../../src/introduction/basic-concepts.md:33 acc7887c65974114996f700a38a7eccc +#: ../../src/introduction/basic-concepts.md:33 b171b72c48d44050a3416a7a42c4021d msgid "" "The model used for the specification version is called Semantic " "Versioning. See the end of this section to [learn more](#learn-more) " "about it." msgstr "" -#: ../../src/introduction/basic-concepts.md:37 d2476d9bcff44f21b8d84a3a0d87a246 +#: ../../src/introduction/basic-concepts.md:37 b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" -#: ../../src/introduction/basic-concepts.md:39 f86415e4d78e48c4a8a76ced81221b98 +#: ../../src/introduction/basic-concepts.md:39 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "" "An implementation of the CWL specification is any software written " "following what is defined in a version of the specification document. " @@ -528,24 +555,24 @@ msgid "" "and commercial licenses." msgstr "" -#: ../../src/introduction/basic-concepts.md:44 c5524d73708c4c779980528864506fd4 +#: ../../src/introduction/basic-concepts.md:44 c3869b4ec5ff47d99e8da79770722e04 msgid "" "CWL is well suited for describing large-scale workflows in cluster, cloud" " and high performance computing environments where tasks are scheduled in" " parallel across many nodes." msgstr "" -#: ../../src/introduction/basic-concepts.md:51 ac46a9f8850a434bac5bc2b41ee6294e +#: ../../src/introduction/basic-concepts.md:51 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "" "A process is a computing unit that takes inputs and produces outputs. The" " behavior of a process can be affected by the inputs, requirements, and " @@ -554,39 +581,39 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: cf2922f645904ac7955428ecddc37b8a msgid "" "A command-line tool is a wrapper for a command-line utility like `echo`, " "`ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "" "An expression tool is a wrapper for a JavaScript expression. It can be " "used to simplify workflows and command-line tools, moving common parts of" @@ -595,7 +622,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: f6f589481d0c4891beaccb63160619ef msgid "" "Operation is an abstract process that also takes inputs, produces " "outputs, and can be used in a workflow. But it is a special operation not" @@ -604,7 +631,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "" "The workflow is a process that contains steps. Steps can be other " "workflows (nested workflows), command-line tools, or expression tools. " @@ -614,7 +641,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "" "The CWL specification allows for implementations to provide extra " "functionality and specify prerequisites to workflows through " @@ -623,24 +650,24 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "" "`InitialWorkDirRequirement` - controls staging files in the input " "directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "" "Some CWL runners may provide requirements that are not in the " "specification. For example, GPU requirements are supported in `cwltool` " @@ -650,7 +677,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: e4643938445b48cc80eb8973ceeb126e msgid "" "Hints are similar to requirements, but while requirements list features " "that are required, hints list optional features. Requirements are " @@ -659,12 +686,12 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "" "The FAIR principles have laid a foundation for sharing and publishing " "digital assets, and in particular, data. The FAIR principles emphasize " @@ -678,7 +705,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: 074af9633627470485e5225326d5f20a msgid "" "CWL has roots in \"make\" and many similar tools that determine order of " "execution, based on dependencies between tasks. However, unlike \"make\"," @@ -687,7 +714,7 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 847951c055b94a83b1e081594cef22ee msgid "" "The benefit of explicitness and isolation are flexibility, portability, " "and scalability; tools and workflows described with CWL can transparently" @@ -696,71 +723,71 @@ msgid "" msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 -#: ../../src/introduction/quick-start.md:94 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 ebf339ed376a4d3b89b15b4d5afe593b +#: ../../src/introduction/quick-start.md:94 3439764fab0e49d2bcb7c9fbae556e65 +#: 65c24244713741e196da08cb9ba237b2 f059896039524095b4deb65d693f8ddf msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "" "The CWL Specification page in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "" "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "" "The list of Implementations in the CWL website: " "" msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "" "CWL Operations are covered in the [Operations](../topics/operations.md) " "section of this user guide." msgstr "" -#: ../../src/introduction/index.md:1 c54984605872472190ae7771809a20db +#: ../../src/introduction/index.md:1 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" -#: ../../src/introduction/index.md:3 01a237b8ec2f46c9acd31d142591ce75 +#: ../../src/introduction/index.md:3 950370f0a36048b38e1bde9b78f80816 msgid "" "This section will guide you through a short introduction to CWL, the " "prerequisites for following this user guide, and some basic concepts that" " are useful to know before reading the rest of the user guide." msgstr "" -#: ../../src/introduction/prerequisites.md:1 3fb9888b666945eab1e3ff109646c574 +#: ../../src/introduction/prerequisites.md:1 f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" -#: ../../src/introduction/prerequisites.md:6 5fb0486762354f93853fff209f835c08 +#: ../../src/introduction/prerequisites.md:6 353b14f06ee845d0a06a829643e31534 msgid "" "The software and configurations listed in this section are prerequisites " "for following this user guide. The CWL standards are implemented by many " @@ -770,11 +797,11 @@ msgid "" "look different (though the exact workflow outputs should be identical)." msgstr "" -#: ../../src/introduction/prerequisites.md:12 5f1e7a608e0b455196d191c845a5c98e +#: ../../src/introduction/prerequisites.md:12 b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" -#: ../../src/introduction/prerequisites.md:14 7ba4b5c51be24f5392949d06ee42e018 +#: ../../src/introduction/prerequisites.md:14 ff2bb4c6504b456bac7ca9c514414dbf msgid "" "There are many implementations of the CWL standards. Some are complete " "CWL runners, while others could be plug-ins or extensions to workflow " @@ -782,29 +809,29 @@ msgid "" "concepts.md#implementations) section." msgstr "" -#: ../../src/introduction/prerequisites.md:19 e2d3e6dd13b14d819a504c35da6fe8e7 +#: ../../src/introduction/prerequisites.md:19 cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" -#: ../../src/introduction/prerequisites.md:21 91251d1f0efb4d4cb083b4517ff3107a +#: ../../src/introduction/prerequisites.md:21 5089fdba8aed4113983fa86e698df98b msgid "" "We recommend using an up-to-date operating system. You can choose any of " "the following options for your operating system:" msgstr "" -#: ../../src/introduction/prerequisites.md:24 6ad263e267514c5fb05794d3d76d418d +#: ../../src/introduction/prerequisites.md:24 dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" -#: ../../src/introduction/prerequisites.md:25 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: ../../src/introduction/prerequisites.md:25 c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" -#: ../../src/introduction/prerequisites.md:26 5195706d9c6c4573aff135fd539759a2 +#: ../../src/introduction/prerequisites.md:26 beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" -#: ../../src/introduction/prerequisites.md:29 9c4506915e4c40599527bc1d2b18645b +#: ../../src/introduction/prerequisites.md:29 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "" "If you are using Windows, you will have to install the [Windows Subsystem" " for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) " @@ -814,11 +841,11 @@ msgid "" "access and a recent version of Python (3.6+)." msgstr "" -#: ../../src/introduction/prerequisites.md:35 37d9eb784ec1425786158f98e3f63890 +#: ../../src/introduction/prerequisites.md:35 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" -#: ../../src/introduction/prerequisites.md:41 572f493a985141a1b92dafbdba92790d +#: ../../src/introduction/prerequisites.md:41 0f2704bf1f7148be95e999e312899f11 msgid "" "The first thing you will need for running CWL workflows is a CWL runner. " "`cwltool` is a Python Open Source project maintained by the CWL " @@ -826,7 +853,7 @@ msgid "" "support everything in the current CWL specification, {{ cwl_version }}." msgstr "" -#: ../../src/introduction/prerequisites.md:46 9606d3c4849f4b17b2e55a298210f055 +#: ../../src/introduction/prerequisites.md:46 86264c9e56104ecea9146407c379aae2 msgid "" "`cwltool` can be installed with `pip`. We recommend using a virtual " "environment like `venv` or `conda`. The following commands will create " @@ -834,26 +861,26 @@ msgid "" "install `cwltool` in that environment:" msgstr "" -#: ../../src/introduction/prerequisites.md:51 754fc59967d94ffa935284676d55ffed +#: ../../src/introduction/prerequisites.md:51 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" -#: ../../src/introduction/prerequisites.md:62 2905c6362d4146e8b35bc74744841972 +#: ../../src/introduction/prerequisites.md:62 f7aaafeee230400da056464c853582c2 msgid "" "Visit the `cwltool` [documentation](https://github.com/common-workflow-" "language/cwltool#install) for other ways to install `cwltool` with `apt` " "and `conda`." msgstr "" -#: ../../src/introduction/prerequisites.md:65 091278ece252483a9838fb771de3e04e +#: ../../src/introduction/prerequisites.md:65 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:67 0928a5c668c3414a945bc9eda147892c +#: ../../src/introduction/prerequisites.md:67 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:73 56f3c481762848298214a88e559fc0f9 +#: ../../src/introduction/prerequisites.md:73 6391e08e0bde49f4b21286d8fdb97433 msgid "" "The `cwltool` command has an option to validate CWL tool and workflow " "descriptions. This option will parse the CWL document, look for syntax " @@ -864,23 +891,23 @@ msgid "" " `cwltool` command:" msgstr "" -#: ../../src/introduction/prerequisites.md:79 710c266ab4a5477b84d6ea987420fa20 +#: ../../src/introduction/prerequisites.md:79 cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:84 cc353db5da2546bb88a77ce1a202ff9d +#: ../../src/introduction/prerequisites.md:84 d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" -#: ../../src/introduction/prerequisites.md:86 b62df08ec96f4cdb887600079856dd76 +#: ../../src/introduction/prerequisites.md:86 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/prerequisites.md:91 97e02557293440d1a58ba659dad21113 +#: ../../src/introduction/prerequisites.md:91 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" -#: ../../src/introduction/prerequisites.md:93 0935c3ff01634c75b5c91546dc36c7b9 +#: ../../src/introduction/prerequisites.md:93 096d0a50f69e48bd9915238d1b4264c1 msgid "" "`cwl-runner` is an implementation-agnostic alias for any CWL compliant " "runner. This simply means that the `cwl-runner` alias command can be " @@ -891,32 +918,32 @@ msgid "" " is convenient for environments with multiple CWL runners." msgstr "" -#: ../../src/introduction/prerequisites.md:101 cfb37fd605164a8d9cc75bf892ce97c0 +#: ../../src/introduction/prerequisites.md:101 f9df974a8e2645a6918e67466bd1fdc2 msgid "" "The CWL community publishes a Python package with the name `cwlref-" "runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" -#: ../../src/introduction/prerequisites.md:104 5f06a7a6aae343d989a5b30979c600f6 +#: ../../src/introduction/prerequisites.md:104 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" -#: ../../src/introduction/prerequisites.md:111 5f956260f3874b6dbeaf3ad7ecc09c9a +#: ../../src/introduction/prerequisites.md:111 746c6fc9c29d466494458a08d4c96672 msgid "" "Now you can validate and run your workflow with the `cwl-runner` " "executable, which will invoke `cwltool`. You should have the same results" " and output as in the previous section." msgstr "" -#: ../../src/introduction/prerequisites.md:115 d35e4effec554a638d6c3047ef3fd05f +#: ../../src/introduction/prerequisites.md:115 b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:120 15a1f944a0d642729d3736ed1c907074 +#: ../../src/introduction/prerequisites.md:120 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" -#: ../../src/introduction/prerequisites.md:125 fa34c808bb494ddfa3f3926bc42e650c +#: ../../src/introduction/prerequisites.md:125 705807fae182425dbf4244dbf2be1226 msgid "" "Another way to execute `cwl-runner` is by invoking the file directly. For" " that, the first thing you need to do is copy `true.cwl` workflow into a " @@ -924,30 +951,30 @@ msgid "" "*shebang*:" msgstr "" -#: ../../src/introduction/prerequisites.md:129 0c15f62eb7534e809f625f3fa213e92d +#: ../../src/introduction/prerequisites.md:129 f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" -#: ../../src/introduction/prerequisites.md:135 d67719a6f0ce4ba1bb6152a10507b729 +#: ../../src/introduction/prerequisites.md:135 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" -#: ../../src/introduction/prerequisites.md:137 1c96e75281844bfab0578bab2e816854 +#: ../../src/introduction/prerequisites.md:137 bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" -#: ../../src/introduction/prerequisites.md:144 bece1fc3c3f842b0b30d8f1b7fbfc200 +#: ../../src/introduction/prerequisites.md:144 695184d1b45a42f393e2da99c3721773 msgid "" "And finally, you can execute it directly in the command-line. On " "execution, the program specified in the shebang (`cwl-runner`) will be " "used to execute the rest of the file." msgstr "" -#: ../../src/introduction/prerequisites.md:148 a7caa36b0f83448b91ef2e76e30abc51 +#: ../../src/introduction/prerequisites.md:148 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" -#: ../../src/introduction/prerequisites.md:154 39321e93e9994fcca20b425aa45c2894 +#: ../../src/introduction/prerequisites.md:154 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "" "The *shebang* is the two-character sequence `#!` at the beginning of a " "script. When the script is executable, the operating system will execute " @@ -957,47 +984,47 @@ msgid "" " the `` program in the system `PATH`," msgstr "" -#: ../../src/introduction/prerequisites.md:161 601cf500d76c4e0287af4429a46b36d2 +#: ../../src/introduction/prerequisites.md:161 eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" -#: ../../src/introduction/prerequisites.md:163 b286d5359e184ef58054c72df4014629 +#: ../../src/introduction/prerequisites.md:163 f6b39b12bd5c495cb53e2795bf9200ed msgid "" "You can use any text editor with CWL, but for syntax highlighting we " "recommend an editor with YAML support. Popular editors are Visual Studio " "Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" -#: ../../src/introduction/prerequisites.md:167 e14423edd829401faed0950772123240 +#: ../../src/introduction/prerequisites.md:167 2fdb62a13f9447bc89183426260ce781 msgid "" "There are extensions for Visual Studio Code and WebStorm that provide " "integration with CWL, and features such as customized syntax highlighting" " and better auto-complete:" msgstr "" -#: ../../src/introduction/prerequisites.md:171 889c44360bd54a0e85e7f0e61aa6593c +#: ../../src/introduction/prerequisites.md:171 1f07135156254f74a6b043bf33d00cc3 msgid "" "Visual Studio Code with the Benten (CWL) plugin - " "" msgstr "" -#: ../../src/introduction/prerequisites.md:172 7b9bff73624947ac90a99c7880e2e911 +#: ../../src/introduction/prerequisites.md:172 de344f356b1c466d9131cdbd4d7353a3 msgid "" "cwl-plugin for IntelliJ - " msgstr "" -#: ../../src/introduction/prerequisites.md:174 c5ff687c86ef4ccaae25d8bcfbd5f873 +#: ../../src/introduction/prerequisites.md:174 3f9324ede11441f58d93875867034cf0 msgid "" "The CWL community also maintains a list of editors and viewers: " "" msgstr "" -#: ../../src/introduction/prerequisites.md:177 0a610a9632064deb824afd0719429d3a +#: ../../src/introduction/prerequisites.md:177 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" -#: ../../src/introduction/prerequisites.md:181 ec0c47438a5242cb99dffa7a4997e95a +#: ../../src/introduction/prerequisites.md:181 40cfd559d6a848d1aae354d3bdaa8e9c msgid "" "`cwltool` uses Docker to run tools, workflows, and workflow steps that " "specify a software container. Follow the instructions in the Docker " @@ -1005,7 +1032,7 @@ msgid "" "." msgstr "" -#: ../../src/introduction/prerequisites.md:185 aae94ac2114641f186eac0f4117223eb +#: ../../src/introduction/prerequisites.md:185 8a9a50b0ebe847ce90593881ffe0d69c msgid "" "You do not need to know how to write and build Docker containers. In the " "rest of the user guide, we will use existing Docker images for running " @@ -1013,57 +1040,57 @@ msgid "" "with and without containers." msgstr "" -#: ../../src/introduction/prerequisites.md:191 209e072724ed4d27b37e9bff6d55d811 +#: ../../src/introduction/prerequisites.md:191 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "" "`cwltool` supports running containers with Docker, Podman, udocker, and " "Singularity. You can also use alternative container registries for " "pulling images." msgstr "" -#: ../../src/introduction/prerequisites.md:198 3bf47876e3694e6cadb05123326459cb +#: ../../src/introduction/prerequisites.md:198 9390b03889de44638141d705e0ef8322 msgid "" "The [Implementations](basic-concepts.md#implementations) topic in the " "next section, Basic Concepts." msgstr "" -#: ../../src/introduction/prerequisites.md:199 459a65b8e67c4a9aaa03138c1abe94ad +#: ../../src/introduction/prerequisites.md:199 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" -#: ../../src/introduction/quick-start.md:1 898eb29ac7714c69840b795633953a05 +#: ../../src/introduction/quick-start.md:1 cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" -#: ../../src/introduction/quick-start.md:3 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: ../../src/introduction/quick-start.md:3 c43d9675ed134b78b02acb5a102a764a msgid "" "This section will show you a brief overview of what CWL is, and where you" " can learn more about it. No previous knowledge of CWL is required, but " "you must be comfortable following instructions for the command-line." msgstr "" -#: ../../src/introduction/quick-start.md:7 32dd2e28cf0f40b6930750f0162355eb +#: ../../src/introduction/quick-start.md:7 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" -#: ../../src/introduction/quick-start.md:12 471c47d311074ecfac071b6d52d9cfb6 +#: ../../src/introduction/quick-start.md:12 cb203354977d42a58112d09357f62565 msgid "" "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). " "The example below shows a simple CWL “Hello World” workflow annotated " "with comments. Note that comments start with `#`:" msgstr "" -#: ../../src/introduction/quick-start.md:16 5078140028ea4d04973cb9cd20f0607e +#: ../../src/introduction/quick-start.md:16 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" -#: ../../src/introduction/quick-start.md:22 ab127d4ba0a44526ab129587a8160923 +#: ../../src/introduction/quick-start.md:22 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "" "The example above is just a wrapper for the `echo` command-line tool. " "Running the workflow above with the default input values will produce the" " same result as the command-line `echo \"Hello World\"`." msgstr "" -#: ../../src/introduction/quick-start.md:27 d5cc6b4295a74f3586f022b0227759b3 +#: ../../src/introduction/quick-start.md:27 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "" "In CWL, there is a distinction between a command-line tool and a " "workflow. But for the sake of simplicity, we are using the term " @@ -1071,11 +1098,11 @@ msgid "" "](basic-concepts.md) section." msgstr "" -#: ../../src/introduction/quick-start.md:32 585a4fe583ce44e180a062742b3b0849 +#: ../../src/introduction/quick-start.md:32 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" -#: ../../src/introduction/quick-start.md:34 0d81b0c9ea58420789d1d71cca32ce88 +#: ../../src/introduction/quick-start.md:34 f3e56aedd56b4b93bdc3894273e8c144 msgid "" "`cwltool` is an implementation of the CWL specification. It is also the " "CWL *Reference Runner* for the specification, and it is compliant with " @@ -1083,11 +1110,11 @@ msgid "" "install `cwltool` using `pip`:" msgstr "" -#: ../../src/introduction/quick-start.md:39 ea4ab0782d8049d8b1b89cea4ae60048 +#: ../../src/introduction/quick-start.md:39 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" -#: ../../src/introduction/quick-start.md:47 f6f3b7453a254f828bd4c9e9fef92bed +#: ../../src/introduction/quick-start.md:47 a81342e756d24c40acc15835d0a768f2 msgid "" "If installing the cwltool using the pip command doesn't work for you, the" " [prerequisites](prerequisites.md) section contains other ways to install" @@ -1095,32 +1122,32 @@ msgid "" "following the rest of this user guide." msgstr "" -#: ../../src/introduction/quick-start.md:51 3bf9050175d4444ebbbabe219412574f +#: ../../src/introduction/quick-start.md:51 c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" -#: ../../src/introduction/quick-start.md:53 e03f72a14dcf4bf38ce8232598ca761d +#: ../../src/introduction/quick-start.md:53 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "" "The usage of the `cwltool` command-line executable is basically `cwltool " "[OPTIONS] [INPUTS_OBJECT]`. You can run the " "`hello_world.cwl` workflow without specifying any option:" msgstr "" -#: ../../src/introduction/quick-start.md:57 3dcfb2facd324dccb3084c02487625dc +#: ../../src/introduction/quick-start.md:57 ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:62 b8531da183964b02bca19f818ec076d4 +#: ../../src/introduction/quick-start.md:62 0d8a788402914ebd8f09a5ca80650011 msgid "" "Or you can override the default value of the input parameter `message`, " "similar to how you would change the argument of the `echo` base command:" msgstr "" -#: ../../src/introduction/quick-start.md:65 7ba1ddebeb2843179fe99fc410b193c6 +#: ../../src/introduction/quick-start.md:65 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" -#: ../../src/introduction/quick-start.md:70 a6dc303e9d284b60bf1102212505ca27 +#: ../../src/introduction/quick-start.md:70 2ea056ab04b6419a9faf350de22a17f2 msgid "" "Another way of passing values to your workflow input parameters is via an" " *Inputs Object*. This is a file containing the input fields with their " @@ -1128,21 +1155,21 @@ msgid "" "YAML. For example:" msgstr "" -#: ../../src/introduction/quick-start.md:74 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: ../../src/introduction/quick-start.md:74 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" -#: ../../src/introduction/quick-start.md:80 6d1d6f42ada2418ba0a1de1371825b9f +#: ../../src/introduction/quick-start.md:80 e76bfcc0c9f84bcdb3f6d5277869a88c msgid "" "You can use this Inputs Object file now to execute the “Hello World” " "workflow:" msgstr "" -#: ../../src/introduction/quick-start.md:82 1cd924fe8ace4a82ad8701f37b5e7d84 +#: ../../src/introduction/quick-start.md:82 d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" -#: ../../src/introduction/quick-start.md:88 aa297c52cd964291a47bb91c0135156b +#: ../../src/introduction/quick-start.md:88 b6d59e4b9c854abab1b3f7a0fa26f504 msgid "" "We used a similar file name for the workflow and for the Inputs Object " "files. The *-job.json* suffix is very common in Inputs Object files, but " @@ -1150,46 +1177,46 @@ msgid "" "Inputs Object files." msgstr "" -#: ../../src/introduction/quick-start.md:96 28b02c90397745bfbacc03c3b1034939 +#: ../../src/introduction/quick-start.md:96 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" -#: ../../src/introduction/quick-start.md:97 ef2a4f39f01049b891868b84d968c0dd +#: ../../src/introduction/quick-start.md:97 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" -#: ../../src/introduction/quick-start.md:98 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: ../../src/introduction/quick-start.md:98 7282abfa7155497ca47c30f9abfb6474 msgid "" "The [`common-workflow-language` organization](https://github.com/common-" "workflow-language) at GitHub." msgstr "" -#: ../../src/introduction/quick-start.md:99 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: ../../src/introduction/quick-start.md:99 176d8d47830f4031bb95dc231ebf1303 msgid "" "[Common Workflow Language at " "Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" -#: ../../src/introduction/quick-start.md:100 46f6f8d050ce4f8c897056167d9707a7 +#: ../../src/introduction/quick-start.md:100 82a7ca3703bc4f0daa18942a1ac8943b msgid "" "[YAML.org](http://yaml.org/) and [YAML at " "Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" -#: ../../src/introduction/quick-start.md:101 5ee00ee409b746dc951ca1d4c360e624 +#: ../../src/introduction/quick-start.md:101 d039a9d6461c44628d4660c00d9ce6ff msgid "" "The {{'[CWL Specification " "VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', " "cwl_version_text) }}." msgstr "" -#: ../../src/introduction/quick-start.md:102 d4af972281174b8999eab55ee0ab1a0e +#: ../../src/introduction/quick-start.md:102 fbc3383d9e1c4eaca7931c3cc4f1752b msgid "" "[Workflow management system at " "Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" -#: ../../src/setup.md:9 80401cfffae042ab9ec4b3754af04b25 +#: ../../src/setup.md:9 1330bd38c4b5495f890b98c669f81a9d msgid "" "This page is out-of-date and was kept here to preserve the links of the " "old User Guide. The information on this page has been migrated to the " @@ -1197,19 +1224,19 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "" "Sometimes tools require additional command line options that don't " "correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "" "In this example, we will wrap the Java compiler to compile a java source " "file to a class file. By default, \"javac\" will create the class files " @@ -1220,37 +1247,37 @@ msgid "" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 -#: ../../src/topics/staging-input-files.md:15 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: ../../src/topics/staging-input-files.md:15 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: 9643449da1da46d7861866dce490cbcb msgid "" "And now invoke `cwltool` providing the tool description and the input " "object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "" "Here we use the `arguments` field to add an additional argument to the " "command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1261,11 +1288,11 @@ msgid "" "Environment][runtime] section of the CWL specification for details." msgstr "" -#: ../../src/topics/best-practices.md:1 109b773789024b2b9c063a6169c6169f +#: ../../src/topics/best-practices.md:1 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" -#: ../../src/topics/best-practices.md:3 959fa04f88e54d42b9b774cc95d85ee0 +#: ../../src/topics/best-practices.md:3 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "" "The following are a set of recommended good practices to keep in mind " "when writing a Common Workflow Language description for a tool or " @@ -1273,13 +1300,13 @@ msgid "" "usefulness: although more is better, not all are required." msgstr "" -#: ../../src/topics/best-practices.md:8 64674980c3f24c45bbfbf3f957dda55e +#: ../../src/topics/best-practices.md:8 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "" "No `type: string` parameters for names of input or reference " "files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" -#: ../../src/topics/best-practices.md:11 90f2e4265919446a902e17627f4420e2 +#: ../../src/topics/best-practices.md:11 4dee8504a8e5496081dadc386ab45540 msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1295,7 +1322,7 @@ msgid "" "license]." msgstr "" -#: ../../src/topics/best-practices.md:20 6b5f91a749fd44b5acfd6071c9913342 +#: ../../src/topics/best-practices.md:20 674c238b25e240eda05e22e399f2f78f msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1305,43 +1332,43 @@ msgid "" "SPDX identifier, provide a URL to the license." msgstr "" -#: ../../src/topics/best-practices.md:26 5fe2962837b14f0e9989063be4a506c3 +#: ../../src/topics/best-practices.md:26 b651f80f47b4442fbf29454a233697fc msgid "" "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-" "Programmer][sci-license]\"" msgstr "" -#: ../../src/topics/best-practices.md:28 4e1bdea962ed4618884cb9d1d59d7509 +#: ../../src/topics/best-practices.md:28 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" -#: ../../src/topics/best-practices.md:37 37eff4ca02e843259f6ffa38e4a87a04 +#: ../../src/topics/best-practices.md:37 3a87a0fb2a364e3da5aaa4017e430b19 msgid "" "For more examples of providing metadata within CWL descriptions, see " "[the Metadata and Authorship section of this User Guide](../topics" "/metadata-and-authorship.md)." msgstr "" -#: ../../src/topics/best-practices.md:40 ae47231c203d40a98c10045038ea9b65 +#: ../../src/topics/best-practices.md:40 ecf2b9c0b1664afe9c4e180610610021 msgid "" "Include [attribution information][license-example] for the author(s) of " "the CWL tool or workflow description. Use unambiguous identifiers like " "[ORCID][orcid]." msgstr "" -#: ../../src/topics/best-practices.md:44 018a6d5dbf1044559b365c7b9017eb3f +#: ../../src/topics/best-practices.md:44 e24cb13d98014e558b6a6946758359e0 msgid "" "In tool descriptions, list dependencies using short name(s) under " "`SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:47 e073d8f990c44b09a73d642cfe49bebd +#: ../../src/topics/best-practices.md:47 f2b14a92374e449d9fb1e8c86ae0dd61 msgid "" "Include [SciCrunch][scicrunch] identifiers for dependencies in " "`https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" -#: ../../src/topics/best-practices.md:50 e04fae88d9b64493ac69eaee24585098 +#: ../../src/topics/best-practices.md:50 928e3df7ca3e479ca6474a8e72cf36eb msgid "" "All `input` and `output` identifiers should reflect their conceptual " "identity. Use informative names like `unaligned_sequences`, " @@ -1349,13 +1376,13 @@ msgid "" "`foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" -#: ../../src/topics/best-practices.md:55 b26b9c9b1c4346a297a31c9721f0172a +#: ../../src/topics/best-practices.md:55 d355f035676446c88b028f327aeb4829 msgid "" "In tool descriptions, include a list of version(s) of the tool that are " "known to work with this description under `SoftwareRequirement`." msgstr "" -#: ../../src/topics/best-practices.md:58 b50500c3c3f54b16a535a16175a44653 +#: ../../src/topics/best-practices.md:58 339b852df24242189d6efcd2898a3396 msgid "" "`format` should be specified for all input and output `File`s. " "Bioinformatics tools should use format identifiers from [EDAM][edam-" @@ -1367,44 +1394,44 @@ msgid "" "let us know about it." msgstr "" -#: ../../src/topics/best-practices.md:66 623f3a804199449bb85e23e00c8bb507 +#: ../../src/topics/best-practices.md:66 3ef57e6862f240bebcf193a52397af0a msgid "" "Mark all input and output `File`s that are read from or written to in a " "streaming compatible way (only once, no random-access), as `streamable: " "true`." msgstr "" -#: ../../src/topics/best-practices.md:69 effea0b1356447c0899ca0746667ea31 +#: ../../src/topics/best-practices.md:69 f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "" "Each `CommandLineTool` description should focus on a single operation " "only, even if the (sub)command is capable of more. Don't overcomplicate " "your tool descriptions with options that you don't need or use." msgstr "" -#: ../../src/topics/best-practices.md:73 00e8ef87864c4ca2b2c1c0548b02b38d +#: ../../src/topics/best-practices.md:73 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "" "Custom types should be defined with one external YAML per type definition" " for re-use." msgstr "" -#: ../../src/topics/best-practices.md:76 6e6f48d70b894a6c959ca30fe6bad772 +#: ../../src/topics/best-practices.md:76 c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" -#: ../../src/topics/best-practices.md:78 02fe08760a4a4ab49e96f4e51316a81d +#: ../../src/topics/best-practices.md:78 fae385da16aa443da996fa23ac03d6ae msgid "" "If useful, include a top-level `doc` as well. This should provide a " "longer, more detailed description than was provided in the top-level " "`label` (see above)." msgstr "" -#: ../../src/topics/best-practices.md:82 172ed7915a654964ba63f860b2d65330 +#: ../../src/topics/best-practices.md:82 92430be71ecc40e18bbbb80d5576c613 msgid "" "Use `type: enum` instead of `type: string` for elements with a fixed list" " of valid values." msgstr "" -#: ../../src/topics/best-practices.md:85 4d0a2871a7484e21b3c39c4dbaaa63fc +#: ../../src/topics/best-practices.md:85 387d83db81024f65aa9a890c2d07874a msgid "" "Evaluate all use of JavaScript for possible elimination or replacement. " "One common example: manipulating `File` names and paths? Consider whether" @@ -1412,31 +1439,31 @@ msgid "" "`nameroot`, `nameext`, etc., could be used instead." msgstr "" -#: ../../src/topics/best-practices.md:90 1eea9f1e284447718141f5417b6bb433 +#: ../../src/topics/best-practices.md:90 d8e2280a75a74916a1630afaa2fe2ae3 msgid "" "Give the tool description to a colleague (preferably at a different " "institution) to test and provide feedback." msgstr "" -#: ../../src/topics/best-practices.md:93 509411d353fe4314b087b81b09ea960b +#: ../../src/topics/best-practices.md:93 f1c1340f9745458980e0fbd641738687 msgid "" "Complex workflows with individual components which can be abstracted " "should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make" " their workflow modular and allow sections of them to be easily reused." msgstr "" -#: ../../src/topics/best-practices.md:97 a54bc80bf08243bba67d98dd682ee134 +#: ../../src/topics/best-practices.md:97 5424e5472c3d466fa2a3d2022c6cb475 msgid "" "Software containers should be made to be conformant to the " "[\"Recommendations for the packaging and containerizing of bioinformatics" " software\"][containers] (also useful to other disciplines)." msgstr "" -#: ../../src/topics/command-line-tool.md:1 69ecdaea24ef42eebef9d86e5d716b11 +#: ../../src/topics/command-line-tool.md:1 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" -#: ../../src/topics/command-line-tool.md:3 3cc5847468d1478bb5589dee68147189 +#: ../../src/topics/command-line-tool.md:3 12f57b2ba76b492abe1816e06bfb1417 msgid "" "A command-line tool is a type of Process object that can be run by itself" " or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, " @@ -1444,52 +1471,52 @@ msgid "" "attribute of the command-line tool CWL document." msgstr "" -#: ../../src/topics/command-line-tool.md:8 98c6bc409420485095ae65d6b0b9a3a0 +#: ../../src/topics/command-line-tool.md:8 e1f657a46ce94a0d83671540e2cc2dab msgid "" "A CWL command-line tool must also have `inputs` and `outputs`. The " "following example contains a minimal example of a CWL command-line tool " "for the `echo` Linux command, using inputs and outputs." msgstr "" -#: ../../src/topics/command-line-tool.md:19 ebe23e5378514f888a9ec32a2adb1e98 +#: ../../src/topics/command-line-tool.md:19 abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" -#: ../../src/topics/command-line-tool.md:50 387cfe85604f424f8d31c4a4c9c15edb +#: ../../src/topics/command-line-tool.md:50 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" -#: ../../src/topics/command-line-tool.md:57 7b1d65754e854693bb60289c97d3fb5d +#: ../../src/topics/command-line-tool.md:57 a5eacdbc9aa142c890b177869da4143d msgid "" "The example above uses a simplified form to define inputs and outputs. " "You will learn more about in the [Inputs](../topics/inputs.md) and in the" " [Outputs](../topics/outputs.md) sections." msgstr "" -#: ../../src/topics/command-line-tool.md:68 f440cef729c8410281432307a4da8d55 +#: ../../src/topics/command-line-tool.md:68 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" -#: ../../src/topics/command-line-tool.md:69 4fbb8ceb1b59480583ac611142167049 +#: ../../src/topics/command-line-tool.md:69 e3bdaceae8784ab0807b2cf356a98580 msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. If a command-line tool is written manually in CWL v1.1+, there is" " a need to specify when network access is required." msgstr "" -#: ../../src/topics/command-line-tool.md:83 b87869204838415bbf694214e3680593 +#: ../../src/topics/command-line-tool.md:83 ed521ac365db4a6ba5a1051fbaa2932e msgid "" "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get " "Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "" "Sometimes you need to create a file on the fly from input parameters, " "such as tools that expect to read their input configuration from a file " @@ -1498,17 +1525,17 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "" "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are " "expanded by the CWL engine before creating the file. Here, insert the " @@ -1516,7 +1543,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 9454a330b9324744b89448f2694b1b03 msgid "" "The _CWL expressions_ are independent of any _shell variables_ used later" " during command line tool invocation. That means that any genuine need " @@ -1526,7 +1553,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "" "To test the above CWL tool, use this job to provide the input value " "`message`:" @@ -1534,13 +1561,13 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 ../../src/topics/outputs.md:77 -#: 294fd83a97a64249bac38f7482159372 9e8eb1542db640ff9e300649ce50dc9d -#: ccec7f73b9d948e79a6cdf32bc124092 +#: 2699fbc4376148af91b7a5a6cdac467c 2d2ef4769b2347e79db827655f1bcdeb +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "" "Before we run this, let us look at each step in a little more detail. The" " base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the " @@ -1548,7 +1575,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "" "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a " "YAML array, we need a `-` on the first line of each element of the array," @@ -1560,7 +1587,7 @@ msgid "" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "" "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the " "formatting." @@ -1570,19 +1597,19 @@ msgstr "" #: ../../src/topics/environment-variables.md:18 #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 ../../src/topics/workflows.md:198 -#: 457756c4e9544f068af897113358cc89 6d5ae75431424ea788c3440606f22940 -#: 98e0548845fa447fb05a29c9fc2f17b5 de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: e9801b2142cd45368a73ef9b121c1d08 +#: 293fb1d428b849aebccad598a932992d 7bbd2d738fc54649aeb10f8d2bc38b6f +#: b372f33c65bb4707b2a462a960bb1373 d6255506eebe44be94c5ce703c44a513 +#: f924d65fed0c4cb5b0a019b084a8b535 msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line:" msgstr "" -#: ../../src/topics/custom-types.md:1 ee2bca9bdbb74b60a706c3118d6a17ba +#: ../../src/topics/custom-types.md:1 cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" -#: ../../src/topics/custom-types.md:3 e63ae9694f40438d872d141ae824a42d +#: ../../src/topics/custom-types.md:3 67573252cc064b27ab13eebc468ac58a msgid "" "Sometimes you may want to write your own custom types for use and reuse " "in CWL descriptions. Use of such custom types can reduce redundancy " @@ -1591,21 +1618,21 @@ msgid "" " need to fiddle with the CWL description directly." msgstr "" -#: ../../src/topics/custom-types.md:9 750fdd4c270e46a09f79e867358f7414 +#: ../../src/topics/custom-types.md:9 73e68b3af9cf41338d843c0c40e50cdc msgid "" "The example below is a CWL description of the [biom convert format][biom]" " tool for converting a standard biom table file to hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:12 b3f688cc82444ef7a7a0aa63dac39cac +#: ../../src/topics/custom-types.md:12 ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" -#: ../../src/topics/custom-types.md:18 3638be18b4f64cf08053d512e590dda3 +#: ../../src/topics/custom-types.md:18 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" -#: ../../src/topics/custom-types.md:24 7d5b9c21739c48f18c13614ca6967f6b +#: ../../src/topics/custom-types.md:24 a999b1acda2641598086648c64aa3831 msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1614,13 +1641,13 @@ msgid "" "`wget`:" msgstr "" -#: ../../src/topics/custom-types.md:30 8fea29993f944d8d8d3181afa29bd0a6 +#: ../../src/topics/custom-types.md:30 f8c12a58cb0b46a488823c6ae95f25ea msgid "" "On line 29, in `inputs:table_type`, a list of allowable table options to " "be used in the table conversion are imported as a custom object:" msgstr "" -#: ../../src/topics/custom-types.md:46 02d0b648d70f49d7892f690be06df585 +#: ../../src/topics/custom-types.md:46 f25a63e0926d4932bbe64b2e4bdabf9e msgid "" "The reference to a custom type is a combination of the name of the file " "in which the object is defined (`biom-convert-table.yaml`) and the name " @@ -1631,15 +1658,15 @@ msgid "" " to create an OTU table in hdf5 format." msgstr "" -#: ../../src/topics/custom-types.md:53 0743bef42b9a42328849c8c2f9da9eed +#: ../../src/topics/custom-types.md:53 b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" -#: ../../src/topics/custom-types.md:55 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: ../../src/topics/custom-types.md:55 fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" -#: ../../src/topics/custom-types.md:61 be848f30769543eb9c0be55263e3f758 +#: ../../src/topics/custom-types.md:61 d718630a296545f3a989c8c71e9ddc77 msgid "" "In order for the custom type to be used in the CWL description, it must " "be imported. Imports are described in " @@ -1647,7 +1674,7 @@ msgid "" "types.cwl` description:" msgstr "" -#: ../../src/topics/custom-types.md:76 cbff44a64ba4432cb59a82f82c2f0103 +#: ../../src/topics/custom-types.md:76 9a97acd430064710bcdf76edbd9f711c msgid "" "Note also that the author of this CWL description has also included " "`ResourceRequirement`s, specifying the minimum amount of RAM and number " @@ -1657,26 +1684,26 @@ msgid "" "chapters of this user guide." msgstr "" -#: ../../src/topics/environment-variables.md:1 617f1c0084cf42d9be4c7a8fa5a48432 +#: ../../src/topics/environment-variables.md:1 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" -#: ../../src/topics/environment-variables.md:3 cee79afa3c6f43c29ef05e06b7843d35 +#: ../../src/topics/environment-variables.md:3 3c821c9c46d841ec89b8a5b1018f3af8 msgid "" "Tools run in a restricted environment and do not inherit most environment" " variables from the parent process. You can set environment variables " "for the tool using `EnvVarRequirement`." msgstr "" -#: ../../src/topics/environment-variables.md:7 225903b11efa417989df42de86ad2451 +#: ../../src/topics/environment-variables.md:7 bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:1 1a5f058290064c1cad05e63eb127fcbb +#: ../../src/topics/expression-tool.md:1 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" -#: ../../src/topics/expression-tool.md:3 74ad8d69cf294ae880dbbe28e25b3545 +#: ../../src/topics/expression-tool.md:3 48deb71f361a43e48a56ed483075bca8 msgid "" "An expression tool is a type of Process that can be run by itself or as a" " Workflow step. It executes a pure JavaScript expression. It is meant to " @@ -1684,32 +1711,32 @@ msgid "" "operate on input data and produce some result as output." msgstr "" -#: ../../src/topics/expression-tool.md:8 5293e8ee9b3b4f59947cfc164ef111c4 +#: ../../src/topics/expression-tool.md:8 716b56506ca7470299899c5d820a9ea2 msgid "" "Similar to the command-line tool it requires `inputs` and `outputs`. But " "instead of `baseCommand`, it requires an `expression` attribute." msgstr "" -#: ../../src/topics/expression-tool.md:17 ffa1955c759942c68e7589429e5ea86b +#: ../../src/topics/expression-tool.md:17 b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" -#: ../../src/topics/expression-tool.md:48 038bc0ba5f6a405a8255a7be76979baf +#: ../../src/topics/expression-tool.md:48 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" -#: ../../src/topics/expression-tool.md:67 fae1c63de02e48c0969a98e4c49b2e06 +#: ../../src/topics/expression-tool.md:67 e3ecac0a8e604f2b98a2a12b0579990a msgid "" "We had to use an `InlineJavascriptRequirement` as our expression contains" " a JavaScript call in `.toUpperCase()`. This means to tools using the " "expression tool that JavaScript is a requirement." msgstr "" -#: ../../src/topics/expressions.md:1 7093a94695524851a5463193f0701b78 +#: ../../src/topics/expressions.md:1 c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" -#: ../../src/topics/expressions.md:3 dc8274ecb15948c29a31db89b12a58bd +#: ../../src/topics/expressions.md:3 007a345b4bad49cf996c4301b8386473 msgid "" "If you need to manipulate input parameters, include the requirement " "`InlineJavascriptRequirement` and then anywhere a parameter reference is " @@ -1717,7 +1744,7 @@ msgid "" "the CWL runner." msgstr "" -#: ../../src/topics/expressions.md:9 cec8eef8a5aa49778ecedd4195ab9f2c +#: ../../src/topics/expressions.md:9 2edbd398eadb458b8eacd5fa5496f0a2 msgid "" "JavaScript expressions should only be used when absolutely necessary. " "When manipulating file names, extensions, paths etc, consider whether one" @@ -1726,67 +1753,67 @@ msgid "" "practices](best-practices.md)." msgstr "" -#: ../../src/topics/expressions.md:16 df100967597043c78112bf43b520cfab +#: ../../src/topics/expressions.md:16 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:22 59ccf4daba39406581a6bc2d9bb1b7d2 +#: ../../src/topics/expressions.md:22 efb5fd14988c4e2a8f834ee5369d4102 msgid "" "As this tool does not require any `inputs` we can run it with an (almost)" " empty job file:" msgstr "" -#: ../../src/topics/expressions.md:25 570cc75699dd4e0a987fc9aca9a01ee4 +#: ../../src/topics/expressions.md:25 e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" -#: ../../src/topics/expressions.md:31 9e123723048546d495ed5110d7177708 +#: ../../src/topics/expressions.md:31 276f688ba7cc471a842f085ca852b1d9 msgid "" "`empty.yml` contains a description of an empty JSON object. JSON objects " "descriptions are contained inside curly brackets `{}`, so an empty object" " is represented simply by a set of empty brackets." msgstr "" -#: ../../src/topics/expressions.md:35 26543894f6e04270b89ab702451bcc89 +#: ../../src/topics/expressions.md:35 ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" -#: ../../src/topics/expressions.md:37 f403c1d4e43a4aa0aef8488d2b5a6262 +#: ../../src/topics/expressions.md:37 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" -#: ../../src/topics/expressions.md:47 249dffb569a944c897ce5862e5f28fad +#: ../../src/topics/expressions.md:47 8b70a1ad70514039b97164fa630c12e4 msgid "" "Note that requirements can be provided with the map syntax, as in the " "example above:" msgstr "" -#: ../../src/topics/expressions.md:54 1641c96aca2f4923885fe8a509eb3a49 +#: ../../src/topics/expressions.md:54 2f28ab412d2843ffa5f14acdc01fc732 msgid "" "Or as an array, with each entry (in this case, only `class: " "InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to" " describe the additional command line arguments." msgstr "" -#: ../../src/topics/expressions.md:62 bc63405a0d964df2bd9493996abc48fe +#: ../../src/topics/expressions.md:62 d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" -#: ../../src/topics/expressions.md:64 5c191d1420db4e26aca31c1b1e34cb75 +#: ../../src/topics/expressions.md:64 cbec9277b5004e50af2728cbda0df740 msgid "" "Just like [parameter references](parameter-references.md), you can use " "JavaScript Expressions only in certain fields. These are:" msgstr "" -#: ../../src/topics/expressions.md:66 d6a5c65e824a4bbc94578df9597d4716 +#: ../../src/topics/expressions.md:66 e259f55f8000479bbd8009e25cf0ca6c msgid "" "From " "[`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 -#: ../../src/topics/parameter-references.md:64 a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: ../../src/topics/parameter-references.md:64 0222780b98ac48e89b1b4f57c9df8590 +#: 1acb064f7a4a482aa0174bdc847c6382 msgid "`arguments`" msgstr "" @@ -1794,32 +1821,32 @@ msgstr "" #: ../../src/topics/expressions.md:89 #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 -#: ../../src/topics/parameter-references.md:86 05c34a5a2e404a14b9d284a9d0c73bd3 -#: 2a2286a9c8494e3b88db35bf63230f33 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba e5b0293e6fcd4e9b8d7be3fc9fc127d3 -#: e7f1993580f0425098a719e83a64cc7f +#: ../../src/topics/parameter-references.md:86 17b10d1e91b24dc582df98fcd2ac850e +#: 224732683a9c41f3ba1b778851e745a8 d44e3cfa661840eb851782e24caf1b68 +#: e4e68011dc5f42e4918c747afa7d764b ef2b8433778a40408f179c3e6f0cf99e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 -#: ../../src/topics/parameter-references.md:66 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: ../../src/topics/parameter-references.md:66 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 -#: ../../src/topics/parameter-references.md:67 3f29e4a3087847e9af6f19166a8def9a -#: 92697d3179ec48898eaea9aba3c24dcd +#: ../../src/topics/parameter-references.md:67 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 -#: ../../src/topics/parameter-references.md:68 c0eaef93bc3743279549bcfb8b014ca3 -#: d6722e3093884ad7b62696fbb2f48fdc +#: ../../src/topics/parameter-references.md:68 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" -#: ../../src/topics/expressions.md:72 37c493fdc2f0410a9748f8faf09ce5b5 +#: ../../src/topics/expressions.md:72 8210b36347a749889450529ecdf4ff0e msgid "" "From " "[CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" @@ -1830,11 +1857,11 @@ msgstr "" #: ../../src/topics/parameter-references.md:70 #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 -#: ../../src/topics/parameter-references.md:90 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 4ff7326e660f42d8b45c3353005554f8 -#: 6020618711d449a48618c11215453487 7b132c6e720f4256859757778f5c4fef -#: 9cfb6ca1255241aa9e5928ea981286e9 c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c +#: ../../src/topics/parameter-references.md:90 1bc510d525f0414e88692e356e67fbbc +#: 801729c7c71b4109824b035437e69bf9 b1446bab2732412e91f721a08067b0bd +#: bd61499b71e64164878dea08d6d7141e d0a92a3792b549e9b5ddce4667d168d2 +#: d2e246ae56a24e4abdd6b7d9812a86e2 e89dbeb22f41430ca39c923d9fdf68cb +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1843,51 +1870,51 @@ msgstr "" #: ../../src/topics/parameter-references.md:71 #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 -#: ../../src/topics/parameter-references.md:91 662b36e3505f4ac3bb5070bb6e055217 -#: 6dfc264200a9496f9d2458fc759993d8 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d a44c278bde5849aeac122c981294332c -#: e193aebe7124444c90be1f6cad81482a ee3d416cc68c4f11a79849bb67395f1b -#: f71216a4b35e4157aece5ffa2602d8bf +#: ../../src/topics/parameter-references.md:91 28b6b5ffa7524374aaa9525ebfafb762 +#: 47def3b078e2402182039be0227090ae 8a1748579de14f0888d5ee9023e37c2d +#: bcb7cd10cb5947bb9d85c040f57f954f cd7a0190511d4613b09600a3b1e9d55f +#: d11f6a19ddf34cf19ec856bacf998e29 da5188d3bedc4997a35bdf417f2f643c +#: f760465a49d64d4c8468ad9c4fea62b1 msgid "`secondaryFiles`" msgstr "" -#: ../../src/topics/expressions.md:75 a3c775a0f04b4541a9b712bfe2e4e69a +#: ../../src/topics/expressions.md:75 23088850ad02459696f6bbd385109aac msgid "" "From " "[`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/expressions.md:77 ef16c4a9a7ea415fa399297b63b9710c +#: ../../src/topics/expressions.md:77 f02257a822ad46ac93c5981531cc85d5 msgid "" "From " "[CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:80 2592e429c74c4ff5b8ba68a36f060c1a +#: ../../src/topics/expressions.md:80 989a1c4aaa1143be9f53b90cd8b6d500 msgid "" "From " "[CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 -#: ../../src/topics/parameter-references.md:78 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: ../../src/topics/parameter-references.md:78 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 -#: ../../src/topics/parameter-references.md:79 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: ../../src/topics/parameter-references.md:79 44b3f123c9b04a308c1161b742a7b34b +#: d555a3d991e344a5a8e1289168d7c6d1 msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 -#: ../../src/topics/parameter-references.md:80 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: ../../src/topics/parameter-references.md:80 0e306cc923974d1db83fdfb45105a11c +#: e9fa9430535c424fa3e8be5d460d2ba4 msgid "From `Workflow`" msgstr "" -#: ../../src/topics/expressions.md:84 f09e7371708b4c0685eef2a314791ccd +#: ../../src/topics/expressions.md:84 d289541e460147aa933f7878996f8649 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1896,32 +1923,32 @@ msgid "" msgstr "" #: ../../src/topics/expressions.md:87 -#: ../../src/topics/parameter-references.md:84 aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: ../../src/topics/parameter-references.md:84 446f1190af7a40a0913ff04ce7aa938c +#: b0290d1a477b48119e17cf1fed9d6dff msgid "From `steps`" msgstr "" -#: ../../src/topics/expressions.md:88 6c37a1ff939748bf83a86c07c3d017fe +#: ../../src/topics/expressions.md:88 81b4d1f23a3642bfa9bb395b94260cd1 msgid "" "From " "[WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 -#: ../../src/topics/parameter-references.md:87 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: ../../src/topics/parameter-references.md:87 557694f82e314baa9ccafba14d6ff2c9 +#: e1cde4aa32c041238ed2596173c6d824 msgid "" "From " "[ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 -#: ../../src/topics/parameter-references.md:88 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: ../../src/topics/parameter-references.md:88 3c939769ede94602a67fc50c435741cf +#: c2a92d3eca7f4ee39cec649170eeea53 msgid "`expression`" msgstr "" -#: ../../src/topics/expressions.md:92 58a1773b1cf546d7890010fdebd47388 +#: ../../src/topics/expressions.md:92 f495da32f05a4a5ba9539be0a54c1a59 msgid "" "From " "[InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -1929,61 +1956,61 @@ msgid "" "[ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/expressions.md:95 230f3227ed1144f7abe0f8c231bebbd5 +#: ../../src/topics/expressions.md:95 bdb4c68a175047ddbe141ca24960127f msgid "" "From " "[`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 -#: ../../src/topics/parameter-references.md:93 5c77dc9f8afe4dd88933943030e836f2 -#: c9534670f5f04769aa3749c3778eb705 +#: ../../src/topics/parameter-references.md:93 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 -#: ../../src/topics/parameter-references.md:94 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: ../../src/topics/parameter-references.md:94 2b25152f6df5494a8632f3ce631c20d8 +#: 718ceee9973240ec9c100977bbcc8921 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 -#: ../../src/topics/parameter-references.md:95 aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: ../../src/topics/parameter-references.md:95 846cd427ae25410eae7c920b237edcb0 +#: c07ab08eb75d4528949c56a3d7c12b28 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 -#: ../../src/topics/parameter-references.md:96 266dfb5fe6a842078baf66073cac9623 -#: fe3b9fb45e01490498c5a35c012b3de8 +#: ../../src/topics/parameter-references.md:96 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 -#: ../../src/topics/parameter-references.md:97 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: ../../src/topics/parameter-references.md:97 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 -#: ../../src/topics/parameter-references.md:98 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: ../../src/topics/parameter-references.md:98 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 -#: ../../src/topics/parameter-references.md:99 09120baec1464afb8aed4edd773bf509 -#: fec70bb106ad4d95a2d55ebdcf711afc +#: ../../src/topics/parameter-references.md:99 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: 2e128858cd06466680fc6bbfb577b818 c98db5b115ee4c4abb211481fe7214b0 +#: 1f39f016524a459895ed03c72d74932b e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" -#: ../../src/topics/expressions.md:104 1dc4148caef748428a7d13caff37b1b1 +#: ../../src/topics/expressions.md:104 97b61352363f47cb890e8937c5613fa3 msgid "" "From " "[`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" @@ -1991,33 +2018,33 @@ msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 568406e34c8642578396177b40043014 8caf296626024598b4450311ade09e56 +#: 9359ef94c41249ea8e76fe629926054e a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" -#: ../../src/topics/expressions.md:106 947b1ca132a54ed39745cd12ebcd65e1 +#: ../../src/topics/expressions.md:106 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 f56fb5fa08994fe08cc8ae8c193828d9 +#: 9d4889c8cec24351a7a9e3c547e331b6 effc0208cf4f4551958db6e526c0528b msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: 063e2ae9a0eb404e8c277ef7090eb6bc c6dbe0a66b9f47e5b4b47c44d9f54519 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 be6c1e85c7b6495d8086c262daad20e7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 39c6edc2866542cfa7da9f842fd3edd0 72acfeef964841e7b65937b62b5850f0 +#: 2183ac54ae10428388649daa57b6a7f4 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" -#: ../../src/topics/expressions.md:110 5fa512d352d945e7a3e0d59b0987cd1b +#: ../../src/topics/expressions.md:110 0bc424ef2ca346099f29b937379908a0 msgid "" "From " "[EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" @@ -2025,22 +2052,22 @@ msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 520bf799546b4700a4f38f950ffd913b 79755be159fb45b0ad06cecce623ce2c +#: 107b54b832df4d408d1315bdba05b4dd 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" -#: ../../src/topics/expressions.md:116 81e91df082834d2cab7ef1f62d8ba57a +#: ../../src/topics/expressions.md:116 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" -#: ../../src/topics/expressions.md:118 e6bfd1dc2e324992b6c3332c11ae3445 +#: ../../src/topics/expressions.md:118 29b73e1dd72744f68377f0a38c10f062 msgid "" "The requirement `InlineJavascriptRequirement` supports an `expressionLib`" " attribute that allows users to load external JavaScript files, or to " "provide inline JavaScript code." msgstr "" -#: ../../src/topics/expressions.md:122 acf10261df2944ec890d754fd56c6b28 +#: ../../src/topics/expressions.md:122 38a2afaf4a6c4d04909af22c93f2808d msgid "" "Entries added to the `expressionLib` attribute are parsed with the " "JavaScript engine of a CWL runner. This can be used to include external " @@ -2048,7 +2075,7 @@ msgid "" " of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:128 bda6b8f398554b0c946c2c7d96308a42 +#: ../../src/topics/expressions.md:128 cd74f34b21af4de9be96fd897efc469b msgid "" "The CWL standards (versions 1.0 through 1.2) " "[states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions)" @@ -2058,54 +2085,54 @@ msgid "" "compliant with ECMAScript 5.1." msgstr "" -#: ../../src/topics/expressions.md:135 454c02c3918647039c90ae387005dea6 +#: ../../src/topics/expressions.md:135 f12e371f3f1a4b0cb2cff9800352d48c msgid "" "For example, we can use `InlineJavascriptRequirement` and write a " "JavaScript function inline in `expressionLib`. That function can then be " "used in other parts of the CWL document:" msgstr "" -#: ../../src/topics/expressions.md:139 e1fad28bf9cb4c4c85eb74dd520ba107 +#: ../../src/topics/expressions.md:139 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" -#: ../../src/topics/expressions.md:146 9835d0b399b84a0084fe5a4d9e7e6405 +#: ../../src/topics/expressions.md:146 8f0e8f050e334ac08334e9215e1dcf61 msgid "" "Running this CWL workflow will invoke the JavaScript function and result " "in the `echo` command printing the input message with capital initial " "letters:" msgstr "" -#: ../../src/topics/expressions.md:149 410ba7a5ac6349a98460c6337ee5c4fb +#: ../../src/topics/expressions.md:149 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" -#: ../../src/topics/expressions.md:155 d2daf50d7f3d4de18331c8fd2c8a5786 +#: ../../src/topics/expressions.md:155 7a6be0005a6441feb67f036d005d7885 msgid "" "Let's move the `capitalizeWords` function to an external file, `custom-" "functions.js`, and import it in our CWL document:" msgstr "" -#: ../../src/topics/expressions.md:158 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ../../src/topics/expressions.md:158 ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" -#: ../../src/topics/expressions.md:164 f0ff919ffc12439d89d7b40f51ade84c +#: ../../src/topics/expressions.md:164 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" -#: ../../src/topics/expressions.md:171 307a17a893fc4dafaec2a63a95704644 +#: ../../src/topics/expressions.md:171 06635145b441418aaae84dc804f3d6ac msgid "" "The `custom-functions.js` file is included in the CWL document with the " "`$include: custom-functions.js` statement. That makes the functions and " "variables available to be used in other parts of the CWL document." msgstr "" -#: ../../src/topics/expressions.md:175 7f393e86b114470f8dda47b2deec63aa +#: ../../src/topics/expressions.md:175 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" -#: ../../src/topics/expressions.md:181 c3f459b87b96435583637b3f1573e658 +#: ../../src/topics/expressions.md:181 04eaf1f7c630450db318dcd8b7626e15 msgid "" "Finally, note that you can have both inline and external JavaScript code " "in your CWL document. In this final example we have added another entry " @@ -2114,15 +2141,15 @@ msgid "" " the external file `custom-functions.js`." msgstr "" -#: ../../src/topics/expressions.md:186 9f676022eb2744839ca2109920250cb6 +#: ../../src/topics/expressions.md:186 c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" -#: ../../src/topics/expressions.md:193 ede7285f77864fb0aee6cfecc2c97fa0 +#: ../../src/topics/expressions.md:193 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" -#: ../../src/topics/expressions.md:200 c55fb184bc614ee2b6e5e64611e5df9b +#: ../../src/topics/expressions.md:200 fd4579a3c9844492b314b5c3c1775fc7 msgid "" "The `$include` statement can be used to include a file from the local " "disk or from a remote location. It works with both relative and absolute " @@ -2131,11 +2158,11 @@ msgid "" "the CWL specification to learn more about it." msgstr "" -#: ../../src/topics/file-formats.md:1 66b522f46ce242149386e79f63b32cf8 +#: ../../src/topics/file-formats.md:1 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" -#: ../../src/topics/file-formats.md:3 64a20285785d48ca86227a0cf6353ad4 +#: ../../src/topics/file-formats.md:3 e024bcb70e04412e90e1838426d1b69a msgid "" "Tools and workflows can take `File` types as input and produce them as " "output. We also recommend indicating the format for `File` types. This " @@ -2143,7 +2170,7 @@ msgid "" "some simple type-checking when creating parameter files." msgstr "" -#: ../../src/topics/file-formats.md:8 5f71bbe2c74e4260b79d4d9230d35397 +#: ../../src/topics/file-formats.md:8 a3db21c0b3114802a8a5b610e252ef13 msgid "" "For file formats, we recommend referencing existing ontologies (like EDAM" " in our example), reference a local ontology for your institution, or do " @@ -2152,34 +2179,34 @@ msgid "" "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" -#: ../../src/topics/file-formats.md:14 63bfff437e3348428f7e33ece7ec55e7 +#: ../../src/topics/file-formats.md:14 0f5bc8520d6a4dafa37c65343da9702a msgid "" "In the next tutorial, we explain the `$namespaces` and `$schemas` " "section of the document in greater detail, so don't worry about these for" " now." msgstr "" -#: ../../src/topics/file-formats.md:17 6ce83d9c06e4436881aa47d94ef41e0b +#: ../../src/topics/file-formats.md:17 5cb830da47464a8b9c3950983fa4d56f msgid "" "Note that for added value `cwltool` can do some basic reasoning based on " "file formats and warn you if there seem to be some obvious mismatches." msgstr "" -#: ../../src/topics/file-formats.md:20 55006c594abf4e70a38e979568fadcf4 +#: ../../src/topics/file-formats.md:20 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d 5c8f1709fe61423bba3ceaca2fc7cf09 +#: f558bcf2a993482195cd418b37761809 fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" -#: ../../src/topics/file-formats.md:32 1a1905ff2d624eca952c8a53b3bee678 +#: ../../src/topics/file-formats.md:32 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" -#: ../../src/topics/file-formats.md:34 368ff92476b14f5c8331260eafc5acb5 +#: ../../src/topics/file-formats.md:34 a2ce43b391864e8bbde16328cc19b32b msgid "" "Below is an example of a parameter file for the example above. We " "encourage checking in working examples of parameter files for your tool. " @@ -2187,11 +2214,11 @@ msgid "" "\"known good\" parameterization." msgstr "" -#: ../../src/topics/file-formats.md:39 5d530afa23f349a79f54d51d40724747 +#: ../../src/topics/file-formats.md:39 aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" -#: ../../src/topics/file-formats.md:45 16f965f86712483aa7f95dfa3f944a17 +#: ../../src/topics/file-formats.md:45 56ee4dcfff6141d5bef80eb96559876d msgid "" "___Note:___ To follow the example below, you need to download the example" " input file, *file-formats.bam*. The file is available from " @@ -2200,80 +2227,80 @@ msgid "" "formats.bam> and can be downloaded e.g. via `wget`:" msgstr "" -#: ../../src/topics/index.md:1 dc629e2c90ed458b96107a6994676434 +#: ../../src/topics/index.md:1 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" -#: ../../src/topics/inputs.md:1 cf2f077cf8044079a7005e6e508dcd8c +#: ../../src/topics/inputs.md:1 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" -#: ../../src/topics/inputs.md:3 129e1d2a71894d28b009f4846754a75d +#: ../../src/topics/inputs.md:3 d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" -#: ../../src/topics/inputs.md:5 d6791bbe575042b9a7282c69407dd907 +#: ../../src/topics/inputs.md:5 96671c56523c4ea9992fb5dfcfa6490e msgid "" "The `inputs` of a tool is a list of input parameters that control how to " "run the tool. Each parameter has an `id` for the name of parameter, and " "`type` describing what types of values are valid for that parameter." msgstr "" -#: ../../src/topics/inputs.md:9 e8da87f8bb664334adf831995601f462 +#: ../../src/topics/inputs.md:9 bcc6246742cb46bfb185e415c4a3431a msgid "" "Available primitive types are *string*, *int*, *long*, *float*, *double*," " and *null*; complex types are *array* and *record*; in addition there " "are special types *File*, *Directory* and *Any*." msgstr "" -#: ../../src/topics/inputs.md:13 de6c322618304207b6d1364d1ec2dc13 +#: ../../src/topics/inputs.md:13 86dce36de687449c88fb5eb9d64eb045 msgid "" "The following example demonstrates some input parameters with different " "types and appearing on the command line in different ways." msgstr "" -#: ../../src/topics/inputs.md:16 43bdcf6dc1b14030bff27fa53289c02c +#: ../../src/topics/inputs.md:16 cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" -#: ../../src/topics/inputs.md:18 056510b42ea64717996ab49c307bda86 +#: ../../src/topics/inputs.md:18 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" -#: ../../src/topics/inputs.md:24 6852f5dbd9094c99bb68f2a88f76c9bc +#: ../../src/topics/inputs.md:24 c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" -#: ../../src/topics/inputs.md:26 f33b6800367248b7927d97ad7b4be5b5 +#: ../../src/topics/inputs.md:26 dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" -#: ../../src/topics/inputs.md:33 8ad812d7e88f4cbba83228ffb1711576 +#: ../../src/topics/inputs.md:33 36ab1d9edafc4831bb1bca5f123b04b0 msgid "" "You can use `cwltool` to create a template input object. That saves you " "from having to type all the input parameters in a input object file:" msgstr "" -#: ../../src/topics/inputs.md:40 cc680bbf091a46f8b4b3dbe6324c040a +#: ../../src/topics/inputs.md:40 7dc630ea86464b1dba3a4e5079260b3b msgid "" "You can redirect the output to a file, i.e. `cwltool --make-template " "inp.cwl > inp-job.yml`, and then modify the default values with your " "desired input values." msgstr "" -#: ../../src/topics/inputs.md:44 446ac81f078d46289a18f494748f482c +#: ../../src/topics/inputs.md:44 ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "" "Notice that \"example_file\", as a `File` type, must be provided as an " "object with the fields `class: File` and `path`." msgstr "" -#: ../../src/topics/inputs.md:47 3d6d958d111943f3a2139b4dbb7810db +#: ../../src/topics/inputs.md:47 651e032007ea4a119d20c820bb61f86b msgid "" "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the" " command line." msgstr "" -#: ../../src/topics/inputs.md:53 ba0ec9157709430c822f4e91459288e2 +#: ../../src/topics/inputs.md:53 0b056dde9e87428996e47870b12119da msgid "" "Now invoke `cwltool` with the tool description and the input object on " "the command line, using the command `cwltool inp.cwl inp-job.yml`. The " @@ -2281,7 +2308,7 @@ msgid "" " from the command line:" msgstr "" -#: ../../src/topics/inputs.md:64 2565f8fd4a15429e887aeb71eacdff1e +#: ../../src/topics/inputs.md:64 628124a1670b4b058bb0fb6e495a099c msgid "" "The CWL reference runner (cwltool) and other runners create temporary " "directories with symbolic (\"soft\") links to your input files to ensure " @@ -2289,7 +2316,7 @@ msgid "" "explicitly specified" msgstr "" -#: ../../src/topics/inputs.md:70 659ed5c64fb546399b741553a347b8e8 +#: ../../src/topics/inputs.md:70 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "" "The field `inputBinding` is optional and indicates whether and how the " "input parameter should appear on the tool's command line. If " @@ -2297,14 +2324,14 @@ msgid "" "line. Let's look at each example in detail." msgstr "" -#: ../../src/topics/inputs.md:83 3d87e69d41374fbab23b26d36c1aee03 +#: ../../src/topics/inputs.md:83 ec2adb3912bc46e28891229e9e0d9a1c msgid "" "Boolean types are treated as a flag. If the input parameter " "\"example_flag\" is \"true\", then `prefix` will be added to the command " "line. If false, no flag is added." msgstr "" -#: ../../src/topics/inputs.md:95 07bc81683e2c4ac68b379462bae95207 +#: ../../src/topics/inputs.md:95 a519be60726a44af9941fdce04735353 msgid "" "String types appear on the command line as literal values. The `prefix` " "is optional, if provided, it appears as a separate argument on the " @@ -2312,7 +2339,7 @@ msgid "" "rendered as `--example-string hello`." msgstr "" -#: ../../src/topics/inputs.md:109 3e304da2150f448d9e39715ac5f5deaa +#: ../../src/topics/inputs.md:109 cb8fc8c4c79e467eac5fab4ca685201e msgid "" "Integer (and floating point) types appear on the command line with " "decimal text representation. When the option `separate` is false (the " @@ -2320,7 +2347,7 @@ msgid "" "argument. In the example above, this is rendered as `-i42`." msgstr "" -#: ../../src/topics/inputs.md:124 fd8a98686e3c4c609f79ae427f1558d3 +#: ../../src/topics/inputs.md:124 a26cc105716f47cb807174c9003153b0 msgid "" "File types appear on the command line as the path to the file. When the " "parameter type ends with a question mark `?` it indicates that the " @@ -2330,13 +2357,13 @@ msgid "" "command line." msgstr "" -#: ../../src/topics/inputs.md:131 f1a2e1bbb1104a4fab5a7f04cac845c7 +#: ../../src/topics/inputs.md:131 cc159dd5fe5748caac838862f5b8c4d1 msgid "" "Input files are read-only. If you wish to update an input file, you must" " [first copy it to the output directory](staging-input-files.md)." msgstr "" -#: ../../src/topics/inputs.md:134 6a7f0ccd227e4f90a8c8ca96744bda68 +#: ../../src/topics/inputs.md:134 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "" "The value of `position` is used to determine where parameter should " "appear on the command line. Positions are relative to one another, not " @@ -2347,17 +2374,17 @@ msgid "" "optional. The default position is 0." msgstr "" -#: ../../src/topics/inputs.md:142 1f79d115d8a145189638c68c3095396c +#: ../../src/topics/inputs.md:142 6812698e9ad84d3385de5e88e9dde0b3 msgid "" "The `baseCommand` field will always appear in the final command line " "before the parameters." msgstr "" -#: ../../src/topics/inputs.md:146 6e1b3e2d90184e34925891099d2b5cc1 +#: ../../src/topics/inputs.md:146 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" -#: ../../src/topics/inputs.md:148 4f6df7f13e42448eb4a53f03bc477b56 +#: ../../src/topics/inputs.md:148 d1f02be278754267893dfce5a940997d msgid "" "It is easy to add arrays of input parameters represented to the command " "line. There are two ways to specify an array parameter. First is to " @@ -2367,23 +2394,23 @@ msgid "" "of that type." msgstr "" -#: ../../src/topics/inputs.md:154 dbc0b52627514ad0908969d0b4ddfdf4 +#: ../../src/topics/inputs.md:154 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" -#: ../../src/topics/inputs.md:160 f173dd96ad124470a53573c86a8df203 +#: ../../src/topics/inputs.md:160 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 ../../src/topics/outputs.md:82 -#: ../../src/topics/outputs.md:105 af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 e0098a77080d4349b05ceb7735a5fdf5 +#: ../../src/topics/outputs.md:105 02adef8ee8204842b5b4a0408f3bac33 +#: 588f0f7f967f4d69af27c9729d6d3119 9db68837918a4a349f32f15f12697a1d msgid "" "Now invoke `cwltool` providing the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/inputs.md:178 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: ../../src/topics/inputs.md:178 75d59e395c66416cae9b352db5081516 msgid "" "The `inputBinding` can appear either on the outer array parameter " "definition or the inner array element definition, and these produce " @@ -2393,7 +2420,7 @@ msgid "" "item separator string." msgstr "" -#: ../../src/topics/inputs.md:185 4459819ba75647d185986a3386939494 +#: ../../src/topics/inputs.md:185 874c6f19abbf45d7ab7d30a378c4048d msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2404,11 +2431,11 @@ msgid "" "and other complex types." msgstr "" -#: ../../src/topics/inputs.md:191 8f163bd34ded4785b6e28c8e2147e0dd +#: ../../src/topics/inputs.md:191 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" -#: ../../src/topics/inputs.md:193 1799e11a7b9c4929a3d1379d7ea45d03 +#: ../../src/topics/inputs.md:193 dea0d4b681f94e73b13965dcfe75cf7d msgid "" "Sometimes an underlying tool has several arguments that must be provided " "together (they are dependent) or several arguments that cannot be " @@ -2416,46 +2443,46 @@ msgid "" "unions to group parameters together to describe these two conditions." msgstr "" -#: ../../src/topics/inputs.md:198 9510c0b431a44b5e84e0b583de7c5446 +#: ../../src/topics/inputs.md:198 ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" -#: ../../src/topics/inputs.md:204 efb4eb6f5e994b50a52fa2c707dad1ce +#: ../../src/topics/inputs.md:204 d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" -#: ../../src/topics/inputs.md:215 34599c6f10ce4104be2359a1b37f91cb +#: ../../src/topics/inputs.md:215 750474486a84482292eeba45f118287f msgid "" "In the first example, you can't provide `itemA` without also providing " "`itemB`." msgstr "" -#: ../../src/topics/inputs.md:217 0663ea7918994d3f9c45c652a3ed12db +#: ../../src/topics/inputs.md:217 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" -#: ../../src/topics/inputs.md:233 a98dda6ca4b14edba467de638bba28fc +#: ../../src/topics/inputs.md:233 1eb0e39bb6d04b8cab300f44a79f3add msgid "" "In the second example, `itemC` and `itemD` are exclusive, so only the " "first matching item (`itemC`) is added to the command line and remaining " "item (`itemD`) is ignored." msgstr "" -#: ../../src/topics/inputs.md:236 10d0e9f8df8c47788703073b17529bc8 +#: ../../src/topics/inputs.md:236 bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" -#: ../../src/topics/inputs.md:252 9a0e1a130fba4d24a9168ca3e455cd23 +#: ../../src/topics/inputs.md:252 4b2ab812f62c4f949dd25c8527f2411c msgid "" "In the third example, only `itemD` is provided, so it appears on the " "command line." msgstr "" -#: ../../src/topics/inputs.md:255 992a8c801ceb4233acf56b6bff315188 +#: ../../src/topics/inputs.md:255 b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" -#: ../../src/topics/inputs.md:257 9027d23fa7074b789c3b86ca5ea17fa4 +#: ../../src/topics/inputs.md:257 2c3b884cb1c54521900cc90782e8a58d msgid "" "If you use exclusive input parameters combined with expressions, you need" " to be aware that the `inputs` JavaScript object will contain one of the " @@ -2463,18 +2490,18 @@ msgid "" "boolean operator to check which values are present." msgstr "" -#: ../../src/topics/inputs.md:262 68b47710a8ea4b978428b42c627944e9 +#: ../../src/topics/inputs.md:262 a1073b6306044dffb414319ae01f68bb msgid "" "Let's use an example that contains an exclusive `file_format` input " "parameter that accepts `null` (i.e. no value provided), or any value from" " an enum." msgstr "" -#: ../../src/topics/inputs.md:265 d33e4cac65d14111a89c838c4d1759b9 +#: ../../src/topics/inputs.md:265 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" -#: ../../src/topics/inputs.md:271 24cea1cf7d774b6ab56959f289cab39d +#: ../../src/topics/inputs.md:271 9a1d92334685449386dfa3b3a899ed48 msgid "" "Note how the JavaScript expression uses the value of the exclusive input " "parameter without taking into consideration a `null` value. If you " @@ -2482,7 +2509,7 @@ msgid "" "your command should execute successfully:" msgstr "" -#: ../../src/topics/inputs.md:280 b866867d6f8e4d3999b62a85e6884ebc +#: ../../src/topics/inputs.md:280 fb623af4c480411b8fde28d01c981411 msgid "" "However, if you do not provide any input value, then `file_format` will " "be evaluated to a `null` value, which does not match the expected type " @@ -2490,7 +2517,7 @@ msgid "" " workflow." msgstr "" -#: ../../src/topics/inputs.md:289 80c49ed168b14d25b2f09b3b0186b44f +#: ../../src/topics/inputs.md:289 e98e165f6bba40809c90473d72f9d592 msgid "" "To correct it, you must remember to use an or operator in your JavaScript" " expression when using exclusive parameters, or any parameter that allows" @@ -2500,12 +2527,12 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "" "Implementation extensions not required for correct execution (for " "example, fields related to GUI presentation) and metadata about the tool " @@ -2520,7 +2547,7 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 80af387fe3ff4e2da999903385bd602b msgid "" "For all developers, we recommend the following minimal metadata for your " "tool and workflows. This example includes metadata allowing others to " @@ -2528,17 +2555,17 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "" "For those that are highly motivated, it is also possible to annotate your" " tool with a much larger amount of metadata. This example includes EDAM " @@ -2548,15 +2575,15 @@ msgid "" msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" -#: ../../src/topics/operations.md:1 5feb559552194ba58da7206c601292fe +#: ../../src/topics/operations.md:1 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" -#: ../../src/topics/operations.md:3 b7124ba4df9042baadc1641ee09545d6 +#: ../../src/topics/operations.md:3 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "" "An Operation is a type of CWL process, just like a workflow, a command-" "line tool, or an expression tool. It is a step of a workflow that " @@ -2564,56 +2591,56 @@ msgid "" "to be executed." msgstr "" -#: ../../src/topics/operations.md:7 d34b698c62114041a64e0abce25ca935 +#: ../../src/topics/operations.md:7 5565c1b2d8a349169a305a9b26b4574d msgid "" "You can create operations to visualize a workflow during development, " "before you are ready to submit the workflow to a CWL runner:" msgstr "" -#: ../../src/topics/operations.md:10 cba2c31262bd450cbafc7ca77f4fb8fa +#: ../../src/topics/operations.md:10 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" -#: ../../src/topics/operations.md:16 b01be5f632104096b5af6193aab34d90 +#: ../../src/topics/operations.md:16 88160cef4cfa4add9020aa89511a5749 msgid "" "The `uppercase` step of the workflow is an operation. It can be used like" " a command line tool or an expression. You can also plot it with the CWL " "Viewer or `cwltool`:" msgstr "" -#: ../../src/topics/operations.md:24 60a6a02c1367403db6df3ec10f75eb69 +#: ../../src/topics/operations.md:24 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "" "The output of the command above can be rendered with a Graphviz renderer." " The following image is rendered with the Sphinx Graphviz directive (this" " user guide is built with Sphinx):" msgstr "" -#: ../../src/topics/operations.md:55 314ea7bc35154f41b2af5fa6683ca389 +#: ../../src/topics/operations.md:55 730ba1434a1445ae847ec6153b6a3b72 msgid "" "If you try running it with `cwltool`, the command will fail since " "`cwltool` does not have enough information to know how to execute it:" msgstr "" -#: ../../src/topics/operations.md:58 d81e679b13474f74bc5e1ce1e31c2bc6 +#: ../../src/topics/operations.md:58 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" -#: ../../src/topics/operations.md:66 d7fb27131ee44bfc82f698ee44b2bae0 +#: ../../src/topics/operations.md:66 a25d0b1e13324b40a6b8fcd227948c4f msgid "" "CWL runners may come up with ways to bind operations to concrete steps. A" " CWL runner could, for instance, use abstract operations with ID's that " "correspond to steps executed by a different workflow engine." msgstr "" -#: ../../src/topics/outputs.md:1 b8ef11eafd1d46e088f1277f4ac372bc +#: ../../src/topics/outputs.md:1 da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" -#: ../../src/topics/outputs.md:3 d2382ed1f644459594655d5b5b4d838a +#: ../../src/topics/outputs.md:3 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" -#: ../../src/topics/outputs.md:5 6651632d977b44479b721174fffeda2d +#: ../../src/topics/outputs.md:5 d661df070e3040869da412d07a71f716 msgid "" "The `outputs` of a tool is a list of output parameters that should be " "returned after running the tool. Each parameter has an `id` for the name" @@ -2621,7 +2648,7 @@ msgid "" "that parameter." msgstr "" -#: ../../src/topics/outputs.md:10 bee5f532554241088764ac9e56abbe85 +#: ../../src/topics/outputs.md:10 a11585474d3849cca5467512ed964743 msgid "" "When a tool runs under CWL, the starting working directory is the " "designated output directory. The underlying tool or script must record " @@ -2630,17 +2657,17 @@ msgid "" "themselves, or come from examining the content of those files." msgstr "" -#: ../../src/topics/outputs.md:16 0c7c506f38be421399073871f64e99b0 +#: ../../src/topics/outputs.md:16 2682f9ca8e604a0c9986f7746fdec960 msgid "" "The following example demonstrates how to return a file that has been " "extracted from a tar file." msgstr "" -#: ../../src/topics/outputs.md:19 8b60286e56cc42a8ab5f751a97adf771 +#: ../../src/topics/outputs.md:19 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" -#: ../../src/topics/outputs.md:21 fa0ad674f15348339a1eee771a6ba9e2 +#: ../../src/topics/outputs.md:21 22447a560f6f4317bf67bd7c4336126c msgid "" "In previous examples, the `baseCommand` was just a string, with any " "arguments passed as CWL inputs. Instead of a single string we can use an " @@ -2648,71 +2675,71 @@ msgid "" "subsequent elements are mandatory command line arguments" msgstr "" -#: ../../src/topics/outputs.md:26 177b5f1b95a34fb9b2eb42f733d79ac8 +#: ../../src/topics/outputs.md:26 f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" -#: ../../src/topics/outputs.md:32 a08a6d8aca8e490482e127a8fd5e650e +#: ../../src/topics/outputs.md:32 ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:38 c2c60f68b1e045f88844076e191fda9b +#: ../../src/topics/outputs.md:38 dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" -#: ../../src/topics/outputs.md:45 6d939f62526e4e6d95acb57d72f60a84 +#: ../../src/topics/outputs.md:45 52703d6b7f914097934bfad13663abeb msgid "" "And now invoke `cwltool` with the tool description and the input object " "on the command line:" msgstr "" -#: ../../src/topics/outputs.md:51 c48edd9034364b81ad42540a98b51d91 +#: ../../src/topics/outputs.md:51 5e1c79df657d4a6e84e055dd6b300a5d msgid "" "The field `outputBinding` describes how to set the value of each output " "parameter." msgstr "" -#: ../../src/topics/outputs.md:62 9ebe0186a7124dfaa30e558e8f59653a +#: ../../src/topics/outputs.md:62 329d2809dfae4f90bc638f5f03a47ee3 msgid "" "The `glob` field consists of the name of a file in the output directory. " "If you don't know name of the file in advance, you can use a wildcard " "pattern like `glob: '*.txt'`." msgstr "" -#: ../../src/topics/outputs.md:65 9381b7d7c9904df0a5e16dac29c2e08f +#: ../../src/topics/outputs.md:65 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" -#: ../../src/topics/outputs.md:67 2aa9c6916e3546b7b92fa64bb83275d1 +#: ../../src/topics/outputs.md:67 c6bcf7c6a8774dd6be41cc775848c3b8 msgid "" "To capture a tool's standard output stream, add the `stdout` field with " "the name of the file where the output stream should go. Then add `type: " "stdout` on the corresponding output parameter." msgstr "" -#: ../../src/topics/outputs.md:71 63afb7a597fc4e459b6a7dbd40bbf6ff +#: ../../src/topics/outputs.md:71 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" -#: ../../src/topics/outputs.md:89 7418915470f041c9af5bd39ea652de36 +#: ../../src/topics/outputs.md:89 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" -#: ../../src/topics/outputs.md:91 f82db001b58c4969b2d8bc1dcbd7cf8a +#: ../../src/topics/outputs.md:91 9647019d8c37466886e7aab6f176634d msgid "" "You can also capture multiple output files into an array of files using " "`glob`." msgstr "" -#: ../../src/topics/outputs.md:93 26d9f0b28d384617a8e490c1f8e26e52 +#: ../../src/topics/outputs.md:93 b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" -#: ../../src/topics/outputs.md:99 cf46c971b31b4e10bf0fefb4cd028c2f +#: ../../src/topics/outputs.md:99 cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" -#: ../../src/topics/outputs.md:112 a4347983fb9945a4a2773af88e426dc9 +#: ../../src/topics/outputs.md:112 cc067051f22f433bbece08f60933e002 msgid "" "As described in the [YAML Guide](yaml-guide.md#arrays), the array of " "expected outputs is specified in `array-outputs-job.yml` with each entry " @@ -2721,11 +2748,11 @@ msgid "" "sections." msgstr "" -#: ../../src/topics/parameter-references.md:1 c5489e0633114372b273098ee2c9ffd9 +#: ../../src/topics/parameter-references.md:1 a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" -#: ../../src/topics/parameter-references.md:3 75de9fd63393429daf1ca10a85339aa7 +#: ../../src/topics/parameter-references.md:3 dbfe2c1123144316aa026374b0f353d3 msgid "" "In a previous example, we extracted a file using the \"tar\" program. " "However, that example was very limited because it assumed that the file " @@ -2738,40 +2765,40 @@ msgid "" "which will allow us to then specify the name of the file to extract." msgstr "" -#: ../../src/topics/parameter-references.md:13 8b5d0ada32d645be9359f43a431f5f91 +#: ../../src/topics/parameter-references.md:13 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" -#: ../../src/topics/parameter-references.md:19 2ed93dc8778e44209194f41b9ad193d5 +#: ../../src/topics/parameter-references.md:19 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" -#: ../../src/topics/parameter-references.md:25 a80dd6d9920540e9880514e04035af86 +#: ../../src/topics/parameter-references.md:25 074cf5d912854d8c864607cc24b15302 msgid "" "Create your input files and invoke `cwltool` with the tool description " "and the input object on the command line:" msgstr "" -#: ../../src/topics/parameter-references.md:36 9de300f7b9da49f59d1c9fd96dec4a8b +#: ../../src/topics/parameter-references.md:36 0290af3e3cbb4b32b0450c8771f3bf95 msgid "" "Certain fields permit parameter references which are enclosed in " "`$(...)`. These are evaluated and replaced with value being referenced." msgstr "" -#: ../../src/topics/parameter-references.md:47 a61f52d3c1024c3692899e05fcea4bee +#: ../../src/topics/parameter-references.md:47 b54240bb94f746bba7511633aa969db0 msgid "" "References are written using a subset of Javascript syntax. In this " "example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and " "`$(inputs['extractfile'])` are equivalent." msgstr "" -#: ../../src/topics/parameter-references.md:51 dafc9ba578c14fd79d075160e6b7bd6b +#: ../../src/topics/parameter-references.md:51 8b70a072aa87414c88e89a3e19af0a51 msgid "" "The value of the \"inputs\" variable is the input object provided when " "the CWL tool was invoked." msgstr "" -#: ../../src/topics/parameter-references.md:54 28ca6cae42904559bcec98fb9d2b07cb +#: ../../src/topics/parameter-references.md:54 eea20f89c45f424a888178df53713b28 msgid "" "Note that because `File` parameters are objects, to get the path to an " "input file you must reference the path field on a file object; to " @@ -2779,45 +2806,45 @@ msgid "" "`$(inputs.tarfile.path)`." msgstr "" -#: ../../src/topics/parameter-references.md:59 616c9ff9fcae489285f0bbbc67f07d29 +#: ../../src/topics/parameter-references.md:59 cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" -#: ../../src/topics/parameter-references.md:61 ac17acd83ddb43dc9fb7a5e595ab1153 +#: ../../src/topics/parameter-references.md:61 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" -#: ../../src/topics/parameter-references.md:63 156573324cde41ee8b3c47deabf43db8 +#: ../../src/topics/parameter-references.md:63 7647e0229a924f988cf02b7812a55c06 msgid "" "From " "[`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" -#: ../../src/topics/parameter-references.md:69 c9725be01e8a401fb3ad9ff01339f81e +#: ../../src/topics/parameter-references.md:69 9d663249666045618a0d3acddb85a9a9 msgid "" "From " "[CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:72 6797335256e2412cbbe7636507931455 +#: ../../src/topics/parameter-references.md:72 5fed4984f6784347b4cbe0630b1dd2c2 msgid "" "From " "[`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:74 05a5f0fcb7454cb697e3d810d55fac26 +#: ../../src/topics/parameter-references.md:74 dbf6153cd02542a6a01c172803122b7f msgid "" "From " "[CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:77 406e68280b5c4ee494632f94b635b7ad +#: ../../src/topics/parameter-references.md:77 b6250cf6fa8a4a0c94b33302e0decca5 msgid "" "From " "[CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" -#: ../../src/topics/parameter-references.md:81 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: ../../src/topics/parameter-references.md:81 fa6ca3bbc6784380a03a950a6f49a180 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2825,13 +2852,13 @@ msgid "" "[WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:85 e71a974b29624210a107fc2d097d4196 +#: ../../src/topics/parameter-references.md:85 b92b516e537a4773ad67b4af586e7a25 msgid "" "From " "[WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" -#: ../../src/topics/parameter-references.md:89 b59df98754e24654bfef0b1fe1d91660 +#: ../../src/topics/parameter-references.md:89 467a701228504d06b971b79a59c69064 msgid "" "From " "[InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter)" @@ -2839,43 +2866,43 @@ msgid "" "[ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" -#: ../../src/topics/parameter-references.md:92 d2bccbff1ce646348fe38c776ad183e1 +#: ../../src/topics/parameter-references.md:92 2634f989eb304009a8568d70ed42786c msgid "" "From " "[`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "" "From " "[`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "" "From " "[EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 574d93d1d592458a985f259519c036cb msgid "" "Often, tool descriptions will be written for a specific version of a " "software. To make it easier for others to use your descriptions, you can " @@ -2885,14 +2912,14 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "" "In this example, the software requirement being described is InterProScan" " version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: 02e40154eac74ecc98d0447d03475b44 msgid "" "Depending on your CWL runner, these hints may be used to check that the " "required software is installed and available before the job is run. To " @@ -2901,7 +2928,7 @@ msgid "" msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "" "As well as a version number, a unique resource identifier (URI) for the " "tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be" @@ -2917,11 +2944,11 @@ msgid "" " to the tool." msgstr "" -#: ../../src/topics/staging-input-files.md:1 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: ../../src/topics/staging-input-files.md:1 b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" -#: ../../src/topics/staging-input-files.md:3 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: ../../src/topics/staging-input-files.md:3 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -2931,26 +2958,26 @@ msgid "" " extract the base name of the input file from its leading directory path." msgstr "" -#: ../../src/topics/staging-input-files.md:9 a03372581fa44f9b8e3e088a4099cdd9 +#: ../../src/topics/staging-input-files.md:9 c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:1 36e082be73464be0ad5d0b681cc510da +#: ../../src/topics/troubleshooting.md:1 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" -#: ../../src/topics/troubleshooting.md:3 4464455b51ad4873ac13c4a63ee5fb54 +#: ../../src/topics/troubleshooting.md:3 fbe0c65b444441f785d0054176d036a6 msgid "" "In this section you will find ways to troubleshoot when you have problems" " executing CWL. We focus on `cwltool` here but some of these techniques " "may apply to other CWL Runners." msgstr "" -#: ../../src/topics/troubleshooting.md:6 ed7ff0753d1743a995f4cfedd6e5dcc2 +#: ../../src/topics/troubleshooting.md:6 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" -#: ../../src/topics/troubleshooting.md:8 4c2dd10dd66446058477a52fb8d2c602 +#: ../../src/topics/troubleshooting.md:8 9a710602e00c4934ae3a3b471aa68458 msgid "" "You can use the `--cachedir` option when running a workflow to tell " "`cwltool` to cache intermediate files (files that are not input nor " @@ -2959,7 +2986,7 @@ msgid "" "separate directory makes accessing them easier." msgstr "" -#: ../../src/topics/troubleshooting.md:14 978b6a5fd5fa425fa9a18d9f0e8788da +#: ../../src/topics/troubleshooting.md:14 21b5be7270a14f0987240c81d1ec879b msgid "" "In the following example `troubleshooting-wf1.cwl` we have two steps, " "`step_a` and `step_b`. The workflow is equivalent to `echo \"Hello " @@ -2969,18 +2996,18 @@ msgid "" " which fails." msgstr "" -#: ../../src/topics/troubleshooting.md:20 000c0d6ae8bf414d9293b9f13fd2e448 +#: ../../src/topics/troubleshooting.md:20 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" -#: ../../src/topics/troubleshooting.md:27 7e91b8811be14f8e80df39ac4c5bd316 +#: ../../src/topics/troubleshooting.md:27 cfe9d8241fe84bd5b74042a5625d933f msgid "" "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` " "value (`cwltool` will create the directory for you if it does not exist " "already):" msgstr "" -#: ../../src/topics/troubleshooting.md:35 d42799cc5bd4484bb6beb309a61e103e +#: ../../src/topics/troubleshooting.md:35 764d933cc4da446abd8dd8f913f05dac msgid "" "The workflow is in the `permanentFail` status due to `step_b` failing to " "execute the non-existent `revv` command. The `step_a` was executed " @@ -2988,7 +3015,7 @@ msgid "" "You can inspect the intermediate files created:" msgstr "" -#: ../../src/topics/troubleshooting.md:44 48bb0f6666ac48648c7d969608b3bd48 +#: ../../src/topics/troubleshooting.md:44 c93efc6d4e004859981ee7f5fa28ed03 msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " @@ -2996,7 +3023,7 @@ msgid "" "visible in the output of the command above." msgstr "" -#: ../../src/topics/troubleshooting.md:48 f8876044db184cbaaca56579d0c773df +#: ../../src/topics/troubleshooting.md:48 546601da44cb49bd9611b1c85807fd90 msgid "" "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev`" " in the `step_b`). After fixing the typo, when you execute `cwltool` with" @@ -3006,7 +3033,7 @@ msgid "" "`step_b` is now of success." msgstr "" -#: ../../src/topics/troubleshooting.md:59 a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: ../../src/topics/troubleshooting.md:59 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "" "In this example the workflow step `step_a` was not re-evaluated as it had" " been cached, and there was no change in its execution or output. " @@ -3016,15 +3043,15 @@ msgid "" "`cwltool` to re-evaluate steps unnecessarily." msgstr "" -#: ../../src/topics/using-containers.md:1 4c240a18c4e6441189489011242c1efd +#: ../../src/topics/using-containers.md:1 eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" -#: ../../src/topics/using-containers.md:3 e37e76ef376a4ee695e600998906ec1c +#: ../../src/topics/using-containers.md:3 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" -#: ../../src/topics/using-containers.md:5 51a307b0ba7c4c1d89309ba8d2250471 +#: ../../src/topics/using-containers.md:5 e07f33d01b804663a25ffb08aad74821 msgid "" "[Docker][docker] containers simplify software installation by providing a" " complete known-good runtime for software and its dependencies. However," @@ -3037,35 +3064,35 @@ msgid "" " containers." msgstr "" -#: ../../src/topics/using-containers.md:15 13cc38d72d34468fa4eb6d91f23ff105 +#: ../../src/topics/using-containers.md:15 7a644506619a4f08958ec7d4540cd557 msgid "" "One of the responsibilities of the CWL runner is to adjust the paths of " "input files to reflect the location where they appear inside the " "container." msgstr "" -#: ../../src/topics/using-containers.md:18 42a48398d3ef4b03bd7395120f2cfb42 +#: ../../src/topics/using-containers.md:18 b5195b7d8eaa419fb2b90cb33a57783a msgid "" "This example runs a simple Node.js script inside a Docker container which" " will then print \"Hello World\" to the standard output." msgstr "" -#: ../../src/topics/using-containers.md:21 d59387b433bc4ecfaf7e72026624db02 +#: ../../src/topics/using-containers.md:21 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" -#: ../../src/topics/using-containers.md:27 d963418ccc0b4803bbc758d718ccb5aa +#: ../../src/topics/using-containers.md:27 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" -#: ../../src/topics/using-containers.md:33 a224d1510c9e46aab23d8bdc03c349dd +#: ../../src/topics/using-containers.md:33 2713594c937d4c528fc8d04d9e9819ed msgid "" "Before we run this, let's just break it down and see what some bits do. " "Most of this has been explained in previous sections, the only part that " "is really new is the `dockerRequirement` section." msgstr "" -#: ../../src/topics/using-containers.md:44 0a82f8a45b0546aaac4c976dcc98014a +#: ../../src/topics/using-containers.md:44 cf94c1424fc2413c85647fd1ee73d951 msgid "" "`baseCommand: node` tells CWL that we will be running this command using " "the Node Js runtime that is meant for Javascript files. We then need to " @@ -3078,23 +3105,23 @@ msgid "" "case we have used a container called `node:slim`." msgstr "" -#: ../../src/topics/using-containers.md:52 bc418a2a535e49359c4cd44b373bbe02 +#: ../../src/topics/using-containers.md:52 dc0452107c604e29bdf32bb289fe5db8 msgid "" "Create a Javascript file named \"hello.js\" and invoke `cwltool` " "providing the tool description and the input object on the command line:" msgstr "" -#: ../../src/topics/using-containers.md:55 a799fba2322944cea00e413c08066536 +#: ../../src/topics/using-containers.md:55 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" -#: ../../src/topics/using-containers.md:69 35379c6b972940bd8451f10b74dd793e +#: ../../src/topics/using-containers.md:69 483181f498fc4d968b5fe6ef427709f7 msgid "" "Notice the CWL runner has constructed a Docker command line to run the " "script." msgstr "" -#: ../../src/topics/using-containers.md:72 2d5265525ad544a0b64ad2cf07aacc26 +#: ../../src/topics/using-containers.md:72 7487485d6aa4458089a4b4bdf107ea64 msgid "" "In this example, the path to the script `hello.js` is " "`/home/me/cwl/user_guide/hello.js` outside the container but " @@ -3102,44 +3129,44 @@ msgid "" "reflected in the invocation of the `node` command." msgstr "" -#: ../../src/topics/workflows.md:1 e2521b89596d42f8a87a3207fd6c32f2 +#: ../../src/topics/workflows.md:1 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" -#: ../../src/topics/workflows.md:3 3676f23b63e142cb8e5715ae07216a47 +#: ../../src/topics/workflows.md:3 b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "" "A workflow is a CWL processing unit that executes command-line tools, " "expression tools, or workflows (sub-workflows) as steps. It must have " "`inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" -#: ../../src/topics/workflows.md:13 00725aed13a440ca8b3c4f9155fbee99 +#: ../../src/topics/workflows.md:13 f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" -#: ../../src/topics/workflows.md:41 2e38a4f9072b4ad9bbb74f943d22084d +#: ../../src/topics/workflows.md:41 5870ac44e4c24b8daf5f06c49f95ce04 msgid "" "The CWL document `echo-uppercase.cwl` defines a workflow that runs the " "command-line tool, and the expression tool showed in the earlier " "examples." msgstr "" -#: ../../src/topics/workflows.md:51 2b9f4035ea864b6db50c861a1819289d +#: ../../src/topics/workflows.md:51 a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" -#: ../../src/topics/workflows.md:81 28e9064780e7418a8e02a22f92e34404 +#: ../../src/topics/workflows.md:81 93188ed43ee949cc98b3ea679ce14feb msgid "" "A command-line tool or expression tool can also be written directly in " "the same CWL document as the workflow. For example, we can rewrite the " "`echo-uppercase.cwl` workflow as a single file:" msgstr "" -#: ../../src/topics/workflows.md:91 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: ../../src/topics/workflows.md:91 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" -#: ../../src/topics/workflows.md:150 8dc00528c3d2426c8a3492a8191f1d81 +#: ../../src/topics/workflows.md:150 1cc17ad26e9c474b895ba5cd20c8b66a msgid "" "Having separate files helps with modularity and code organization. But it" " can be helpful writing everything in a single file for development. " @@ -3147,33 +3174,33 @@ msgid "" "`cwltool --pack`) discussed further in other sections of this user guide." msgstr "" -#: ../../src/topics/workflows.md:160 f9ef5e258f7c4971a8543d1dfed711a8 +#: ../../src/topics/workflows.md:160 24aca0bea4d94e3593b844cf0586cffe msgid "" "For a sub-workflows you need to enable the requirement " "`SubworkflowFeatureRequirement`. It is covered in another section of this" " user guide in more detail." msgstr "" -#: ../../src/topics/workflows.md:165 324bc51071d743ea80124c23880ddc0a +#: ../../src/topics/workflows.md:165 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" -#: ../../src/topics/workflows.md:167 d8c13e01976b43a1af34c11a7bc36897 +#: ../../src/topics/workflows.md:167 9c56528acd5f49deb139e034dfbfac7c msgid "" "This workflow extracts a java source file from a tar file and then " "compiles it." msgstr "" -#: ../../src/topics/workflows.md:170 43910a8ab4484e529a17df418b1aedbb +#: ../../src/topics/workflows.md:170 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 ../../src/topics/workflows.md:180 -#: 56917e39cfa34470a7a88b52b1f955d9 eab3ac7490f24645bbf0babb20aa9df0 +#: 23af7bd2facf4043b2b1c4373fce15fa 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" -#: ../../src/topics/workflows.md:180 7ad12d67e815400c94080804b9285629 +#: ../../src/topics/workflows.md:180 a2dd833fdca4443181648e41051a5232 msgid "" "[![Visualization of 1st-" "workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-" @@ -3186,34 +3213,34 @@ msgid "" "-1st-workflow/1st-workflow.cwl)" msgstr "" -#: ../../src/topics/workflows.md:183 457d5a31c79143acae2683d95d27f7a3 +#: ../../src/topics/workflows.md:183 7e40cc9f9e1341c195e843c009575b94 msgid "" "Use a YAML or a JSON object in a separate file to describe the input of a" " run:" msgstr "" -#: ../../src/topics/workflows.md:185 a2a73901bf634547900d08b9a1ac8889 +#: ../../src/topics/workflows.md:185 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:191 f347d80e62384b14acf6423675e5359a +#: ../../src/topics/workflows.md:191 6fcf8ad3d1bd49afa4a105622437bd59 msgid "" "Next, create a sample Java file and add it to a tar file to use with the " "command-line tool." msgstr "" -#: ../../src/topics/workflows.md:205 2a845a4f3f98428fb82f3ca7ce038a6e +#: ../../src/topics/workflows.md:205 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" -#: ../../src/topics/workflows.md:212 e2007c74d5f449a882809d6b91c010bf +#: ../../src/topics/workflows.md:212 def35d6021394def80a53ae49a2cdbde msgid "" "The `cwlVersion` field indicates the version of the CWL spec used by the " "document. The `class` field indicates this document describes a " "workflow." msgstr "" -#: ../../src/topics/workflows.md:221 7f5e53ee7cf94be2bff45ef64db28a24 +#: ../../src/topics/workflows.md:221 ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "" "The `inputs` section describes the inputs of the workflow. This is a " "list of input parameters where each parameter consists of an identifier " @@ -3221,7 +3248,7 @@ msgid "" "specific workflows steps." msgstr "" -#: ../../src/topics/workflows.md:233 a0d076b7b8b048478580c99ef0c8429f +#: ../../src/topics/workflows.md:233 c84d4450bc6a475dbf34e0b22cea9130 msgid "" "The `outputs` section describes the outputs of the workflow. This is a " "list of output parameters where each parameter consists of an identifier " @@ -3230,7 +3257,7 @@ msgid "" "`compiled_class`." msgstr "" -#: ../../src/topics/workflows.md:248 7fd926c18ad548e98845e9b5134dd6f2 +#: ../../src/topics/workflows.md:248 cca9665f6daa44b49233baf34ab9fcc7 msgid "" "The `steps` section describes the actual steps of the workflow. In this " "example, the first step extracts a file from a tar file, and the second " @@ -3241,7 +3268,7 @@ msgid "" "another may run in parallel." msgstr "" -#: ../../src/topics/workflows.md:256 789fbd47f8564cceb430ef3c0bc90e9b +#: ../../src/topics/workflows.md:256 547edbf5fa424b8286cc21674ff159b0 msgid "" "The first step, `untar` runs `tar-param.cwl` (described previously in " "[Parameter References](parameter-references.md)). This tool has two input" @@ -3249,7 +3276,7 @@ msgid "" "`extracted_file`." msgstr "" -#: ../../src/topics/workflows.md:261 45c4d0492d6143ca9cebe81e9b2cf3ae +#: ../../src/topics/workflows.md:261 7ca248888b9d484cb544cd76ba538662 msgid "" "The ``in`` section of the workflow step connects these two input " "parameters to the inputs of the workflow, `tarball` and " @@ -3259,13 +3286,13 @@ msgid "" "`extractfile` in order to run the tool." msgstr "" -#: ../../src/topics/workflows.md:267 73bd3da2af8545928d5ea71d0f7454f6 +#: ../../src/topics/workflows.md:267 ae6b240718104380b08db5552d7355ea msgid "" "The `out` section of the workflow step lists the output parameters that " "are expected from the tool." msgstr "" -#: ../../src/topics/workflows.md:278 15ce3d2700424f0fbb280d602ccebcf6 +#: ../../src/topics/workflows.md:278 e5a8b7f84be64020b191099f3fad30ed msgid "" "The second step `compile` depends on the results from the first step by " "connecting the input parameter `src` to the output parameter of `untar` " @@ -3275,11 +3302,11 @@ msgid "" "the `outputs` section for the Workflow, described above." msgstr "" -#: ../../src/topics/workflows.md:285 af4268f19202436eb0a7e8c6bed5e386 +#: ../../src/topics/workflows.md:285 f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" -#: ../../src/topics/workflows.md:287 94a4eadca6b949d79de2990a0150eee8 +#: ../../src/topics/workflows.md:287 12a06d8358534102b202965d4258c18e msgid "" "Workflows are ways to combine multiple tools to perform a larger " "operations. We can also think of a workflow as being a tool itself; a CWL" @@ -3287,17 +3314,17 @@ msgid "" "engine supports the `SubworkflowFeatureRequirement`:" msgstr "" -#: ../../src/topics/workflows.md:297 09c1619e8cbd4febbb637f7e99ad5890 +#: ../../src/topics/workflows.md:297 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "" "Here's an example workflow that uses our `1st-workflow.cwl` as a nested " "workflow:" msgstr "" -#: ../../src/topics/workflows.md:300 677ea7a27eb64568ab3689142d6efe70 +#: ../../src/topics/workflows.md:300 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" -#: ../../src/topics/workflows.md:309 097e6d47f9394e62b80110700492783a +#: ../../src/topics/workflows.md:309 b7f93705e5b8416696be01850072e8c0 msgid "" "This two-step workflow starts with the `create-tar` step which is " "connected to the `compile` step in orange; `compile` is another workflow," @@ -3305,7 +3332,7 @@ msgid "" "`\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" -#: ../../src/topics/workflows.md:314 e93affce8c104bf6977182047c1f1077 +#: ../../src/topics/workflows.md:314 e87045829b344089ab59dc27063ddd7a msgid "" "" msgstr "" -#: ../../src/topics/workflows.md:322 06c9e04ba890473b851240a0fa9c3b12 +#: ../../src/topics/workflows.md:322 42ef2f145b824d69b63abc1da175c216 msgid "" "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, " "its CWL file is included with `run`. The workflow inputs (`tarball` and " @@ -3327,7 +3354,7 @@ msgid "" "mapped to become the step's input/outputs." msgstr "" -#: ../../src/topics/workflows.md:336 0380dc1fe3aa48e4b62283b7b2a611d8 +#: ../../src/topics/workflows.md:336 c61cedf543664d388183e04b3939cc39 msgid "" "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when " "running it we had to provide a job file to denote the tar file and " @@ -3336,7 +3363,7 @@ msgid "" "the same workflow." msgstr "" -#: ../../src/topics/workflows.md:341 49b251f7a313492ea60504b00109e526 +#: ../../src/topics/workflows.md:341 9e39e3f1501c4fcaab3e8962e090f6be msgid "" "Here we use `default:` to hard-code `\"Hello.java\"` as the " "`name_of_file_to_extract` input, however our workflow also requires a tar" @@ -3346,7 +3373,7 @@ msgid "" "as a tool." msgstr "" -#: ../../src/topics/workflows.md:347 7ee55702d7dd4679a24ff052f6f0cbeb +#: ../../src/topics/workflows.md:347 03e2f767c4da461982fc3c0f3ba94762 msgid "" "It is also possible to do a less generic approach and avoid external " "dependencies in the job file. So in this workflow we can generate a hard-" @@ -3354,14 +3381,14 @@ msgid "" "`InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" -#: ../../src/topics/workflows.md:366 85d7e2e270874aa6b9f477cec0f48154 +#: ../../src/topics/workflows.md:366 3bea5822b8694e2aa32c446e1c54a045 msgid "" "In this case our step can assume `Hello.java` rather than be " "parameterized, so we can use hardcoded values `hello.tar` and " "`Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" -#: ../../src/topics/workflows.md:383 570e94513c984c09ad6aa255f534216d +#: ../../src/topics/workflows.md:383 426023bd6e3a471cbb30dbda3d6f9e57 msgid "" "Did you notice that we didn't split out the `tar --create` tool to a " "separate file, but rather embedded it within the CWL Workflow file? This " @@ -3370,7 +3397,7 @@ msgid "" "coded with filenames that only make sense within this workflow." msgstr "" -#: ../../src/topics/workflows.md:389 a107258662fb4bd4a9a3d8754e34d1e9 +#: ../../src/topics/workflows.md:389 0d498cd4caf54c15891ca1afe58e2727 msgid "" "In this example we had to prepare a tar file outside, but only because " "our inner workflow was designed to take that as an input. A better " @@ -3379,7 +3406,7 @@ msgid "" "workflows." msgstr "" -#: ../../src/topics/workflows.md:394 fc1a6502d831458ab8371a575cea47e2 +#: ../../src/topics/workflows.md:394 b2d75045e02741b4850f5ff1243f7858 msgid "" "Nested workflows can be a powerful feature to generate higher-level " "functional and reusable workflow units - but just like for creating a CWL" @@ -3387,11 +3414,11 @@ msgid "" "multiple workflows." msgstr "" -#: ../../src/topics/workflows.md:398 2d10806bf1ce4e26b92adda61efc0862 +#: ../../src/topics/workflows.md:398 cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" -#: ../../src/topics/workflows.md:400 046c5e134de94b629cc22d416f3c9182 +#: ../../src/topics/workflows.md:400 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "" "Now that we know how to write workflows, we can start utilizing the " "`ScatterFeatureRequirement`. This feature tells the runner that you wish " @@ -3402,7 +3429,7 @@ msgid "" "generate many different commands or input yaml files." msgstr "" -#: ../../src/topics/workflows.md:411 52fa22d3277940049fbb589a3ea73433 +#: ../../src/topics/workflows.md:411 5fa79c62049a447c8328ebf9db54ebf4 msgid "" "The most common reason a new user might want to use scatter is to perform" " the same analysis on different samples. Let's start with a simple " @@ -3410,23 +3437,23 @@ msgid "" "array of strings as input to the workflow:" msgstr "" -#: ../../src/topics/workflows.md:415 6043beb96c2c49648011ec556aa9e986 +#: ../../src/topics/workflows.md:415 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:421 5ac4310515124e2986724425bed5651f +#: ../../src/topics/workflows.md:421 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "" "Aside from the `requirements` section including " "`ScatterFeatureRequirement`, what is going on here?" msgstr "" -#: ../../src/topics/workflows.md:429 7958e91d5c2f4046aa9d2070a900f9ae +#: ../../src/topics/workflows.md:429 f1cb55fc59824cc18a95fd6dcb32cf4c msgid "" "First of all, notice that the main workflow level input here requires an " "array of strings." msgstr "" -#: ../../src/topics/workflows.md:441 2db234d776fe4fd38bab07245dcb783a +#: ../../src/topics/workflows.md:441 d947c54933d64aad90df392a1cedd63f msgid "" "Here we've added a new field to the step `echo` called `scatter`. This " "field tells the runner that we'd like to scatter over this input for this" @@ -3434,7 +3461,7 @@ msgid "" "one of the step's input, not a workflow level input." msgstr "" -#: ../../src/topics/workflows.md:445 7cfb17230e284ee7b6e2a00efe8eeb74 +#: ../../src/topics/workflows.md:445 651d35997332404186aa6d5711da4a3d msgid "" "For our first scatter, it's as simple as that! Since our tool doesn't " "collect any outputs, we still use `outputs: []` in our workflow, but if " @@ -3442,59 +3469,59 @@ msgid "" "outputs to collect, be sure to update that to an array type as well!" msgstr "" -#: ../../src/topics/workflows.md:450 4311ac98544e4fb0b2f4b24985710a01 +#: ../../src/topics/workflows.md:450 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" -#: ../../src/topics/workflows.md:452 780f9c72e6c34c39918642c7e2477355 +#: ../../src/topics/workflows.md:452 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" -#: ../../src/topics/workflows.md:458 cc4a7316db644b438cbaa181ad9ef2d3 +#: ../../src/topics/workflows.md:458 b662c1a5a4424c8d8350a806356acc61 msgid "" "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply" " calls the command `echo` on a message. If we invoke `cwltool scatter-" "workflow.cwl scatter-job.yml` on the command line:" msgstr "" -#: ../../src/topics/workflows.md:466 dfc461a03fe8487794837904febb8b63 +#: ../../src/topics/workflows.md:466 04d6babfd87343d7a5f13867ea02b65f msgid "" "You can see that the workflow calls echo multiple times on each element " "of our `message_array`. Ok, so how about if we want to scatter over two " "steps in a workflow?" msgstr "" -#: ../../src/topics/workflows.md:469 1e83485b00b64dfaba897bd8d772e0f0 +#: ../../src/topics/workflows.md:469 2eaacf1a90204a2b9bd621344560f2a1 msgid "" "Let's perform a simple echo like above, but capturing `stdout` by adding " "the following lines instead of `outputs: []`" msgstr "" -#: ../../src/topics/workflows.md:472 d0321d6805ec4d3abf3877d02a0a417f +#: ../../src/topics/workflows.md:472 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" -#: ../../src/topics/workflows.md:480 d7d77e807b3048c7bdf89558f76804cb +#: ../../src/topics/workflows.md:480 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "" "And add a second step that uses `wc` to count the characters in each " "file. See the tool below:" msgstr "" -#: ../../src/topics/workflows.md:483 8d9b8be147fc4a71922dde858842e543 +#: ../../src/topics/workflows.md:483 e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" -#: ../../src/topics/workflows.md:489 34b7705416a745a6a42e6d402c0757ed +#: ../../src/topics/workflows.md:489 e3a7182f00f440b8b5461da91194a64b msgid "" "Now, how do we incorporate scatter? Remember the scatter field is under " "each step:" msgstr "" -#: ../../src/topics/workflows.md:491 257adcee9da64d5c987f3b64efd20ab0 +#: ../../src/topics/workflows.md:491 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" -#: ../../src/topics/workflows.md:497 fa6ed5d0c14f42f4aa3c5144648db22c +#: ../../src/topics/workflows.md:497 b5338f39e8c74ff28e139da68089a742 msgid "" "Here we have placed the scatter field under each step. This is fine for " "this example since it runs quickly, but if you're running many samples " @@ -3512,7 +3539,7 @@ msgid "" "might not scale well." msgstr "" -#: ../../src/topics/workflows.md:509 333e8ce458d54de394526769f96d12d2 +#: ../../src/topics/workflows.md:509 f6d92156d67c4a339bcfd194cff897df msgid "" "Ok, so how do we scatter on steps that can proceed independent of other " "samples? Remember from [Nested Workflows](#nested-workflows), that we can" @@ -3520,38 +3547,38 @@ msgid "" "two-step workflow to a single step subworkflow:" msgstr "" -#: ../../src/topics/workflows.md:513 b819e8a5df6e4fa495924095709669ef +#: ../../src/topics/workflows.md:513 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:519 f1955468a1364d44a930db77c9c4b495 +#: ../../src/topics/workflows.md:519 d80ab383eec9402faba997b548fe42eb msgid "" "Now the scatter acts on a single step, but that step consists of two " "steps so each step is performed in parallel." msgstr "" -#: ../../src/topics/workflows.md:522 8c3b9b645a204d02b2c73a205e8ec296 +#: ../../src/topics/workflows.md:522 f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" -#: ../../src/topics/workflows.md:524 4d88b9c186cd4502adbf752e8a70b6ce +#: ../../src/topics/workflows.md:524 49217c02f58c43ff9ec00f10da8d4e84 msgid "" "This workflow contains a conditional step and is executed based on the " "input. This allows workflows to skip additional steps based on input " "parameters given at the start of the program or by previous steps." msgstr "" -#: ../../src/topics/workflows.md:527 9927673564024ba5833b5ac271737857 +#: ../../src/topics/workflows.md:527 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" -#: ../../src/topics/workflows.md:566 84f4ed7ce2004742b8db9087104a469a +#: ../../src/topics/workflows.md:566 8dbd56473f8c40c0bb12a48be06117e3 msgid "" "The first thing you'll notice is that this workflow is only compatible " "for version 1.2 or greater of the CWL standards." msgstr "" -#: ../../src/topics/workflows.md:573 2b5f9757adca4490a149c7f45e14fcb5 +#: ../../src/topics/workflows.md:573 78d7f3ede2c746d482042adef050b2c4 msgid "" "The first step of the workflow (step1) contains two input properties and " "will execute foo.cwl when the conditions are met. The new property `when`" @@ -3560,7 +3587,7 @@ msgid "" "executed." msgstr "" -#: ../../src/topics/workflows.md:587 0418de720813442f81ecff293c9448b5 +#: ../../src/topics/workflows.md:587 cbbf93c70fe04ba7932ba25758ddc611 msgid "" "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value" " will pass the first conditional step and will therefore be executed and " @@ -3568,62 +3595,62 @@ msgid "" "is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" -#: ../../src/topics/workflows.md:607 524eec63be8248ae982939c975ef50a2 +#: ../../src/topics/workflows.md:607 cfa1c1fde4454df283f87cc54a9c59ec msgid "" "When a value of 3 is given the first conditional step will not be " "executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" -#: ../../src/topics/workflows.md:627 5e99f9912cc549a7890e2934425eb943 +#: ../../src/topics/workflows.md:627 1a8be2950cbb475bbb2617e005f0fac9 msgid "" "If no conditions are met for example when using `--val 2` the workflow " "will raise a permanentFail." msgstr "" -#: ../../src/topics/yaml-guide.md:1 b0121ee087d6424fbb0ea5957a7b0b8c +#: ../../src/topics/yaml-guide.md:1 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" -#: ../../src/topics/yaml-guide.md:6 49e9f6b3a06840289decf3f557860f87 +#: ../../src/topics/yaml-guide.md:6 5d83c56102e141cc978500f678dd0c1c msgid "" "[YAML][yaml] is a file format designed to be readable by both computers " "and humans. This guide introduces the features of YAML that are relevant " "when writing CWL descriptions and input parameter files." msgstr "" -#: ../../src/topics/yaml-guide.md:13 ed9eebec0b3d4b72ba65507d37757a37 +#: ../../src/topics/yaml-guide.md:13 c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" -#: ../../src/topics/yaml-guide.md:16 bf9b255a24a84f3ba989a223492b8f41 +#: ../../src/topics/yaml-guide.md:16 fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" -#: ../../src/topics/yaml-guide.md:18 e79fa0b7f8b14810a3a20908ef92bc55 +#: ../../src/topics/yaml-guide.md:18 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" -#: ../../src/topics/yaml-guide.md:19 290e2035f903417cbecb5dc5f09d6ebe +#: ../../src/topics/yaml-guide.md:19 b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" -#: ../../src/topics/yaml-guide.md:20 d420730151534f1a89076588a3358f09 +#: ../../src/topics/yaml-guide.md:20 b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" -#: ../../src/topics/yaml-guide.md:21 a6b5378bbe1e4bee9e37a765bddf75f7 +#: ../../src/topics/yaml-guide.md:21 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" -#: ../../src/topics/yaml-guide.md:22 6e4d9465dc2b454d96b02d7ad1817795 +#: ../../src/topics/yaml-guide.md:22 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" -#: ../../src/topics/yaml-guide.md:24 a649d4af5f434dac9395e013ec4836bb +#: ../../src/topics/yaml-guide.md:24 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" -#: ../../src/topics/yaml-guide.md:26 446190a298834b73bda068286e8490cf +#: ../../src/topics/yaml-guide.md:26 cda73485875d4c8e9464679a20558616 msgid "" "Fundamentally, a file written in YAML consists of a set of _key-value " "pairs_. Each pair is written as `key: value`, where whitespace after the " @@ -3633,7 +3660,7 @@ msgid "" "otherwise. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:42 2f35c012ff174721bffe66a3f58a804f +#: ../../src/topics/yaml-guide.md:42 98cae24919b74c088a5d89706aec581b msgid "" "The YAML above defines four keys - `first_name`, `last_name`, " "`age_years`, and `home` - with their four respective values. Values can " @@ -3642,7 +3669,7 @@ msgid "" "types (see below)." msgstr "" -#: ../../src/topics/yaml-guide.md:51 43127c98c9d94aedac61cee67929c1a6 +#: ../../src/topics/yaml-guide.md:51 b4b0940b4b5743c09637b36b964202d0 msgid "" "Values may be wrapped in quotation marks, but be aware that this may " "change the way that they are interpreted i.e. `\"1234\"` will be treated " @@ -3653,28 +3680,28 @@ msgid "" "wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" -#: ../../src/topics/yaml-guide.md:61 dc4fe561203c4c38a9caea5bd6eff2cd +#: ../../src/topics/yaml-guide.md:61 dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" -#: ../../src/topics/yaml-guide.md:63 f924e4896db2424d99ce8c9da14c599a +#: ../../src/topics/yaml-guide.md:63 9ca3554d771d45998e88aaede525b227 msgid "" "You may use `#` to add comments to your CWL and parameter files. Any " "characters to the right of ` #` will be ignored by the program " "interpreting the YAML. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:76 bf7646f5f925485c842a6d34140e40b8 +#: ../../src/topics/yaml-guide.md:76 3fca839cede94cfd8e4f605c73ba699d msgid "" "If there is anything on the line before the comment, be sure to add at " "least one space before the `#`!" msgstr "" -#: ../../src/topics/yaml-guide.md:79 c483e61dec8949fa96bb893d422888a0 +#: ../../src/topics/yaml-guide.md:79 da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" -#: ../../src/topics/yaml-guide.md:81 85fcb523d0e34a499eae04d304887f7b +#: ../../src/topics/yaml-guide.md:81 3ded0f125249485c921994b6e6b93ac9 msgid "" "When describing a tool or workflow with CWL, it is usually necessary to " "construct more complex, nested representations. Referred to as _maps_, " @@ -3685,7 +3712,7 @@ msgid "" "with two spaces (⇥tab characters are not allowed). For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:104 83d47c8736a34f3cbf09e3997845e4f4 +#: ../../src/topics/yaml-guide.md:104 53ece35d309a4c8d99f1efb2122a7092 msgid "" "The YAML above illustrates how to build up complex nested object " "descriptions relatively quickly. The `inputs` map contains a single key, " @@ -3698,11 +3725,11 @@ msgid "" "object it describes." msgstr "" -#: ../../src/topics/yaml-guide.md:127 c698fb3d37bc403e9aeb679b8fc0e15e +#: ../../src/topics/yaml-guide.md:127 d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" -#: ../../src/topics/yaml-guide.md:129 ae8af2f0eeda4aec97201211dfa965c7 +#: ../../src/topics/yaml-guide.md:129 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "" "In certain circumstances, it is necessary to provide multiple values or " "objects for a single key. As we've already seen in the [Maps](#maps) " @@ -3713,26 +3740,26 @@ msgid "" "preceded by `-`. For example:" msgstr "" -#: ../../src/topics/yaml-guide.md:146 2ee87aa465cd41fda16a61e242f8c9d0 +#: ../../src/topics/yaml-guide.md:146 fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" -#: ../../src/topics/yaml-guide.md:167 0a6fd4469ff24b61b3ad001b09eead18 +#: ../../src/topics/yaml-guide.md:167 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" -#: ../../src/topics/yaml-guide.md:169 b96ba19bce9341d39c46054e1f10fe8f +#: ../../src/topics/yaml-guide.md:169 87bafb845c714b109874f6137b84462d msgid "" "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and " "arrays can also be defined in YAML using the native JSON syntax. For " "example:" msgstr "" -#: ../../src/topics/yaml-guide.md:177 903f30af3d0c45cfb61063936a8097a7 +#: ../../src/topics/yaml-guide.md:177 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" -#: ../../src/topics/yaml-guide.md:184 ede8db7c0a58432e8a1c416e937a06d2 +#: ../../src/topics/yaml-guide.md:184 fcd05b1ef31a4046946a2399c7fc5575 msgid "" "Native JSON can be useful in indicating where a field is intentionally " "left empty (such as `[]` for an empty array), as well as where it makes " @@ -3742,64 +3769,52 @@ msgid "" "readability of a YAML file, and should be used sparingly." msgstr "" -#: ../../src/topics/yaml-guide.md:194 c8b53615476a4a1fbef2420d93bac94e +#: ../../src/topics/yaml-guide.md:194 f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" -#: ../../src/topics/yaml-guide.md:196 ea03cb5525cc491f9feb5c4780b38fee +#: ../../src/topics/yaml-guide.md:196 859368c1f25c4a4aad57abfd046c63f5 msgid "" "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for" " us while we wrote this guide, though it also covers features that are " "not valid in CWL." msgstr "" -#: ../../src/tutorials.md:1 92fd3a5e31714eab859dd630af2e78cf +#: ../../src/tutorials.md:1 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" -#: ../../src/tutorials.md:5 de660ecdb5b44c97a0e519d00b232497 +#: ../../src/tutorials.md:5 5d92464923c245818c070fbef102be89 msgid "" "This is a list of tutorials provided by the CWL community. Use the `Edit " "this page` link in the menu if you would like to add another tutorial to " "the list." msgstr "" -#: ../../src/tutorials.md:7 5afc1e1288e74ed0985e61e5164479c7 +#: ../../src/tutorials.md:7 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" -#: ../../src/tutorials.md:9 862dc7ac81e54b1fb3d4c2f961b8810e +#: ../../src/tutorials.md:9 13d7e2e92e96432787c712cf6a595424 msgid "" "[Introduction to Workflows with Common Workflow Language: For " "Contributors.](https://carpentries-incubator.github.io/cwl-novice-" "tutorial/)" msgstr "" -#: ../../src/tutorials.md:11 e2c94c0e1c7048d38cd7aa2c465a859d +#: ../../src/tutorials.md:11 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" -#: ../../src/tutorials.md:13 b63253780f51467a95207d820d13ac39 +#: ../../src/tutorials.md:13 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" -#: ../../src/tutorials.md:15 6d06ca7ed5df4560aaed286f4fe33928 +#: ../../src/tutorials.md:15 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" -#: ../../src/tutorials.md:17 5448df4a6a8f431d80e269bcd480e19e +#: ../../src/tutorials.md:17 a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" -#~ msgid "" -#~ "Unless required by applicable law or " -#~ "agreed to in writing, software " -#~ "distributed under the License is " -#~ "distributed on an \"AS IS\" BASIS, " -#~ "WITHOUT WARRANTIES OR CONDITIONS OF ANY" -#~ " KIND, either express or implied. See" -#~ " the License for the specific " -#~ "language governing permissions and limitations" -#~ " under the License." -#~ msgstr "" - diff --git a/locales/user_guide.pot b/locales/user_guide.pot index a806cea1..0a669946 100644 --- a/locales/user_guide.pot +++ b/locales/user_guide.pot @@ -8,7 +8,7 @@ msgid "" msgstr "" "Project-Id-Version: Common Workflow Language User Guide \n" "Report-Msgid-Bugs-To: \n" -"POT-Creation-Date: 2023-01-25 16:53+0100\n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" "PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" "Last-Translator: FULL NAME \n" "Language-Team: LANGUAGE \n" @@ -16,1273 +16,1273 @@ msgstr "" "Content-Type: text/plain; charset=UTF-8\n" "Content-Transfer-Encoding: 8bit\n" -#: ../../LICENSE.rst:2 -#: 75de2be8809847b8bf1ccd42aa694a24 +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 msgid "Licenses" msgstr "" -#: ../../LICENSE.rst:5 -#: 2edd71801f6245ef821887a74f21b94c +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 msgid "Instructional Material" msgstr "" -#: ../../LICENSE.rst:7 -#: 3c0a9704ed8f4367893242a4f75d703f -msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the `Creative Commons Attribution license `_. The following is a human-readable summary of (and not a substitute for) the `full legal text of the CC BY 4.0 license `_." +#: ../../LICENSE.md:6 +#: 747f9dd48bc54f44adcd8b18c57f4d9d +msgid "All Common Workflow Language project instructional material and changes to the structure are also made available under the [Creative Commons Attribution license][cc-by-human]. The following is a human-readable summary of (and not a substitute for) the [full legal text of the CC BY 4.0 license][cc-by-legal]." msgstr "" -#: ../../LICENSE.rst:12 -#: 90cc755d172e4c82b882b4ee620fe652 +#: ../../LICENSE.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 msgid "You are free:" msgstr "" -#: ../../LICENSE.rst:14 -#: e5246890525144bda8547106b6643382 -msgid "to **Share**—copy and redistribute the material in any medium or format" +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" msgstr "" -#: ../../LICENSE.rst:16 -#: 4d96baa7ca7a4240b75be213696558ba -msgid "to **Adapt**—remix, transform, and build upon the material" +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" msgstr "" -#: ../../LICENSE.rst:18 -#: e19adbba09d14d069534251a7ef70993 +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 msgid "for any purpose, even commercially." msgstr "" -#: ../../LICENSE.rst:20 -#: 8bc6672f4a33428296226112a1be6fbe +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" msgstr "" -#: ../../LICENSE.rst:23 -#: be38276e7b374f57b9997391bf898a62 -msgid "**Attribution**—You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a `link to the license `_, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." +#: ../../LICENSE.md:24 +#: 8fb7a2946c384364814c6ec3910997d3 +msgid "**Attribution**---You must give appropriate credit (mentioning that your work is derived from work that is Copyright © the Common Workflow Language project, and, where practical, linking to https://www.commonwl.org/ ), provide a [link to the license][cc-by-human], and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use." msgstr "" -#: ../../LICENSE.rst:31 -#: f00d5c3846034c2ea116c2f74786d9fc -msgid "**No additional restrictions**—You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" +#: ../../LICENSE.md:32 +#: 8161753b7526445db319210044566200 +msgid "**No additional restrictions**---You may not apply legal terms or technological measures that legally restrict others from doing anything the license permits. With the understanding that:" msgstr "" -#: ../../LICENSE.rst:35 -#: 1798d65c10104040923c2fea2199bab2 +#: ../../LICENSE.md:36 +#: 15314ba527864eaa834cf1185cfcc4e3 msgid "You do not have to comply with the license for elements of the material in the public domain or where your use is permitted by an applicable exception or limitation." msgstr "" -#: ../../LICENSE.rst:38 -#: c65198b804f8436ba783643d51bc72d9 +#: ../../LICENSE.md:39 +#: b351ddf9847d48b1a2a87fc78eaba4d2 msgid "No warranties are given. The license may not give you all of the permissions necessary for your intended use. For example, other rights such as publicity, privacy, or moral rights may limit how you use the material." msgstr "" -#: ../../LICENSE.rst:44 -#: 4777f6a958394b138c5b68eee0367734 +#: ../../LICENSE.md:44 +#: a091addc2dea4830a06bb72ead56c5ea msgid "Software" msgstr "" -#: ../../LICENSE.rst:46 -#: 7dec2236137f4de5ac7df7a8c8eaf98b -msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the `OSI`_-approved `Apache 2.0 license `_." +#: ../../LICENSE.md:46 +#: 84b2c685bbab48449fdc72d2a1e42bf4 +msgid "Except where otherwise noted, the example programs and other software provided by Common Workflow Language project are made available under the [OSI][osi]-approved [Apache 2.0 license][apache-2.0-license]." msgstr "" -#: ../../LICENSE.rst:50 -#: 9c4d58a1129a4d4eb4db1bfabbeddb6e -msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." +#: ../../LICENSE.md:51 +#: 0f68eafafaef4b54accba7e13bfaa702 +msgid "Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an \"AS IS\" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License." msgstr "" #: ../../src/_includes/what-is-cwl.md:1 #: ../../src/_includes/what-is-cwl.md:2 -#: bdd540403a5746ff99edf2dcad0e3122 -#: 5ad4be9b62d54c95a913795b514676fd -#: dfc7702e073140c985cf47272a20214d +#: eab02dc13915490bb3c9ba744d78b6a7 +#: d4f35995b0f6494d9771a4be0a82538f +#: d6ccd4b546254f56a597d67dd4fdc5d6 msgid "CWL is a way to describe command-line tools and connect them together to create workflows. Because CWL is a specification and not a specific piece of software, tools and workflows described using CWL are portable across a variety of platforms that support the CWL standard." msgstr "" #: ../../src/episodes.md:5 #: ../../src/setup.md:5 -#: f1b89ae4325343f783bce8b7c9971047 -#: 810c4e8dd79247d6a6fd51a8f65d3975 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f msgid "This page has moved" msgstr "" #: ../../src/episodes.md:9 -#: 3060770b3bef41d7bcfcdfb413d7689c +#: cc11f5d29206492d9f2f0922882b6159 msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. Please use the new [Table of Contents](index.md#table-of-contents) to browse the User Guide." msgstr "" #: ../../src/faq.md:1 -#: 48bb9f628b344ba1a3b67ae1cb264e3c +#: e2ed894d325a4f50a5e2dc69da5531a1 msgid "FAQ" msgstr "" #: ../../src/faq.md:11 -#: 7e3684e9672643738846756e1ebafd18 +#: 61edb787dab04ca2ad3ed07616d878a0 msgid "Non \"`File`\" Types Using `evalFrom`" msgstr "" #: ../../src/faq.md:41 -#: 187ceabb7fd9480bb8cf0f2da47f65ef +#: d5321589e7ed4f0db3c630cc39800791 msgid "Rename an Input File" msgstr "" #: ../../src/faq.md:43 -#: b548b76bcc85420a9b30792386105139 +#: fc62427c0a004810b055dee90ec5e2d9 msgid "This example demonstrates how to change the name of an input file as part of a tool description. This could be useful when you are taking files produced from another step in a workflow, and don't want to work with the default names that these files were given when they were created." msgstr "" #: ../../src/faq.md:59 -#: 9ce692b78ead47e4b0f8cdae8837d35b +#: 1c6b8a4194a14611b4061b1540c3807f msgid "Rename an Output File" msgstr "" #: ../../src/faq.md:61 -#: 6df1201c159343da9e7515379980d6a0 +#: bc7ad10c929848a3a9a240a3c501d299 msgid "This example demonstrates how to change the name of an output file from the default name given to it by a tool:" msgstr "" #: ../../src/faq.md:82 -#: f9ab1d0dc1c842b6abb5385268c1d3bd +#: 7225a993d281421b95c8e3df2846a0e3 msgid "Referencing a Local Script" msgstr "" #: ../../src/faq.md:84 -#: 9f6a84ab6a9343b6ad7db826f8964362 +#: 7ef1dbb81993473f948d9c6f3c64b381 msgid "There are two ways to reference a local script:" msgstr "" #: ../../src/faq.md:86 -#: fa50e4fa990b42d1ba4c0f4ae1e5caa1 +#: 450edf800a18423195bea4fe8793a2cb msgid "The first method involves adding the folder containing your scripts to the `PATH` environment variable. This allows you to run the shell script directly without using `sh` or `bash` commands." msgstr "" #: ../../src/faq.md:89 -#: 3a871012fcfd4f3ebeca0cb86ec93435 +#: 1a8cc75ea6174b9297871b2e58971077 msgid "Start with adding a _shebang_ at the top of your file:" msgstr "" #: ../../src/faq.md:95 -#: d954edfff2584288ac8c600733070d2e +#: a7d84f740a714ec588503ee084fbbc34 msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" msgstr "" #: ../../src/faq.md:97 -#: af6b1e37d6be4450a761854480ec9aab +#: 569d553abe85450c9d1c37456bf412f4 msgid "Finally, modify your `PATH` to add the directory where your script is located. (It is good practice to use `$HOME/bin` for storing your own scripts)." msgstr "" #: ../../src/faq.md:104 -#: 31f4a2d43062493ca64c648f80afc8e9 +#: 95f5dbbd21084a318413b9528fb867be msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." msgstr "" #: ../../src/faq.md:113 -#: 41c54e71b6cd4f63b2a619a515240d34 +#: 1b3cae80fa9a40ffb2259b8c1cd2b468 msgid "When you wish to share your work later, you can place your script in a software container in the Docker format." msgstr "" #: ../../src/faq.md:115 -#: 8edc3541ad134ab5a1d23c724f1f0a4e +#: 8d86baa239364f799d4f9d5ea2b0e314 msgid "The second method involves including an input of `type: File` in the script itself:" msgstr "" #: ../../src/faq.md:135 -#: ac0ea81eba8842a18801ab03cbf80a57 +#: f2c109998c76434893ff16b17fdb2bd0 msgid "In CWL, everything must be directly stated." msgstr "" #: ../../src/faq.md:138 -#: 52be1a5640234feabe958ff7ade33653 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 msgid "Setting `self`-based Input Bindings for Optional Inputs" msgstr "" #: ../../src/faq.md:140 -#: c6db734d5aef4f4f99676bdebf9c83c9 +#: 2c38cc58cbb340bc935a5f00e96ba95c msgid "Currently, `cwltool` can't cope with missing optional inputs if their input binding makes use of `self`. Below is an example workaround for this, pending a more sophisticated fix." msgstr "" #: ../../src/faq.md:165 -#: a9f7b47c0dd741739795da39bf114879 +#: ce6db54bd0f54839a5beb948530a21f0 msgid "Model a \"one-or-the-other\" Parameter" msgstr "" #: ../../src/faq.md:167 -#: e3fdd9228b924905a4a1f4b2b7ad7159 +#: d06cbf89028b4638ad54c2529bcbfa25 msgid "Below is an example showing how to specify different strings to be added to a command line, based on the value given to a Boolean parameter." msgstr "" #: ../../src/faq.md:188 -#: 3f7cda1437cc48f18745a827ebb74582 +#: d53fb28dcad04e7788cba9e280a2343c msgid "Connect a Solo Value to an Input that Expects an Array of that Type" msgstr "" #: ../../src/faq.md:190 -#: 5aeaba2cae64442e816bbd458aee833a +#: d9e30e11533b4d53a144f5df7041268d msgid "Using [`MultipleInputFeatureRequirement`](https://www.commonwl.org/v1.0/Workflow.html#MultipleInputFeatureRequirement) along with [`linkMerge: merge_nested`](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/faq.md:194 -#: 5af827a402834978addd82c70be6b5ab +#: 941077158ec54ae19bfa2e2ad6662da1 msgid "merge_nested" msgstr "" #: ../../src/faq.md:196 -#: 6d69e42bd8e443c4b19d80807c7efd6b +#: 937cb94a370640c788fbc3fe0b19f2e5 msgid "The input must be an array consisting of exactly one entry for each input link. If \"merge_nested\" is specified with a single link, the value from the link must be wrapped in a single-item list." msgstr "" #: ../../src/faq.md:199 -#: 404640397b6e40c2a2cd5cf85ab3b1c0 +#: a1d57e15656548128a76a8b975c564c9 msgid "Which means \"create a list with exactly these sources as elements\"" msgstr "" #: ../../src/faq.md:201 -#: 1682c2486e224770b62269709a8663cf +#: c8c235a9bf6240628f0b5493ffebf7e0 msgid "Or in other words: if the destination is of type `File[]` (an array of `File`s) and the source is a single `File` then add `MultipleInputFeatureRequirement` to the Workflow level `requirements` and add `linkMerge: merge_nested` under the appropriate `in` entry of the destination step." msgstr "" #: ../../src/faq.md:229 -#: 9078fc009bc145808813c9cc2b734b58 +#: 3da4dcb043eb4423a53a14182949d9cd msgid "Optional Inputs 💯" msgstr "" #: ../../src/faq.md:231 -#: d4b5a54a400c409cb7984428f6a03ec8 +#: 89b90d3bf1ea4ebd88482d435241fac5 msgid "To make an input parameter optional, add a question mark to the type declaration." msgstr "" #: ../../src/faq.md:247 -#: 9e8dbee6e8f84d08b1a54fffa06394ef +#: a854006054ce4ffe94bbfa73bdbecbf2 msgid "" msgstr "" #: ../../src/faq.md:248 -#: 1d846bfb5f054d09a4afad1da8e4b642 +#: f80eb714e9df417fbba555b5dd5f4d8c msgid "Enum Inputs ⚜️" msgstr "" #: ../../src/faq.md:250 -#: 2d0e95fec8084787b734388d60188574 +#: 10af80fa13af4158aec7060550485350 msgid "For command line flags that require a specific input as the argument an enum type can be declared in CWL. **Specifying null here is known as long form style. It does the same thing as the question mark on the other inputs.**" msgstr "" #: ../../src/faq.md:267 -#: eccc4a364330470fa474dcaaa3433390 +#: ad1c26711ccd4efd8fdb25f9293d33fd msgid "" msgstr "" #: ../../src/faq.md:268 -#: e945f6a337af4e4686bed482a4fe6c39 +#: 49e2095b51f84f609f5d4bc088ad9745 msgid "Record Inputs 📀" msgstr "" #: ../../src/faq.md:270 -#: 8a3efaa0ad1548428bcfd6e01d135cdc +#: 52b8538177c64090af51f5f6a696c28c msgid "For commandline flags that are either **mutually exclusive** or **dependent** a special record type can be defined. You can also specify null here to create optional inputs." msgstr "" #: ../../src/faq.md:322 -#: cdab644adc5643708870fb08c06cbfca +#: f96c9257e3734b8aa0cc5e065f74f944 msgid "Setting Mutually Exclusive Parameters" msgstr "" #: ../../src/faq.md:324 -#: 089a5a0b076b44aeaab4d69ee3c79f97 +#: 7dc0540508084a3495ff3b2ac90fd323 msgid "To properly set fields in a record input type, you need to pass a dictionary to the input to properly set the parameters. This is done by using inline JavaScript and returning the dictionary with the key of the field you want to set. The source field is set to indicate the input from the workflow to be used as the value." msgstr "" #: ../../src/faq.md:342 -#: 561172559c6f41a68819608fd9e58bb0 +#: b53dc77466b24a67b52b8aadf4fab724 msgid "Setting Booleans" msgstr "" #: ../../src/faq.md:344 -#: c5ee4946d2e840abaa3dc796a62652c7 +#: cf4e7f3977ae4f9b877072c2b1c4b533 msgid "These can be set by using the default field" msgstr "" #: ../../src/faq.md:349 -#: 4f2069a2113c414db18eca95550e9e09 +#: 99b37739ef18443ca7c0e715a131e0c7 msgid "Concatenating Strings in Inputs" msgstr "" #: ../../src/faq.md:351 -#: 31f3390e6771414ba7bf57c044c4b0c4 +#: 9b00b5a55ee941e1adbfe89e133791e3 msgid "The valueFrom field must be used instead of default." msgstr "" #: ../../src/faq.md:359 -#: 3b77ce4930ae46d5be9f6965e8c54727 +#: 07922147f7ab487ba2a1e7c43c9f410c msgid "`cwltool` Errors due to Filenames with Space Characters Inside" msgstr "" #: ../../src/faq.md:361 -#: 06f36bbe4d3840229b7374f27b86ae80 +#: 7a11806f0c7045b48fe58a271f814797 msgid "`cwltool` does not allow some characters in filenames by default." msgstr "" #: ../../src/faq.md:363 -#: 3cb2f70d00274a4dafd972ccd8c519c2 +#: fdaec25650ab4b0fb1c527610e24ae5a msgid "For example, the filename `a space is here.txt` includes 3 space characters." msgstr "" #: ../../src/faq.md:371 -#: 093a1529262043ef84a99675054938e0 +#: 182959fc9f4746d082994e07d05c8cde msgid "If you can not avoid these dangerous characters, then pass `--relax-path-checks` to `cwltool`." msgstr "" #: ../../src/faq.md:373 -#: 45b6d9acbfaa47e5984184f7da554d0a +#: cc7752e9989e4a6d957682f479d6fc60 msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" msgstr "" #: ../../src/faq.md:375 -#: 5705c9bacca5405ca6f14315a5575db8 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 msgid "If `cwltool --validate` returns valid" msgstr "" #: ../../src/faq.md:384 -#: 82bfc285b59a439ca97d3278997f0fce +#: 3de2513c7d7b4569ba63f7e6d29137b7 msgid "But executing it causes an error like:" msgstr "" #: ../../src/faq.md:396 -#: 181d5130101d45ccb22aebae3d154c2f +#: ae3a9188706649e28f97bc4ec34c0821 msgid "The file is here" msgstr "" #: ../../src/faq.md:410 -#: e864390b5ddb423aaa10e9d33d257dc1 +#: e1ac97ab6ad3449b8c54933d25257f73 msgid "Problem caused by `-` (hyphen character)." msgstr "" #: ../../src/faq.md:423 -#: fe637c32fb15427a9045679b5da42ec5 +#: f6c402f7f6974edbbb5582c8e22f3869 msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" msgstr "" #: ../../src/faq.md:436 -#: 1f8004b9df8547029d82e57f9abdc979 +#: 190099a242a645c9b9f8bc3ce89d920d msgid "If it is not possible to change the input identifier, then you can use an alternative CWL Parameter Reference syntax:" msgstr "" #: ../../src/faq.md:442 -#: 70990dc5a0034099921ceb89c89e2dcc +#: 06a4f6ffc2da4d43b453d4784b42efd3 msgid "Use CWL and cwltool with Singularity" msgstr "" #: ../../src/faq.md:445 -#: f679e26f18d9455f945fd13361a9c906 +#: 1901c34201054a9cae199b0dbb8b945e msgid "The CWL standards are built around (optional) Docker format containers. The reference runner and several other CWL implementations support running those Docker format containers using the Singularity engine. Directly specifying a Singularity format container is not part of the CWL standards." msgstr "" #: ../../src/faq.md:450 -#: fcd0273dbdd84e728cfd8fbe239f2a01 +#: 2d498470524d47f18f9936ace6acebb0 msgid "Debug JavaScript Expressions" msgstr "" #: ../../src/faq.md:452 -#: 173ddbd1e7c64927a8dcb12a2a2140f8 +#: d7b044f5224a48eda09bc949cf645193 msgid "You can use the --js-console option of cwltool, or you can try creating a JavaScript or TypeScript project for your code, and load it using expressionLib, e.g.: https://github.com/common-workflow-language/common-workflow-language/blob/master/v1.0/v1.0/template-tool.cwl#L6-L8" msgstr "" #: ../../src/index.md:1 -#: 662fe273e2fb4042b688512955e450a1 +#: 2754519265eb426b940bbbd2b8d64e1e msgid "Common Workflow Language User Guide" msgstr "" #: ../../src/index.md:3 -#: a15b52205f0145feaac298510e4d678a +#: f8d6e4cd54cb42c88182a43171d97bab msgid "This guide will introduce you to writing workflows using the [Common Workflow Language](https://www.commonwl.org/) (CWL) open standards. This guide describes the latest specification {{ cwl_version }}." msgstr "" #: ../../src/index.md:7 -#: 512aa0c7166b429e8116f71eef007f79 +#: 132d40fee3b84469afa80d5ff613bf77 msgid "Contributions and Feedback are Welcome!" msgstr "" #: ../../src/index.md:9 -#: b1b19e17a18540939cb3bb7f8a700cab +#: 0f47157605a34ea58770ea898deebae4 msgid "If you find that something is missing from this guide, or if you would like to provide other feedback, file an Issue on the [project repository for this guide][repo]. You can also suggest changes directly in a Pull Request by clicking the \"Edit this page\" button at the right sidebar of each page." msgstr "" #: ../../src/index.md:16 -#: d58b36ac43ac44139897be752fbb1f87 +#: 6d269e8d70184034bcb56385a6ca198f msgid "Navigating the User Guide" msgstr "" #: ../../src/index.md:18 -#: 6726cf3585a646a8b4cbeb543cf84a38 +#: ed74c9a4b623464480e2c184668fcec0 msgid "If you are a beginner user get started with the [Introduction](/introduction/index.md) section. For advanced users the subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." msgstr "" #: ../../src/index.md:23 -#: 2e504aa7c46a426fa959e7254e9a84a5 +#: cfa67cf5521b414da6f7d34cbed283f7 msgid "The Table of Contents is displayed at the top menu and also on the left sidebar. It also appears further down this page but with links to subsections. The right sidebar contains links to the sections of each page, and the Search form is on the left sidebar." msgstr "" #: ../../src/index.md:28 -#: e7be0df0838b432d9c7f296d777f120b +#: ee6b82bd86264e4bb1e8e4065b1e6b9c msgid "Table of Contents" msgstr "" #: ../../src/introduction/basic-concepts.md:1 -#: 173e0816db20432c8d9dba1de5393dee +#: e208c8a7506e41dcac9a403c5d2850c1 msgid "Basic Concepts" msgstr "" #: ../../src/introduction/basic-concepts.md:3 -#: 30eacc583f6841719e2142d283811d97 +#: ac62d326a68145b695e46b714d4e8156 msgid "This section describes the basic concepts for users to get started on working with Common Workflow Language (CWL) workflows. Readers are expected to be familiar with workflow managers, YAML, and comfortable with following instructions for the command-line. The other sections of the user guide cover the same concepts, but in more detail. If you are already familiar with CWL or you are looking for more advanced content, you may want to skip this section." msgstr "" #: ../../src/introduction/basic-concepts.md:10 -#: 791b8f38a14147bbaa174c7eb595f17e +#: 984e6676b9d04c7092bc492f195dfb91 msgid "The CWL Specification" msgstr "" #: ../../src/introduction/basic-concepts.md:21 -#: 1a3989dcbb9844b39d84bf6df6b352ed +#: cbe1d761da5b403d9605fa1fb8e62fdf msgid "The CWL specification is a document written and maintained by the CWL community. The specification has different versions. The version covered in this user guide is the {{ cwl_version }}." msgstr "" #: ../../src/introduction/basic-concepts.md:25 -#: db1bbc6e980f404f9f3fcd08e92ee9a3 +#: 3a71b269bd3c49eb913cf69b60373c24 msgid "The specification version can have up to three numbers separated by `.`s (dots). The first number is the major release, used for backward-incompatible changes like the removal of deprecated features. The second number is the minor release, used for new features or smaller changes that are backward-compatible. The last number is used for bug fixes, like typos and other corrections to the specification." msgstr "" #: ../../src/introduction/basic-concepts.md:33 -#: acc7887c65974114996f700a38a7eccc +#: b171b72c48d44050a3416a7a42c4021d msgid "The model used for the specification version is called Semantic Versioning. See the end of this section to [learn more](#learn-more) about it." msgstr "" #: ../../src/introduction/basic-concepts.md:37 -#: d2476d9bcff44f21b8d84a3a0d87a246 +#: b3df1607e9d242d78b22dc44335fbe2d msgid "Implementations" msgstr "" #: ../../src/introduction/basic-concepts.md:39 -#: f86415e4d78e48c4a8a76ced81221b98 +#: 078b58ffc1cc4d25a7c4eea3bb76e025 msgid "An implementation of the CWL specification is any software written following what is defined in a version of the specification document. However, implementations may not implement every aspect of the specification. CWL implementations are licensed under both Open Source and commercial licenses." msgstr "" #: ../../src/introduction/basic-concepts.md:44 -#: c5524d73708c4c779980528864506fd4 +#: c3869b4ec5ff47d99e8da79770722e04 msgid "CWL is well suited for describing large-scale workflows in cluster, cloud and high performance computing environments where tasks are scheduled in parallel across many nodes." msgstr "" #: ../../src/introduction/basic-concepts.md:51 -#: ac46a9f8850a434bac5bc2b41ee6294e +#: 2482c84831fc4dfab629e7bfcfb41cbf msgid "CWL specification, implementations, and other tools." msgstr "" #: ../../src/introduction/basic-concepts.md:105 -#: 9bba7c4f783942e4a299603430601363 +#: a5ebc727fb3443f78e81d6b7ed5ac750 msgid "Processes and Requirements" msgstr "" #: ../../src/introduction/basic-concepts.md:107 -#: e2140e0f0e7747ef8383887c20a7945a +#: 86e6a06992dc4228bfda7add48e28ca3 msgid "A process is a computing unit that takes inputs and produces outputs. The behavior of a process can be affected by the inputs, requirements, and hints. There are four types of processes defined in the CWL specification {{ cwl_version }}:" msgstr "" #: ../../src/introduction/basic-concepts.md:112 -#: 15bf490724cd46dcbcfab44633c5a9a2 +#: 8c9772f96caf4169924d22eb929a4f0f msgid "A command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:113 -#: 51d52d051e654a8395239f88df7c9d8c +#: 4fac209a62114798b79e4810f7a0148b msgid "An expression tool." msgstr "" #: ../../src/introduction/basic-concepts.md:114 -#: eb496cc818524fa7bae5a22ddd00a19c +#: b97ba368fd664caab0494e2392795697 msgid "An operation." msgstr "" #: ../../src/introduction/basic-concepts.md:115 -#: c4a22d12e7f149ff901d27de32b9361d +#: 903a6796e3304a19ad885b2428b0e80f msgid "A workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:118 -#: 7618de899a7043989d77baacf62eb7b2 +#: 6e352ac1f8e144c392ac5adf18c28298 msgid "The processing units available in the CWL objects model." msgstr "" #: ../../src/introduction/basic-concepts.md:119 -#: 6f1544a220664b79b04bf008058b5a91 +#: cf2922f645904ac7955428ecddc37b8a msgid "A command-line tool is a wrapper for a command-line utility like `echo`, `ls`, and `tar`. A command-line tool can be called from a workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:122 -#: fbd14ac9a2f541478a320ed4cbc69e13 +#: 5f47aae608c041aeb4134d59dad314d2 msgid "An expression tool is a wrapper for a JavaScript expression. It can be used to simplify workflows and command-line tools, moving common parts of a workflow execution into reusable JavaScript code that takes inputs and produces outputs like a command-line tool." msgstr "" #: ../../src/introduction/basic-concepts.md:127 -#: da4dba50d25d4533b3dbb92f54d32a30 +#: f6f589481d0c4891beaccb63160619ef msgid "Operation is an abstract process that also takes inputs, produces outputs, and can be used in a workflow. But it is a special operation not so commonly used. It is discussed in the [Operations section](../topics/operations.md) of this user guide." msgstr "" #: ../../src/introduction/basic-concepts.md:131 -#: ce11c9f8d65c4268984d0384d95144cc +#: 73b0c1ccb18c4b74a2c0fdf9706eca85 msgid "The workflow is a process that contains steps. Steps can be other workflows (nested workflows), command-line tools, or expression tools. The inputs of a workflow can be passed to any of its steps, while the outputs produced by its steps can be used in the final output of the workflow." msgstr "" #: ../../src/introduction/basic-concepts.md:137 -#: 3a201aa497e84f70855bb2251e7e3281 +#: 4ace6b92f4e04a07aa202840ebe36417 msgid "The CWL specification allows for implementations to provide extra functionality and specify prerequisites to workflows through *requirements*. There are many requirements defined in the CWL specification, for instance:" msgstr "" #: ../../src/introduction/basic-concepts.md:141 -#: b78f7fa2be1c4bb090f6da895457ad1e +#: cc6cd8cb81564cadb8e6a4c49423b7f7 msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." msgstr "" #: ../../src/introduction/basic-concepts.md:142 -#: f7e95d264ffa4e2db0864faccd9e5a0e +#: 2d9f53b6ed5041dbb6c0b54835897856 msgid "`SubworkflowFeatureRequirement` - enables nested workflows." msgstr "" #: ../../src/introduction/basic-concepts.md:143 -#: 3f1e5b01e49a4dc1b1c99936a4589afc +#: 907674a4ecff4826a2b880e28fc38f33 msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." msgstr "" #: ../../src/introduction/basic-concepts.md:145 -#: 03c3048f38ae4938a484cf02001877b3 +#: 037cd0e5ceda482eaeaca03d51745aee msgid "Some CWL runners may provide requirements that are not in the specification. For example, GPU requirements are supported in `cwltool` through the `cwltool:CUDARequirement` requirement, but it is not part of the {{ cwl_version }} specification and may not be supported by other CWL runners." msgstr "" #: ../../src/introduction/basic-concepts.md:151 -#: f9715b5ec65c405c849bb030c1927060 +#: e4643938445b48cc80eb8973ceeb126e msgid "Hints are similar to requirements, but while requirements list features that are required, hints list optional features. Requirements are explained in detail in the [Requirements](../topics/requirements-and-hints.md) section." msgstr "" #: ../../src/introduction/basic-concepts.md:155 -#: 442662f50e9e4620970ce32b1b127969 +#: c4c3315c96714e81b364f8cc003b87e6 msgid "FAIR Workflows" msgstr "" #: ../../src/introduction/basic-concepts.md:157 -#: 2b34c786af3840e88f29d214e19dc837 +#: 3eb6a013a2a4478ca2ad134661f65c58 msgid "The FAIR principles have laid a foundation for sharing and publishing digital assets, and in particular, data. The FAIR principles emphasize machine accessibility and that all digital assets should be Findable, Accessible, Interoperable, and Reusable. Workflows encode the methods by which the scientific process is conducted and via which data are created. It is thus important that workflows support the creation of FAIR data and adhere to the FAIR principles. — [FAIR Computational Workflows](https://workflows.community/groups/fair/), Workflows Community Initiative." msgstr "" #: ../../src/introduction/basic-concepts.md:167 -#: dd6aadff8cf54ce78ea6b317afbaddb0 +#: 074af9633627470485e5225326d5f20a msgid "CWL has roots in \"make\" and many similar tools that determine order of execution, based on dependencies between tasks. However, unlike \"make\", CWL tasks are isolated, and you must be explicit about your inputs and outputs." msgstr "" #: ../../src/introduction/basic-concepts.md:171 -#: fe7f1f0b28434f8aaf0f6ac6589a83f0 +#: 847951c055b94a83b1e081594cef22ee msgid "The benefit of explicitness and isolation are flexibility, portability, and scalability; tools and workflows described with CWL can transparently leverage technologies such as Docker and be used with CWL implementations from different vendors." msgstr "" #: ../../src/introduction/basic-concepts.md:176 -#: d10cf45b3c7f49dc98bc0e5d1246f224 +#: 44bde1fae06b4678bcac4f3224601296 msgid "`cwltool` also uses the PROV-O standard ontology for data provenance." msgstr "" #: ../../src/introduction/basic-concepts.md:178 #: ../../src/introduction/prerequisites.md:196 #: ../../src/introduction/quick-start.md:94 -#: ebf339ed376a4d3b89b15b4d5afe593b -#: 332b6e8b831e4bc5aed3745938230a57 -#: ce7fc63b808d4499b9bf9828c2dafe35 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 msgid "Learn More" msgstr "" #: ../../src/introduction/basic-concepts.md:180 -#: 8badec9987ba40609cf1f626172b2b2d +#: 9d5100c7d0a040aea1020bf633ad17de msgid "Semantic Versioning - " msgstr "" #: ../../src/introduction/basic-concepts.md:181 -#: c75a8b4bf0e24781bf6713cf6f013cd1 +#: 36eb4b3b966640af90faa55db3789cb6 msgid "The CWL Specification page in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:182 -#: 79b146ffe6d74e1b8f6019251dc4b7c2 +#: 2ccb956baa6b4376a04ad9fcc4654631 msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" msgstr "" #: ../../src/introduction/basic-concepts.md:183 -#: 07cca9a33d8f4b77ac6ad35ca8b95655 +#: 72889b830c514afe9a7cb1e64b5666a0 msgid "The list of Implementations in the CWL website: " msgstr "" #: ../../src/introduction/basic-concepts.md:184 -#: 31db11c8ddf2423192a8b2063b3e91c2 +#: e29bd7f973544600be589c3b3f84cf63 msgid "PROV-O: The PROV Ontology - " msgstr "" #: ../../src/introduction/basic-concepts.md:185 -#: d81dd96143ea444aa78ff45cfa0584b3 +#: c377a7f5dbe645cebbb6c7eccf831a0b msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." msgstr "" #: ../../src/introduction/index.md:1 -#: c54984605872472190ae7771809a20db +#: 1769a0cbf4de4d77879c1f202cd11af9 msgid "Introduction" msgstr "" #: ../../src/introduction/index.md:3 -#: 01a237b8ec2f46c9acd31d142591ce75 +#: 950370f0a36048b38e1bde9b78f80816 msgid "This section will guide you through a short introduction to CWL, the prerequisites for following this user guide, and some basic concepts that are useful to know before reading the rest of the user guide." msgstr "" #: ../../src/introduction/prerequisites.md:1 -#: 3fb9888b666945eab1e3ff109646c574 +#: f01faaf1b253407cbbc2f353c24774f3 msgid "Prerequisites" msgstr "" #: ../../src/introduction/prerequisites.md:6 -#: 5fb0486762354f93853fff209f835c08 +#: 353b14f06ee845d0a06a829643e31534 msgid "The software and configurations listed in this section are prerequisites for following this user guide. The CWL standards are implemented by many different workflow runners and platforms. This list of requirements focuses on the CWL reference runner, `cwltool`. You can use another CWL-compatible runner or workflow system, but the results and interface may look different (though the exact workflow outputs should be identical)." msgstr "" #: ../../src/introduction/prerequisites.md:12 -#: 5f1e7a608e0b455196d191c845a5c98e +#: b5a0607096814c0aa577f977c3b57c54 msgid "CWL Implementations" msgstr "" #: ../../src/introduction/prerequisites.md:14 -#: 7ba4b5c51be24f5392949d06ee42e018 +#: ff2bb4c6504b456bac7ca9c514414dbf msgid "There are many implementations of the CWL standards. Some are complete CWL runners, while others could be plug-ins or extensions to workflow engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." msgstr "" #: ../../src/introduction/prerequisites.md:19 -#: e2d3e6dd13b14d819a504c35da6fe8e7 +#: cbbcce4c2a96471b8b0ae3593ad59de4 msgid "Operating System" msgstr "" #: ../../src/introduction/prerequisites.md:21 -#: 91251d1f0efb4d4cb083b4517ff3107a +#: 5089fdba8aed4113983fa86e698df98b msgid "We recommend using an up-to-date operating system. You can choose any of the following options for your operating system:" msgstr "" #: ../../src/introduction/prerequisites.md:24 -#: 6ad263e267514c5fb05794d3d76d418d +#: dbaa4bae22fe4d05b18d7351967ddbc3 msgid "Linux" msgstr "" #: ../../src/introduction/prerequisites.md:25 -#: 8a3bfd72dccf4a8c874a96aebcbe5cb7 +#: c05187af85be41b782678b79627f8fbf msgid "macOS" msgstr "" #: ../../src/introduction/prerequisites.md:26 -#: 5195706d9c6c4573aff135fd539759a2 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 msgid "Windows" msgstr "" #: ../../src/introduction/prerequisites.md:29 -#: 9c4506915e4c40599527bc1d2b18645b +#: 3b5fdc4c2ebd45dcb3703e59d2b3ef25 msgid "If you are using Windows, you will have to install the [Windows Subsystem for Linux 2](https://learn.microsoft.com/en-us/windows/wsl/install) (WSL2). Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool/blob/main/README.rst#ms-windows-users) for details on installing WSL2. Your operating system also needs internet access and a recent version of Python (3.6+)." msgstr "" #: ../../src/introduction/prerequisites.md:35 -#: 37d9eb784ec1425786158f98e3f63890 +#: 56d78c95daa54135b6aa9b2bfdc34d01 msgid "CWL Runner" msgstr "" #: ../../src/introduction/prerequisites.md:41 -#: 572f493a985141a1b92dafbdba92790d +#: 0f2704bf1f7148be95e999e312899f11 msgid "The first thing you will need for running CWL workflows is a CWL runner. `cwltool` is a Python Open Source project maintained by the CWL community. It is also the CWL reference runner, which means it must support everything in the current CWL specification, {{ cwl_version }}." msgstr "" #: ../../src/introduction/prerequisites.md:46 -#: 9606d3c4849f4b17b2e55a298210f055 +#: 86264c9e56104ecea9146407c379aae2 msgid "`cwltool` can be installed with `pip`. We recommend using a virtual environment like `venv` or `conda`. The following commands will create and activate a Python virtual environment using the `venv` module, and install `cwltool` in that environment:" msgstr "" #: ../../src/introduction/prerequisites.md:51 -#: 754fc59967d94ffa935284676d55ffed +#: 0a0f0e5151ab4c498b4f8a12c016f28d msgid "Installing `cwltool` with `pip` and `venv`." msgstr "" #: ../../src/introduction/prerequisites.md:62 -#: 2905c6362d4146e8b35bc74744841972 +#: f7aaafeee230400da056464c853582c2 msgid "Visit the `cwltool` [documentation](https://github.com/common-workflow-language/cwltool#install) for other ways to install `cwltool` with `apt` and `conda`." msgstr "" #: ../../src/introduction/prerequisites.md:65 -#: 091278ece252483a9838fb771de3e04e +#: 5eced7e4cd084e8a806b1d3b12d0c000 msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:67 -#: 0928a5c668c3414a945bc9eda147892c +#: 040c019b6e844eda8c8c2b210852516b msgid "`true.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:73 -#: 56f3c481762848298214a88e559fc0f9 +#: 6391e08e0bde49f4b21286d8fdb97433 msgid "The `cwltool` command has an option to validate CWL tool and workflow descriptions. This option will parse the CWL document, look for syntax errors, and verify that the workflow descriptions are compliant with the CWL standards. However, these actions will be performed without running the document. To validate CWL workflows (or even a standalone command line tool description like the above) pass the `--validate` option to the `cwltool` command:" msgstr "" #: ../../src/introduction/prerequisites.md:79 -#: 710c266ab4a5477b84d6ea987420fa20 +#: cdef47fca304479c9a9df75afc0afb35 msgid "Validating `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:84 -#: cc353db5da2546bb88a77ce1a202ff9d +#: d41c4bc740aa474ea09a7cbd267c8840 msgid "You can run the CWL tool description by omitting the `--validate` option:" msgstr "" #: ../../src/introduction/prerequisites.md:86 -#: b62df08ec96f4cdb887600079856dd76 +#: 24d7be55d3994f0b82c38da47918e0c9 msgid "Running `true.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/prerequisites.md:91 -#: 97e02557293440d1a58ba659dad21113 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 msgid "Cwl-runner Python Module" msgstr "" #: ../../src/introduction/prerequisites.md:93 -#: 0935c3ff01634c75b5c91546dc36c7b9 +#: 096d0a50f69e48bd9915238d1b4264c1 msgid "`cwl-runner` is an implementation-agnostic alias for any CWL compliant runner. This simply means that the `cwl-runner` alias command can be invoked independently, and is not reliant on a particular CWL runner program name. Users can invoke `cwl-runner` instead of invoking a CWL runner like `cwltool` directly. The `cwl-runner` is installed by a system administrator or user to point to the preferred CWL implementation. This is convenient for environments with multiple CWL runners." msgstr "" #: ../../src/introduction/prerequisites.md:101 -#: cfb37fd605164a8d9cc75bf892ce97c0 +#: f9df974a8e2645a6918e67466bd1fdc2 msgid "The CWL community publishes a Python package with the name `cwlref-runner` that installs an alias for `cwltool` under the name `cwl-runner`" msgstr "" #: ../../src/introduction/prerequisites.md:104 -#: 5f06a7a6aae343d989a5b30979c600f6 +#: 71ebe91d4bda473abe87578929433212 msgid "Installing `cwl-runner` alias for cwltool with `pip`." msgstr "" #: ../../src/introduction/prerequisites.md:111 -#: 5f956260f3874b6dbeaf3ad7ecc09c9a +#: 746c6fc9c29d466494458a08d4c96672 msgid "Now you can validate and run your workflow with the `cwl-runner` executable, which will invoke `cwltool`. You should have the same results and output as in the previous section." msgstr "" #: ../../src/introduction/prerequisites.md:115 -#: d35e4effec554a638d6c3047ef3fd05f +#: b9cc5a843a0f49daad56e9303657bdd5 msgid "Validating `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:120 -#: 15a1f944a0d642729d3736ed1c907074 +#: 34ab40437ab646488ba3ee86cd7fe071 msgid "Running `true.cwl` with `cwl-runner`." msgstr "" #: ../../src/introduction/prerequisites.md:125 -#: fa34c808bb494ddfa3f3926bc42e650c +#: 705807fae182425dbf4244dbf2be1226 msgid "Another way to execute `cwl-runner` is by invoking the file directly. For that, the first thing you need to do is copy `true.cwl` workflow into a new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" msgstr "" #: ../../src/introduction/prerequisites.md:129 -#: 0c15f62eb7534e809f625f3fa213e92d +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a msgid "`true_shebang.cwl`" msgstr "" #: ../../src/introduction/prerequisites.md:135 -#: d67719a6f0ce4ba1bb6152a10507b729 +#: 164c438baab54ec19bbb4584a10dd411 msgid "Now you can make the file `true_shebang.cwl` executable with `chmod u+x`." msgstr "" #: ../../src/introduction/prerequisites.md:137 -#: 1c96e75281844bfab0578bab2e816854 +#: bf8be77af6154326b28442c5d2e2b852 msgid "Making `true.cwl` executable." msgstr "" #: ../../src/introduction/prerequisites.md:144 -#: bece1fc3c3f842b0b30d8f1b7fbfc200 +#: 695184d1b45a42f393e2da99c3721773 msgid "And finally, you can execute it directly in the command-line. On execution, the program specified in the shebang (`cwl-runner`) will be used to execute the rest of the file." msgstr "" #: ../../src/introduction/prerequisites.md:148 -#: a7caa36b0f83448b91ef2e76e30abc51 +#: 7c4f45b3e7b549e186126693aa4a3d4f msgid "Running `true_shebang.cwl` with a shebang." msgstr "" #: ../../src/introduction/prerequisites.md:154 -#: 39321e93e9994fcca20b425aa45c2894 +#: 3ba23b4ea01c46848e4e43bbeff5f5a1 msgid "The *shebang* is the two-character sequence `#!` at the beginning of a script. When the script is executable, the operating system will execute the script using the executable specified after the shebang. It is considered a good practice to use `/usr/bin/env ` rather than using a hard-coded location, since `/usr/bin/env ` looks for the `` program in the system `PATH`," msgstr "" #: ../../src/introduction/prerequisites.md:161 -#: 601cf500d76c4e0287af4429a46b36d2 +#: eec6c07455384630809ff1c532bfe7d4 msgid "Text Editor" msgstr "" #: ../../src/introduction/prerequisites.md:163 -#: b286d5359e184ef58054c72df4014629 +#: f6b39b12bd5c495cb53e2795bf9200ed msgid "You can use any text editor with CWL, but for syntax highlighting we recommend an editor with YAML support. Popular editors are Visual Studio Code, Sublime, WebStorm, vim/neovim, and Emacs." msgstr "" #: ../../src/introduction/prerequisites.md:167 -#: e14423edd829401faed0950772123240 +#: 2fdb62a13f9447bc89183426260ce781 msgid "There are extensions for Visual Studio Code and WebStorm that provide integration with CWL, and features such as customized syntax highlighting and better auto-complete:" msgstr "" #: ../../src/introduction/prerequisites.md:171 -#: 889c44360bd54a0e85e7f0e61aa6593c +#: 1f07135156254f74a6b043bf33d00cc3 msgid "Visual Studio Code with the Benten (CWL) plugin - " msgstr "" #: ../../src/introduction/prerequisites.md:172 -#: 7b9bff73624947ac90a99c7880e2e911 +#: de344f356b1c466d9131cdbd4d7353a3 msgid "cwl-plugin for IntelliJ - " msgstr "" #: ../../src/introduction/prerequisites.md:174 -#: c5ff687c86ef4ccaae25d8bcfbd5f873 +#: 3f9324ede11441f58d93875867034cf0 msgid "The CWL community also maintains a list of editors and viewers: " msgstr "" #: ../../src/introduction/prerequisites.md:177 -#: 0a610a9632064deb824afd0719429d3a +#: 6ce8b81560e341c580d316d69202b268 msgid "Docker" msgstr "" #: ../../src/introduction/prerequisites.md:181 -#: ec0c47438a5242cb99dffa7a4997e95a +#: 40cfd559d6a848d1aae354d3bdaa8e9c msgid "`cwltool` uses Docker to run tools, workflows, and workflow steps that specify a software container. Follow the instructions in the Docker documentation to install it for your operating system: ." msgstr "" #: ../../src/introduction/prerequisites.md:185 -#: aae94ac2114641f186eac0f4117223eb +#: 8a9a50b0ebe847ce90593881ffe0d69c msgid "You do not need to know how to write and build Docker containers. In the rest of the user guide, we will use existing Docker images for running examples, and to clarify the differences between the execution models with and without containers." msgstr "" #: ../../src/introduction/prerequisites.md:191 -#: 209e072724ed4d27b37e9bff6d55d811 +#: 923cf9dd6d6c417aabe42f9fa62ffa35 msgid "`cwltool` supports running containers with Docker, Podman, udocker, and Singularity. You can also use alternative container registries for pulling images." msgstr "" #: ../../src/introduction/prerequisites.md:198 -#: 3bf47876e3694e6cadb05123326459cb +#: 9390b03889de44638141d705e0ef8322 msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." msgstr "" #: ../../src/introduction/prerequisites.md:199 -#: 459a65b8e67c4a9aaa03138c1abe94ad +#: 12042e411482458f8c35a2491f9433e0 msgid "The Python `venv` module: " msgstr "" #: ../../src/introduction/quick-start.md:1 -#: 898eb29ac7714c69840b795633953a05 +#: cdd4196f9aa34beba115901ec97913b6 msgid "Quick Start" msgstr "" #: ../../src/introduction/quick-start.md:3 -#: 2a658bd2d8ce4533ab7e056fc3a3ffcf +#: c43d9675ed134b78b02acb5a102a764a msgid "This section will show you a brief overview of what CWL is, and where you can learn more about it. No previous knowledge of CWL is required, but you must be comfortable following instructions for the command-line." msgstr "" #: ../../src/introduction/quick-start.md:7 -#: 32dd2e28cf0f40b6930750f0162355eb +#: 280936bb2a22469799b2c9e9ba22adee msgid "“Hello World”" msgstr "" #: ../../src/introduction/quick-start.md:12 -#: 471c47d311074ecfac071b6d52d9cfb6 +#: cb203354977d42a58112d09357f62565 msgid "CWL documents are written in [YAML](../topics/index.md) (and/or JSON). The example below shows a simple CWL “Hello World” workflow annotated with comments. Note that comments start with `#`:" msgstr "" #: ../../src/introduction/quick-start.md:16 -#: 5078140028ea4d04973cb9cd20f0607e +#: 9e51962a7e5c47248f3e20703ae101eb msgid "`hello_world.cwl`" msgstr "" #: ../../src/introduction/quick-start.md:22 -#: ab127d4ba0a44526ab129587a8160923 +#: 7e475e3f3c4a4404bb0236124c0f7ce7 msgid "The example above is just a wrapper for the `echo` command-line tool. Running the workflow above with the default input values will produce the same result as the command-line `echo \"Hello World\"`." msgstr "" #: ../../src/introduction/quick-start.md:27 -#: d5cc6b4295a74f3586f022b0227759b3 +#: 82613ca4e32b4ccab1b7735f5ba2d5a1 msgid "In CWL, there is a distinction between a command-line tool and a workflow. But for the sake of simplicity, we are using the term “workflow” here. You will learn more about this in the [basic concepts](basic-concepts.md) section." msgstr "" #: ../../src/introduction/quick-start.md:32 -#: 585a4fe583ce44e180a062742b3b0849 +#: 498a43362a4749f3b8b433709d34a1d5 msgid "Installing a CWL Runner" msgstr "" #: ../../src/introduction/quick-start.md:34 -#: 0d81b0c9ea58420789d1d71cca32ce88 +#: f3e56aedd56b4b93bdc3894273e8c144 msgid "`cwltool` is an implementation of the CWL specification. It is also the CWL *Reference Runner* for the specification, and it is compliant with the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" msgstr "" #: ../../src/introduction/quick-start.md:39 -#: ea4ab0782d8049d8b1b89cea4ae60048 +#: 81481f5b82e4488398f87f0a169bd359 msgid "Installing `cwltool` with `pip`." msgstr "" #: ../../src/introduction/quick-start.md:47 -#: f6f3b7453a254f828bd4c9e9fef92bed +#: a81342e756d24c40acc15835d0a768f2 msgid "If installing the cwltool using the pip command doesn't work for you, the [prerequisites](prerequisites.md) section contains other ways to install `cwltool` and a more detailed list of software and libraries used for following the rest of this user guide." msgstr "" #: ../../src/introduction/quick-start.md:51 -#: 3bf9050175d4444ebbbabe219412574f +#: c12cf89f8b9a421ebd05330326e219b3 msgid "Running \"Hello World\"" msgstr "" #: ../../src/introduction/quick-start.md:53 -#: e03f72a14dcf4bf38ce8232598ca761d +#: 9b68bcb1a41849dc9601ab47c5bbb0fe msgid "The usage of the `cwltool` command-line executable is basically `cwltool [OPTIONS] [INPUTS_OBJECT]`. You can run the `hello_world.cwl` workflow without specifying any option:" msgstr "" #: ../../src/introduction/quick-start.md:57 -#: 3dcfb2facd324dccb3084c02487625dc +#: ce04027dfcfe4b7b91ea3c2136b18b23 msgid "Running `hello_world.cwl` with `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:62 -#: b8531da183964b02bca19f818ec076d4 +#: 0d8a788402914ebd8f09a5ca80650011 msgid "Or you can override the default value of the input parameter `message`, similar to how you would change the argument of the `echo` base command:" msgstr "" #: ../../src/introduction/quick-start.md:65 -#: 7ba1ddebeb2843179fe99fc410b193c6 +#: 6d0b679efab24813a7a3b709ade940d1 msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." msgstr "" #: ../../src/introduction/quick-start.md:70 -#: a6dc303e9d284b60bf1102212505ca27 +#: 2ea056ab04b6419a9faf350de22a17f2 msgid "Another way of passing values to your workflow input parameters is via an *Inputs Object*. This is a file containing the input fields with their corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" msgstr "" #: ../../src/introduction/quick-start.md:74 -#: 59ac7830ae3e4d7cb1bf503e8c90fe30 +#: 1a44a545434b448aa956005deeed90a8 msgid "`hello_world-job.json`" msgstr "" #: ../../src/introduction/quick-start.md:80 -#: 6d1d6f42ada2418ba0a1de1371825b9f +#: e76bfcc0c9f84bcdb3f6d5277869a88c msgid "You can use this Inputs Object file now to execute the “Hello World” workflow:" msgstr "" #: ../../src/introduction/quick-start.md:82 -#: 1cd924fe8ace4a82ad8701f37b5e7d84 +#: d4cdbe870a6f4a68b542ca719d989062 msgid "Passing an Inputs Object file to `cwltool`." msgstr "" #: ../../src/introduction/quick-start.md:88 -#: aa297c52cd964291a47bb91c0135156b +#: b6d59e4b9c854abab1b3f7a0fa26f504 msgid "We used a similar file name for the workflow and for the Inputs Object files. The *-job.json* suffix is very common in Inputs Object files, but it is not a requirement. You can choose any name for your workflows and Inputs Object files." msgstr "" #: ../../src/introduction/quick-start.md:96 -#: 28b02c90397745bfbacc03c3b1034939 +#: 5535b98e8b1342f09f003ec6db2b44b1 msgid "Continue reading the next sections of this User Guide!" msgstr "" #: ../../src/introduction/quick-start.md:97 -#: ef2a4f39f01049b891868b84d968c0dd +#: 77e43c7117fd4c52b140f0dd52cc3963 msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." msgstr "" #: ../../src/introduction/quick-start.md:98 -#: 89e3fa8dceda4f0cb1cfdfd1f17fe4df +#: 7282abfa7155497ca47c30f9abfb6474 msgid "The [`common-workflow-language` organization](https://github.com/common-workflow-language) at GitHub." msgstr "" #: ../../src/introduction/quick-start.md:99 -#: 7cd178223ba94d1ab3ee8cc5f13a8dcf +#: 176d8d47830f4031bb95dc231ebf1303 msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." msgstr "" #: ../../src/introduction/quick-start.md:100 -#: 46f6f8d050ce4f8c897056167d9707a7 +#: 82a7ca3703bc4f0daa18942a1ac8943b msgid "[YAML.org](http://yaml.org/) and [YAML at Wikipedia](https://en.wikipedia.org/wiki/YAML)." msgstr "" #: ../../src/introduction/quick-start.md:101 -#: 5ee00ee409b746dc951ca1d4c360e624 +#: d039a9d6461c44628d4660c00d9ce6ff msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." msgstr "" #: ../../src/introduction/quick-start.md:102 -#: d4af972281174b8999eab55ee0ab1a0e +#: fbc3383d9e1c4eaca7931c3cc4f1752b msgid "[Workflow management system at Wikipedia](https://en.wikipedia.org/wiki/Workflow_management_system)." msgstr "" #: ../../src/setup.md:9 -#: 80401cfffae042ab9ec4b3754af04b25 +#: 1330bd38c4b5495f890b98c669f81a9d msgid "This page is out-of-date and was kept here to preserve the links of the old User Guide. The information on this page has been migrated to the [FAQ](/faq.md) section of the new user guide." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:1 -#: 32f86f911ebe4a4c94975f81742333f3 +#: 9c87c76c690948ac8e18088a0fffe679 msgid "Additional Arguments and Parameters" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:3 -#: d5f1ad2b95ad46d48f8f2ca5e357bb5d +#: ad00d94d4fb64bbdac356e64dd3803b9 msgid "Sometimes tools require additional command line options that don't correspond exactly to input parameters." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:6 -#: c53ceee943ad4acea779e072b9137889 +#: d8110ed19da94ad8a9f56e7006c4a2cf msgid "In this example, we will wrap the Java compiler to compile a java source file to a class file. By default, \"javac\" will create the class files in the same directory as the source file. However, CWL input files (and the directories in which they appear) may be read-only, so we need to instruct \"javac\" to write the class file to the designated output directory instead." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:13 -#: 7dfe9dffbf5744299bf232599644c7f6 +#: a74935dc31664e979ca8f90a6a4ba53c msgid "`arguments.cwl`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:19 #: ../../src/topics/staging-input-files.md:15 -#: 00709fa451134ee09a0d808e101f28ed -#: 991172e201ec4796992a349dee44f090 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 msgid "`arguments-job.yml`" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:24 -#: 1f3c23a4769043ca985b8ddfed19391d +#: 6359191b4f684d5aa3602e4aaf394883 msgid "Next, create a sample Java file to use with the command-line tool." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:30 -#: f81b43c7cb194a1cad8672129223c833 +#: 9643449da1da46d7861866dce490cbcb msgid "And now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:36 -#: a20073a8f5374eb1bc8531ff33e622b6 +#: 713666580a0a4466b4ba6e3eb2b54f0a msgid "Here we use the `arguments` field to add an additional argument to the command line that isn't tied to a specific input parameter." msgstr "" #: ../../src/topics/additional-arguments-and-parameters.md:43 -#: d08869beca3a4774baf1097b63e79474 +#: d50574c8b9694f83aa376d39b9a6fcd6 msgid "This example references a runtime parameter. Runtime parameters provide information about the hardware or software environment when the tool is actually executed. The `$(runtime.outdir)` parameter is the path to the designated output directory. Other parameters include `$(runtime.tmpdir)`, `$(runtime.ram)`, `$(runtime.cores)`, `$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime Environment][runtime] section of the CWL specification for details." msgstr "" #: ../../src/topics/best-practices.md:1 -#: 109b773789024b2b9c063a6169c6169f +#: 612c4a66c36a43d4ac5d74c1757d6845 msgid "Best Practices" msgstr "" #: ../../src/topics/best-practices.md:3 -#: 959fa04f88e54d42b9b774cc95d85ee0 +#: 939cd9e9eaff4e3ab74fe707a5d4eb21 msgid "The following are a set of recommended good practices to keep in mind when writing a Common Workflow Language description for a tool or workflow. These guidelines are presented for consideration on a scale of usefulness: although more is better, not all are required." msgstr "" #: ../../src/topics/best-practices.md:8 -#: 64674980c3f24c45bbfbf3f957dda55e +#: 4bcb84707acb40a0bfe2ea0853cb10b7 msgid "No `type: string` parameters for names of input or reference files/directories; use `type: File` or `type: Directory` as appropriate." msgstr "" #: ../../src/topics/best-practices.md:11 -#: 90f2e4265919446a902e17627f4420e2 +#: 4dee8504a8e5496081dadc386ab45540 msgid "A CWL document (in conjunction with any external components like `Dockerfile`s) is software code. Workflow developers should be aware that the usual rules of software licensing apply to this document. For example, if the workflow is shared publicly, licensing terms must be clear so that a future user understands under what conditions they can run the workflow, modify it and/or combine it with other workflows. For this reason, please consider including a license field in the document. The authors of this guide urge you to choose a pre-existing license rather than trying to write your own (see the link below to learn more about choosing a license), and our recommended practice is to choose a license that allows for re-use by anyone, e.g. [Apache 2.0][apache-license]." msgstr "" #: ../../src/topics/best-practices.md:20 -#: 6b5f91a749fd44b5acfd6071c9913342 +#: 674c238b25e240eda05e22e399f2f78f msgid "If possible, the license should be specified with its corresponding [SPDX identifier][spdx]. Construct the metadata field for the license by providing a URL of the form `https://spdx.org/licenses/[SPDX-ID]` where `SPDX-ID` is taken from the list of identifiers linked above. See the example snippet below for guidance. For non-standard licenses without an SPDX identifier, provide a URL to the license." msgstr "" #: ../../src/topics/best-practices.md:26 -#: 5fe2962837b14f0e9989063be4a506c3 +#: b651f80f47b4442fbf29454a233697fc msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" msgstr "" #: ../../src/topics/best-practices.md:28 -#: 4e1bdea962ed4618884cb9d1d59d7509 +#: 263a127a77cf4c41af76854f22f1f260 msgid "_Example of metadata field for license with SPDX identifier:_" msgstr "" #: ../../src/topics/best-practices.md:37 -#: 37eff4ca02e843259f6ffa38e4a87a04 +#: 3a87a0fb2a364e3da5aaa4017e430b19 msgid "For more examples of providing metadata within CWL descriptions, see [the Metadata and Authorship section of this User Guide](../topics/metadata-and-authorship.md)." msgstr "" #: ../../src/topics/best-practices.md:40 -#: ae47231c203d40a98c10045038ea9b65 +#: ecf2b9c0b1664afe9c4e180610610021 msgid "Include [attribution information][license-example] for the author(s) of the CWL tool or workflow description. Use unambiguous identifiers like [ORCID][orcid]." msgstr "" #: ../../src/topics/best-practices.md:44 -#: 018a6d5dbf1044559b365c7b9017eb3f +#: e24cb13d98014e558b6a6946758359e0 msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:47 -#: e073d8f990c44b09a73d642cfe49bebd +#: f2b14a92374e449d9fb1e8c86ae0dd61 msgid "Include [SciCrunch][scicrunch] identifiers for dependencies in `https://identifiers.org/rrid/RRID:SCR_NNNNNN` format." msgstr "" #: ../../src/topics/best-practices.md:50 -#: e04fae88d9b64493ac69eaee24585098 +#: 928e3df7ca3e479ca6474a8e72cf36eb msgid "All `input` and `output` identifiers should reflect their conceptual identity. Use informative names like `unaligned_sequences`, `reference_genome`, `phylogeny`, or `aligned_sequences` instead of `foo_input`, `foo_file`, `result`, `input`, `output`, and so forth." msgstr "" #: ../../src/topics/best-practices.md:55 -#: b26b9c9b1c4346a297a31c9721f0172a +#: d355f035676446c88b028f327aeb4829 msgid "In tool descriptions, include a list of version(s) of the tool that are known to work with this description under `SoftwareRequirement`." msgstr "" #: ../../src/topics/best-practices.md:58 -#: b50500c3c3f54b16a535a16175a44653 +#: 339b852df24242189d6efcd2898a3396 msgid "`format` should be specified for all input and output `File`s. Bioinformatics tools should use format identifiers from [EDAM][edam-example]. See also `iana:text/plain`, `iana:text/tab-separated-values` with `$namespaces: { iana: \"https://www.iana.org/assignments/media-types/\" }`. [Full IANA media type list][iana-types] (also known as MIME types). For non-bioinformatics tools, use or build an appropriate ontology/controlled vocabulary in the same way. Please edit this page to let us know about it." msgstr "" #: ../../src/topics/best-practices.md:66 -#: 623f3a804199449bb85e23e00c8bb507 +#: 3ef57e6862f240bebcf193a52397af0a msgid "Mark all input and output `File`s that are read from or written to in a streaming compatible way (only once, no random-access), as `streamable: true`." msgstr "" #: ../../src/topics/best-practices.md:69 -#: effea0b1356447c0899ca0746667ea31 +#: f1a7c4f896a04a80b0c5f6a1db61ff8c msgid "Each `CommandLineTool` description should focus on a single operation only, even if the (sub)command is capable of more. Don't overcomplicate your tool descriptions with options that you don't need or use." msgstr "" #: ../../src/topics/best-practices.md:73 -#: 00e8ef87864c4ca2b2c1c0548b02b38d +#: 1ac4c3d8c3e44bd1af3fc5df70051926 msgid "Custom types should be defined with one external YAML per type definition for re-use." msgstr "" #: ../../src/topics/best-practices.md:76 -#: 6e6f48d70b894a6c959ca30fe6bad772 +#: c858f64e66f048a5b0032ef3e4d83694 msgid "Include a top-level short `label` summarising the tool/workflow." msgstr "" #: ../../src/topics/best-practices.md:78 -#: 02fe08760a4a4ab49e96f4e51316a81d +#: fae385da16aa443da996fa23ac03d6ae msgid "If useful, include a top-level `doc` as well. This should provide a longer, more detailed description than was provided in the top-level `label` (see above)." msgstr "" #: ../../src/topics/best-practices.md:82 -#: 172ed7915a654964ba63f860b2d65330 +#: 92430be71ecc40e18bbbb80d5576c613 msgid "Use `type: enum` instead of `type: string` for elements with a fixed list of valid values." msgstr "" #: ../../src/topics/best-practices.md:85 -#: 4d0a2871a7484e21b3c39c4dbaaa63fc +#: 387d83db81024f65aa9a890c2d07874a msgid "Evaluate all use of JavaScript for possible elimination or replacement. One common example: manipulating `File` names and paths? Consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc., could be used instead." msgstr "" #: ../../src/topics/best-practices.md:90 -#: 1eea9f1e284447718141f5417b6bb433 +#: d8e2280a75a74916a1630afaa2fe2ae3 msgid "Give the tool description to a colleague (preferably at a different institution) to test and provide feedback." msgstr "" #: ../../src/topics/best-practices.md:93 -#: 509411d353fe4314b087b81b09ea960b +#: f1c1340f9745458980e0fbd641738687 msgid "Complex workflows with individual components which can be abstracted should utilise the [`SubworkflowFeatureRequirement`][subworkflow] to make their workflow modular and allow sections of them to be easily reused." msgstr "" #: ../../src/topics/best-practices.md:97 -#: a54bc80bf08243bba67d98dd682ee134 +#: 5424e5472c3d466fa2a3d2022c6cb475 msgid "Software containers should be made to be conformant to the [\"Recommendations for the packaging and containerizing of bioinformatics software\"][containers] (also useful to other disciplines)." msgstr "" #: ../../src/topics/command-line-tool.md:1 -#: 69ecdaea24ef42eebef9d86e5d716b11 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 msgid "Command Line Tool" msgstr "" #: ../../src/topics/command-line-tool.md:3 -#: 3cc5847468d1478bb5589dee68147189 +#: 12f57b2ba76b492abe1816e06bfb1417 msgid "A command-line tool is a type of Process object that can be run by itself or as a Workflow step. It is a wrapper for a command like `ls`, `echo`, `tar`, etc. The command-line tool is defined in the `baseCommand` attribute of the command-line tool CWL document." msgstr "" #: ../../src/topics/command-line-tool.md:8 -#: 98c6bc409420485095ae65d6b0b9a3a0 +#: e1f657a46ce94a0d83671540e2cc2dab msgid "A CWL command-line tool must also have `inputs` and `outputs`. The following example contains a minimal example of a CWL command-line tool for the `echo` Linux command, using inputs and outputs." msgstr "" #: ../../src/topics/command-line-tool.md:19 -#: ebe23e5378514f888a9ec32a2adb1e98 +#: abb83f0097654a43bd78639d3dbb2bc8 msgid "CWL command-line tool." msgstr "" #: ../../src/topics/command-line-tool.md:50 -#: 387cfe85604f424f8d31c4a4c9c15edb +#: 3b1a9ae3412f4d6e96a39b9a16934232 msgid "`echo.cwl`" msgstr "" #: ../../src/topics/command-line-tool.md:57 -#: 7b1d65754e854693bb60289c97d3fb5d +#: a5eacdbc9aa142c890b177869da4143d msgid "The example above uses a simplified form to define inputs and outputs. You will learn more about in the [Inputs](../topics/inputs.md) and in the [Outputs](../topics/outputs.md) sections." msgstr "" #: ../../src/topics/command-line-tool.md:68 -#: f440cef729c8410281432307a4da8d55 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e msgid "Network Access" msgstr "" #: ../../src/topics/command-line-tool.md:69 -#: 4fbb8ceb1b59480583ac611142167049 +#: e3bdaceae8784ab0807b2cf356a98580 msgid "This indicates whether a process requires outgoing IPv4/IPv6 network access. If a command-line tool is written manually in CWL v1.1+, there is a need to specify when network access is required." msgstr "" #: ../../src/topics/command-line-tool.md:83 -#: b87869204838415bbf694214e3680593 +#: ed521ac365db4a6ba5a1051fbaa2932e msgid "CWL v1.0 command-line tools that are upgraded to v1.1 or v1.2 get Network Access automatically." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:1 -#: 12cf5f2264504c44a2173e858bb2c283 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b msgid "Creating Files at Runtime" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:3 -#: 7694f9cabfe04308bbddd2c88ae6d9b9 +#: 0cf51b6da6884065ae42032abc20eb0d msgid "Sometimes you need to create a file on the fly from input parameters, such as tools that expect to read their input configuration from a file rather than the command line parameters, or need a small wrapper shell script." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:7 -#: b557dc4f8ef549b98f59412a918643de +#: 2df3a3a9094d4b79b1d5dd99195f3bff msgid "To generate such files, we can use the `InitialWorkDirRequirement`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:9 -#: 3011eb003c084285b30cfa56a8da45b6 +#: d3f74c3b094a427fbec831afab657d50 msgid "`createfile.cwl`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:15 -#: 9f9c90a2bb4b4d3b8e99b63cb0e72f76 +#: cfffc518ba6e4ed1a80762ed6f7d25df msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:20 -#: ce78b2d147054da895beba66d0ecdab4 +#: 9454a330b9324744b89448f2694b1b03 msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` must be **escaped** with `\\`. For instance, `\\${PREFIX}` above is expanded to `${PREFIX}` in the generated file to be evaluated by the shell script instead of the CWL engine." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:27 -#: a973846ec5a946eeaff02c5b00997da9 +#: 7f8d99a30b644457a62ac1523d0c72aa msgid "To test the above CWL tool, use this job to provide the input value `message`:" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:29 #: ../../src/topics/environment-variables.md:13 #: ../../src/topics/outputs.md:77 -#: ccec7f73b9d948e79a6cdf32bc124092 -#: 9e8eb1542db640ff9e300649ce50dc9d -#: 294fd83a97a64249bac38f7482159372 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 msgid "`echo-job.yml`" msgstr "" #: ../../src/topics/creating-files-at-runtime.md:35 -#: 22948f19cb78485f8f86244686a35c09 +#: 10d1373bb14a4a3cacd3b92a2f83382d msgid "Before we run this, let us look at each step in a little more detail. The base command `baseCommand: [\"sh\", \"example.sh\"]` will execute the command `sh example.sh`. This will run the file we create in the shell." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 -#: 001d9579bfce438e865377fb9c2df776 +#: 70e257091bdb456e8957f90a8fa90e8c msgid "`InitialWorkDirRequirement` requires a `listing`. As the `listing` is a YAML array, we need a `-` on the first line of each element of the array, in this case we have just one element. `entryname:` can have any value, but it must match what was specified in the `baseCommand`. The final part is `entry:`, this is followed by `|-` which is YAML quoting syntax, and means that you are using a multiline string (without it, we would need to write the whole script on one line)." msgstr "" #: ../../src/topics/creating-files-at-runtime.md:51 -#: e62618db8995428bb3f260e03ac8f459 +#: 1741804e33aa43ce88b4320c11ae5973 msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." msgstr "" @@ -1291,193 +1291,193 @@ msgstr "" #: ../../src/topics/file-formats.md:52 #: ../../src/topics/staging-input-files.md:20 #: ../../src/topics/workflows.md:198 -#: 98e0548845fa447fb05a29c9fc2f17b5 -#: e9801b2142cd45368a73ef9b121c1d08 -#: 457756c4e9544f068af897113358cc89 -#: de5e8aad4e3046bf9bfc2ad8ccba17d0 -#: 6d5ae75431424ea788c3440606f22940 +#: b372f33c65bb4707b2a462a960bb1373 +#: 293fb1d428b849aebccad598a932992d +#: f924d65fed0c4cb5b0a019b084a8b535 +#: d6255506eebe44be94c5ce703c44a513 +#: 7bbd2d738fc54649aeb10f8d2bc38b6f msgid "Now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/custom-types.md:1 -#: ee2bca9bdbb74b60a706c3118d6a17ba +#: cb34fd4c8cb04053ada491a227651048 msgid "Custom Types" msgstr "" #: ../../src/topics/custom-types.md:3 -#: e63ae9694f40438d872d141ae824a42d +#: 67573252cc064b27ab13eebc468ac58a msgid "Sometimes you may want to write your own custom types for use and reuse in CWL descriptions. Use of such custom types can reduce redundancy between multiple descriptions that all use the same type, and also allow for additional customisation/configuration of a tool/analysis without the need to fiddle with the CWL description directly." msgstr "" #: ../../src/topics/custom-types.md:9 -#: 750fdd4c270e46a09f79e867358f7414 +#: 73e68b3af9cf41338d843c0c40e50cdc msgid "The example below is a CWL description of the [biom convert format][biom] tool for converting a standard biom table file to hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:12 -#: b3f688cc82444ef7a7a0aa63dac39cac +#: ef5f35acb97f4ddfad7b688712f53484 msgid "`custom-types.cwl`" msgstr "" #: ../../src/topics/custom-types.md:18 -#: 3638be18b4f64cf08053d512e590dda3 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c msgid "`custom-types.yml`" msgstr "" #: ../../src/topics/custom-types.md:24 -#: 7d5b9c21739c48f18c13614ca6967f6b +#: a999b1acda2641598086648c64aa3831 msgid "___Note:___ To follow the example below, you need to [download the example input file](https://github.com/common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via `wget`:" msgstr "" #: ../../src/topics/custom-types.md:30 -#: 8fea29993f944d8d8d3181afa29bd0a6 +#: f8c12a58cb0b46a488823c6ae95f25ea msgid "On line 29, in `inputs:table_type`, a list of allowable table options to be used in the table conversion are imported as a custom object:" msgstr "" #: ../../src/topics/custom-types.md:46 -#: 02d0b648d70f49d7892f690be06df585 +#: f25a63e0926d4932bbe64b2e4bdabf9e msgid "The reference to a custom type is a combination of the name of the file in which the object is defined (`biom-convert-table.yaml`) and the name of the object within that file (`table_type`) that defines the custom type. In this case the `symbols` array from the imported `biom-convert-table.yaml` file define the allowable table options. For example, in `custom-types.yml`, we pass `OTU table` as an `input` that tells the tool to create an OTU table in hdf5 format." msgstr "" #: ../../src/topics/custom-types.md:53 -#: 0743bef42b9a42328849c8c2f9da9eed +#: b0a4df0fd3ca42338cff4689235dcf4e msgid "The contents of the YAML file describing the custom type are given below:" msgstr "" #: ../../src/topics/custom-types.md:55 -#: 85c5d0cbbc6243a6823f5eeac0f85dd9 +#: fecfbb44456640d8ba05e519bf2ff564 msgid "`biom-convert-table.yaml`" msgstr "" #: ../../src/topics/custom-types.md:61 -#: be848f30769543eb9c0be55263e3f758 +#: d718630a296545f3a989c8c71e9ddc77 msgid "In order for the custom type to be used in the CWL description, it must be imported. Imports are described in `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" msgstr "" #: ../../src/topics/custom-types.md:76 -#: cbff44a64ba4432cb59a82f82c2f0103 +#: 9a97acd430064710bcdf76edbd9f711c msgid "Note also that the author of this CWL description has also included `ResourceRequirement`s, specifying the minimum amount of RAM and number of cores required for the tool to run successfully, as well as details of the version of the software that the description was written for and other useful metadata. These features are discussed further in other chapters of this user guide." msgstr "" #: ../../src/topics/environment-variables.md:1 -#: 617f1c0084cf42d9be4c7a8fa5a48432 +#: 59014808cbef4c02aaef03129d8a29b0 msgid "Environment Variables" msgstr "" #: ../../src/topics/environment-variables.md:3 -#: cee79afa3c6f43c29ef05e06b7843d35 +#: 3c821c9c46d841ec89b8a5b1018f3af8 msgid "Tools run in a restricted environment and do not inherit most environment variables from the parent process. You can set environment variables for the tool using `EnvVarRequirement`." msgstr "" #: ../../src/topics/environment-variables.md:7 -#: 225903b11efa417989df42de86ad2451 +#: bfdebb32440a4034beb42135e38884e8 msgid "`env.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:1 -#: 1a5f058290064c1cad05e63eb127fcbb +#: 777d4a52f7554eff84db2df6d4d0f729 msgid "Expression Tool" msgstr "" #: ../../src/topics/expression-tool.md:3 -#: 74ad8d69cf294ae880dbbe28e25b3545 +#: 48deb71f361a43e48a56ed483075bca8 msgid "An expression tool is a type of Process that can be run by itself or as a Workflow step. It executes a pure JavaScript expression. It is meant to be used as a way to isolate complex JavaScript expressions that need to operate on input data and produce some result as output." msgstr "" #: ../../src/topics/expression-tool.md:8 -#: 5293e8ee9b3b4f59947cfc164ef111c4 +#: 716b56506ca7470299899c5d820a9ea2 msgid "Similar to the command-line tool it requires `inputs` and `outputs`. But instead of `baseCommand`, it requires an `expression` attribute." msgstr "" #: ../../src/topics/expression-tool.md:17 -#: ffa1955c759942c68e7589429e5ea86b +#: b63e6f5a2e89431c8fc7d04f47fd69fe msgid "CWL expression tool." msgstr "" #: ../../src/topics/expression-tool.md:48 -#: 038bc0ba5f6a405a8255a7be76979baf +#: 39727e9058f24b62b8746a46d3f812c2 msgid "`uppercase.cwl`" msgstr "" #: ../../src/topics/expression-tool.md:67 -#: fae1c63de02e48c0969a98e4c49b2e06 +#: e3ecac0a8e604f2b98a2a12b0579990a msgid "We had to use an `InlineJavascriptRequirement` as our expression contains a JavaScript call in `.toUpperCase()`. This means to tools using the expression tool that JavaScript is a requirement." msgstr "" #: ../../src/topics/expressions.md:1 -#: 7093a94695524851a5463193f0701b78 +#: c8d648b765ec499a8e9c464590838492 msgid "Expressions" msgstr "" #: ../../src/topics/expressions.md:3 -#: dc8274ecb15948c29a31db89b12a58bd +#: 007a345b4bad49cf996c4301b8386473 msgid "If you need to manipulate input parameters, include the requirement `InlineJavascriptRequirement` and then anywhere a parameter reference is legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." msgstr "" #: ../../src/topics/expressions.md:9 -#: cec8eef8a5aa49778ecedd4195ab9f2c +#: 2edbd398eadb458b8eacd5fa5496f0a2 msgid "JavaScript expressions should only be used when absolutely necessary. When manipulating file names, extensions, paths etc, consider whether one of the [built in `File` properties][file-prop] like `basename`, `nameroot`, `nameext`, etc, could be used instead. See the [list of best practices](best-practices.md)." msgstr "" #: ../../src/topics/expressions.md:16 -#: df100967597043c78112bf43b520cfab +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 msgid "`expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:22 -#: 59ccf4daba39406581a6bc2d9bb1b7d2 +#: efb5fd14988c4e2a8f834ee5369d4102 msgid "As this tool does not require any `inputs` we can run it with an (almost) empty job file:" msgstr "" #: ../../src/topics/expressions.md:25 -#: 570cc75699dd4e0a987fc9aca9a01ee4 +#: e833649b951841c49397796f996d29f3 msgid "`empty.yml`" msgstr "" #: ../../src/topics/expressions.md:31 -#: 9e123723048546d495ed5110d7177708 +#: 276f688ba7cc471a842f085ca852b1d9 msgid "`empty.yml` contains a description of an empty JSON object. JSON objects descriptions are contained inside curly brackets `{}`, so an empty object is represented simply by a set of empty brackets." msgstr "" #: ../../src/topics/expressions.md:35 -#: 26543894f6e04270b89ab702451bcc89 +#: ebf399ea4d5f47b9be03e24f04c69f2d msgid "We can then run `expression.cwl`:" msgstr "" #: ../../src/topics/expressions.md:37 -#: f403c1d4e43a4aa0aef8488d2b5a6262 +#: 65e0cdd505b944caa40f65e612cdddfc msgid "Running `expression.cwl`" msgstr "" #: ../../src/topics/expressions.md:47 -#: 249dffb569a944c897ce5862e5f28fad +#: 8b70a1ad70514039b97164fa630c12e4 msgid "Note that requirements can be provided with the map syntax, as in the example above:" msgstr "" #: ../../src/topics/expressions.md:54 -#: 1641c96aca2f4923885fe8a509eb3a49 +#: 2f28ab412d2843ffa5f14acdc01fc732 msgid "Or as an array, with each entry (in this case, only `class: InlineJavascriptRequirement`) marked by a `-`. The same syntax is used to describe the additional command line arguments." msgstr "" #: ../../src/topics/expressions.md:62 -#: bc63405a0d964df2bd9493996abc48fe +#: d957f55a6377422c9834f85d45e35009 msgid "Where are JavaScript expressions allowed?" msgstr "" #: ../../src/topics/expressions.md:64 -#: 5c191d1420db4e26aca31c1b1e34cb75 +#: cbec9277b5004e50af2728cbda0df740 msgid "Just like [parameter references](parameter-references.md), you can use JavaScript Expressions only in certain fields. These are:" msgstr "" #: ../../src/topics/expressions.md:66 -#: d6a5c65e824a4bbc94578df9597d4716 +#: e259f55f8000479bbd8009e25cf0ca6c msgid "From [`CommandLineTool`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/expressions.md:67 #: ../../src/topics/parameter-references.md:64 -#: a7ff51fe564748229a88a0d3044dbc17 -#: c12625211cc542b68cb51365a63eef00 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 msgid "`arguments`" msgstr "" @@ -1487,38 +1487,38 @@ msgstr "" #: ../../src/topics/parameter-references.md:65 #: ../../src/topics/parameter-references.md:73 #: ../../src/topics/parameter-references.md:86 -#: 3a64ccbbf70447d1a813a725e528b6fe -#: 5fb932af34a54a0ea691260d43053eba -#: 2a2286a9c8494e3b88db35bf63230f33 -#: e7f1993580f0425098a719e83a64cc7f -#: 05c34a5a2e404a14b9d284a9d0c73bd3 -#: e5b0293e6fcd4e9b8d7be3fc9fc127d3 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 msgid "`valueFrom`" msgstr "" #: ../../src/topics/expressions.md:69 #: ../../src/topics/parameter-references.md:66 -#: 2fd5b42cafe34d3185888de041818dff -#: c158e9ee5fbf4e868b152a0a5880092f +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff msgid "`stdin`" msgstr "" #: ../../src/topics/expressions.md:70 #: ../../src/topics/parameter-references.md:67 -#: 92697d3179ec48898eaea9aba3c24dcd -#: 3f29e4a3087847e9af6f19166a8def9a +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 msgid "`stdout`" msgstr "" #: ../../src/topics/expressions.md:71 #: ../../src/topics/parameter-references.md:68 -#: d6722e3093884ad7b62696fbb2f48fdc -#: c0eaef93bc3743279549bcfb8b014ca3 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 msgid "`stderr`" msgstr "" #: ../../src/topics/expressions.md:72 -#: 37c493fdc2f0410a9748f8faf09ce5b5 +#: 8210b36347a749889450529ecdf4ff0e msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" @@ -1530,14 +1530,14 @@ msgstr "" #: ../../src/topics/parameter-references.md:75 #: ../../src/topics/parameter-references.md:82 #: ../../src/topics/parameter-references.md:90 -#: 9cfb6ca1255241aa9e5928ea981286e9 -#: 4ff7326e660f42d8b45c3353005554f8 -#: 04e3eefe4ec445cb90c2fa42344aaed5 -#: 07611b01b06a4afb808322a0dccccf30 -#: 6020618711d449a48618c11215453487 -#: c358a25b1f9543598b90d3df7c012b85 -#: c610220d06484d589313dc29faf8222c -#: 7b132c6e720f4256859757778f5c4fef +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 msgid "`format`" msgstr "" @@ -1549,1574 +1549,1574 @@ msgstr "" #: ../../src/topics/parameter-references.md:76 #: ../../src/topics/parameter-references.md:83 #: ../../src/topics/parameter-references.md:91 -#: e193aebe7124444c90be1f6cad81482a -#: 74652fdbeaf14d82b9c5053e322504da -#: 93d2b17bb236426286ffd51bbecda61d -#: a44c278bde5849aeac122c981294332c -#: 6dfc264200a9496f9d2458fc759993d8 -#: f71216a4b35e4157aece5ffa2602d8bf -#: 662b36e3505f4ac3bb5070bb6e055217 -#: ee3d416cc68c4f11a79849bb67395f1b +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae msgid "`secondaryFiles`" msgstr "" #: ../../src/topics/expressions.md:75 -#: a3c775a0f04b4541a9b712bfe2e4e69a +#: 23088850ad02459696f6bbd385109aac msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/expressions.md:77 -#: ef16c4a9a7ea415fa399297b63b9710c +#: f02257a822ad46ac93c5981531cc85d5 msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:80 -#: 2592e429c74c4ff5b8ba68a36f060c1a +#: 989a1c4aaa1143be9f53b90cd8b6d500 msgid "From [CommandOutputBinding](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/expressions.md:81 #: ../../src/topics/parameter-references.md:78 -#: 5cca4c2ad617400eb6efad4066b1839b -#: ba1fff3ebb274dfba845b3ee20ebd71f +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 msgid "`glob`" msgstr "" #: ../../src/topics/expressions.md:82 #: ../../src/topics/parameter-references.md:79 -#: 6914526c0a7c43a2a05438519508ee0f -#: 722d3bd7184841639b9f9a38914002da +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b msgid "`outputEval`" msgstr "" #: ../../src/topics/expressions.md:83 #: ../../src/topics/parameter-references.md:80 -#: 737b0f9392154241ae5b56c6caa823f5 -#: 7b46d408e7e7481b91a950b2d4010c9a +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c msgid "From `Workflow`" msgstr "" #: ../../src/topics/expressions.md:84 -#: f09e7371708b4c0685eef2a314791ccd +#: d289541e460147aa933f7878996f8649 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:87 #: ../../src/topics/parameter-references.md:84 -#: aa6ca1def2024c98b9d5542de1a81425 -#: e9fc5f7fa4474dfc95039b94167fe894 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c msgid "From `steps`" msgstr "" #: ../../src/topics/expressions.md:88 -#: 6c37a1ff939748bf83a86c07c3d017fe +#: 81b4d1f23a3642bfa9bb395b94260cd1 msgid "From [WorkflowStepInput](https://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/expressions.md:90 #: ../../src/topics/parameter-references.md:87 -#: 3a8126b0a0334df890b2be2c693ea5d5 -#: 61744122b7d7494890cbe6b2fb72b9f7 +#: e1cde4aa32c041238ed2596173c6d824 +#: 557694f82e314baa9ccafba14d6ff2c9 msgid "From [ExpressionTool](https://www.commonwl.org/v1.0/Workflow.html#ExpressionTool)" msgstr "" #: ../../src/topics/expressions.md:91 #: ../../src/topics/parameter-references.md:88 -#: 93cb9015dacc4b50a4ef177ce4ece2e7 -#: e0c7ccc8f8664cf794cbb7330355f3fe +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf msgid "`expression`" msgstr "" #: ../../src/topics/expressions.md:92 -#: 58a1773b1cf546d7890010fdebd47388 +#: f495da32f05a4a5ba9539be0a54c1a59 msgid "From [InputParameter](https://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](https://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/expressions.md:95 -#: 230f3227ed1144f7abe0f8c231bebbd5 +#: bdb4c68a175047ddbe141ca24960127f msgid "From [`ResourceRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/expressions.md:96 #: ../../src/topics/parameter-references.md:93 -#: c9534670f5f04769aa3749c3778eb705 -#: 5c77dc9f8afe4dd88933943030e836f2 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 msgid "`coresMin`" msgstr "" #: ../../src/topics/expressions.md:97 #: ../../src/topics/parameter-references.md:94 -#: 4ec8bbac5fb14371a6a4cd53d7cd6450 -#: 7b0887a8caed41b2acccf7021bb323d3 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 msgid "`coresMax`" msgstr "" #: ../../src/topics/expressions.md:98 #: ../../src/topics/parameter-references.md:95 -#: aceedfb558b246bc87eb3eaedea187fd -#: e5e8b8c75f0f43cbb6e160e5bf810c6e +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 msgid "`ramMin`" msgstr "" #: ../../src/topics/expressions.md:99 #: ../../src/topics/parameter-references.md:96 -#: fe3b9fb45e01490498c5a35c012b3de8 -#: 266dfb5fe6a842078baf66073cac9623 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 msgid "`ramMax`" msgstr "" #: ../../src/topics/expressions.md:100 #: ../../src/topics/parameter-references.md:97 -#: 85f424cbfc85460f9da310aee1ff0b82 -#: ddf82b12b12d416fb65f3ce3f51bbdf0 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 msgid "`tmpdirMin`" msgstr "" #: ../../src/topics/expressions.md:101 #: ../../src/topics/parameter-references.md:98 -#: 966e88656ae5402a975022ee60646283 -#: af14fda3cca645fbb2f3c5825fe0788e +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 msgid "`tmpdirMax`" msgstr "" #: ../../src/topics/expressions.md:102 #: ../../src/topics/parameter-references.md:99 -#: fec70bb106ad4d95a2d55ebdcf711afc -#: 09120baec1464afb8aed4edd773bf509 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 msgid "`outdirMin`" msgstr "" #: ../../src/topics/expressions.md:103 #: ../../src/topics/parameter-references.md:100 -#: c98db5b115ee4c4abb211481fe7214b0 -#: 2e128858cd06466680fc6bbfb577b818 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 msgid "`outdirMax`" msgstr "" #: ../../src/topics/expressions.md:104 -#: 1dc4148caef748428a7d13caff37b1b1 +#: 97b61352363f47cb890e8937c5613fa3 msgid "From [`InitialWorkDirRequirement`](https://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/expressions.md:105 #: ../../src/topics/parameter-references.md:102 -#: 8caf296626024598b4450311ade09e56 -#: 568406e34c8642578396177b40043014 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 msgid "`listing`" msgstr "" #: ../../src/topics/expressions.md:106 -#: 947b1ca132a54ed39745cd12ebcd65e1 +#: 8d0b142bb7ed4e61b8fb03de197240ce msgid "in [Dirent](https://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/expressions.md:107 #: ../../src/topics/parameter-references.md:104 -#: 3af8e4ce750048e6b9de12d26b9647a6 -#: f56fb5fa08994fe08cc8ae8c193828d9 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 msgid "`entry`" msgstr "" #: ../../src/topics/expressions.md:108 #: ../../src/topics/parameter-references.md:105 -#: c6dbe0a66b9f47e5b4b47c44d9f54519 -#: 063e2ae9a0eb404e8c277ef7090eb6bc +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 msgid "`entryname`" msgstr "" #: ../../src/topics/expressions.md:109 #: ../../src/topics/parameter-references.md:106 -#: 72acfeef964841e7b65937b62b5850f0 -#: 39c6edc2866542cfa7da9f842fd3edd0 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 msgid "From `EnvVarRequirement`" msgstr "" #: ../../src/topics/expressions.md:110 -#: 5fa512d352d945e7a3e0d59b0987cd1b +#: 0bc424ef2ca346099f29b937379908a0 msgid "From [EnvironmentDef](https://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/expressions.md:111 #: ../../src/topics/parameter-references.md:108 -#: 79755be159fb45b0ad06cecce623ce2c -#: 520bf799546b4700a4f38f950ffd913b +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 msgid "`envValue`" msgstr "" #: ../../src/topics/expressions.md:116 -#: 81e91df082834d2cab7ef1f62d8ba57a +#: 10d36a1adfd04144b401c993b12b4094 msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" msgstr "" #: ../../src/topics/expressions.md:118 -#: e6bfd1dc2e324992b6c3332c11ae3445 +#: 29b73e1dd72744f68377f0a38c10f062 msgid "The requirement `InlineJavascriptRequirement` supports an `expressionLib` attribute that allows users to load external JavaScript files, or to provide inline JavaScript code." msgstr "" #: ../../src/topics/expressions.md:122 -#: acf10261df2944ec890d754fd56c6b28 +#: 38a2afaf4a6c4d04909af22c93f2808d msgid "Entries added to the `expressionLib` attribute are parsed with the JavaScript engine of a CWL runner. This can be used to include external files or to create JavaScript functions that can be called in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:128 -#: bda6b8f398554b0c946c2c7d96308a42 +#: cd74f34b21af4de9be96fd897efc469b msgid "The CWL standards (versions 1.0 through 1.2) [states](https://www.commonwl.org/v1.0/CommandLineTool.html#Expressions) that the only version of JavaScript valid in CWL expressions is [ECMAScript 5.1](https://262.ecma-international.org/5.1/). This means that any code that you include or write in your CWL Document must be compliant with ECMAScript 5.1." msgstr "" #: ../../src/topics/expressions.md:135 -#: 454c02c3918647039c90ae387005dea6 +#: f12e371f3f1a4b0cb2cff9800352d48c msgid "For example, we can use `InlineJavascriptRequirement` and write a JavaScript function inline in `expressionLib`. That function can then be used in other parts of the CWL document:" msgstr "" #: ../../src/topics/expressions.md:139 -#: e1fad28bf9cb4c4c85eb74dd520ba107 +#: 49d0fda2fc144e0b8b7c92afc1d8945e msgid "`hello-world-expressionlib-inline.cwl`" msgstr "" #: ../../src/topics/expressions.md:146 -#: 9835d0b399b84a0084fe5a4d9e7e6405 +#: 8f0e8f050e334ac08334e9215e1dcf61 msgid "Running this CWL workflow will invoke the JavaScript function and result in the `echo` command printing the input message with capital initial letters:" msgstr "" #: ../../src/topics/expressions.md:149 -#: 410ba7a5ac6349a98460c6337ee5c4fb +#: 26c74b11bb1849cea0763bb74ec43e42 msgid "Running `hello-world-expressionlib-inline.cwl`." msgstr "" #: ../../src/topics/expressions.md:155 -#: d2daf50d7f3d4de18331c8fd2c8a5786 +#: 7a6be0005a6441feb67f036d005d7885 msgid "Let's move the `capitalizeWords` function to an external file, `custom-functions.js`, and import it in our CWL document:" msgstr "" #: ../../src/topics/expressions.md:158 -#: 8f2015c12b2b4d5d9a800ddeaf428f25 +#: ed590f9e6f4f425da886b110295c45db msgid "`custom-functions.js`" msgstr "" #: ../../src/topics/expressions.md:164 -#: f0ff919ffc12439d89d7b40f51ade84c +#: 093235307d6f47d4858e559b780ef5e5 msgid "`hello-world-expressionlib-external.cwl`" msgstr "" #: ../../src/topics/expressions.md:171 -#: 307a17a893fc4dafaec2a63a95704644 +#: 06635145b441418aaae84dc804f3d6ac msgid "The `custom-functions.js` file is included in the CWL document with the `$include: custom-functions.js` statement. That makes the functions and variables available to be used in other parts of the CWL document." msgstr "" #: ../../src/topics/expressions.md:175 -#: 7f393e86b114470f8dda47b2deec63aa +#: 973a9b257b1a4f0dbd4444d4f11dadd7 msgid "Running `hello-world-expressionlib-external.cwl`." msgstr "" #: ../../src/topics/expressions.md:181 -#: c3f459b87b96435583637b3f1573e658 +#: 04eaf1f7c630450db318dcd8b7626e15 msgid "Finally, note that you can have both inline and external JavaScript code in your CWL document. In this final example we have added another entry to the `expressionLib` attribute with the new function `createHelloWorldMessage`, that calls the `capitalizeWords` function from the external file `custom-functions.js`." msgstr "" #: ../../src/topics/expressions.md:186 -#: 9f676022eb2744839ca2109920250cb6 +#: c4098489fbb049789f022cd3e5c3d49b msgid "`hello-world-expressionlib.cwl`" msgstr "" #: ../../src/topics/expressions.md:193 -#: ede7285f77864fb0aee6cfecc2c97fa0 +#: 5979e4ae5c424276bdbc47f69b379d0f msgid "Running `hello-world-expressionlib.cwl`." msgstr "" #: ../../src/topics/expressions.md:200 -#: c55fb184bc614ee2b6e5e64611e5df9b +#: fd4579a3c9844492b314b5c3c1775fc7 msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$include`](https://www.commonwl.org/v1.0/SchemaSalad.html#Include) from the CWL specification to learn more about it." msgstr "" #: ../../src/topics/file-formats.md:1 -#: 66b522f46ce242149386e79f63b32cf8 +#: 3f038e7371f84ed9b4547358dfb55a11 msgid "File Formats" msgstr "" #: ../../src/topics/file-formats.md:3 -#: 64a20285785d48ca86227a0cf6353ad4 +#: e024bcb70e04412e90e1838426d1b69a msgid "Tools and workflows can take `File` types as input and produce them as output. We also recommend indicating the format for `File` types. This helps document for others how to use your tool while allowing you to do some simple type-checking when creating parameter files." msgstr "" #: ../../src/topics/file-formats.md:8 -#: 5f71bbe2c74e4260b79d4d9230d35397 +#: a3db21c0b3114802a8a5b610e252ef13 msgid "For file formats, we recommend referencing existing ontologies (like EDAM in our example), reference a local ontology for your institution, or do not add a file format initially for quick development before sharing your tool with others. You can browse existing [IANA file format listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" #: ../../src/topics/file-formats.md:14 -#: 63bfff437e3348428f7e33ece7ec55e7 +#: 0f5bc8520d6a4dafa37c65343da9702a msgid "In the next tutorial, we explain the `$namespaces` and `$schemas` section of the document in greater detail, so don't worry about these for now." msgstr "" #: ../../src/topics/file-formats.md:17 -#: 6ce83d9c06e4436881aa47d94ef41e0b +#: 5cb830da47464a8b9c3950983fa4d56f msgid "Note that for added value `cwltool` can do some basic reasoning based on file formats and warn you if there seem to be some obvious mismatches." msgstr "" #: ../../src/topics/file-formats.md:20 -#: 55006c594abf4e70a38e979568fadcf4 +#: 0535d5de416b4ea3b2f5996583deecc1 msgid "`metadata_example.cwl`" msgstr "" #: ../../src/topics/file-formats.md:26 #: ../../src/topics/metadata-and-authorship.md:22 -#: 12ba2083a9ae4c78bf502ab762a29c7d -#: 5c8f1709fe61423bba3ceaca2fc7cf09 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 msgid "The equivalent of this CWL description in command line format is:" msgstr "" #: ../../src/topics/file-formats.md:32 -#: 1a1905ff2d624eca952c8a53b3bee678 +#: 74b28c1b09c6429b82e462e4ec61808e msgid "Sample Parameter Files" msgstr "" #: ../../src/topics/file-formats.md:34 -#: 368ff92476b14f5c8331260eafc5acb5 +#: a2ce43b391864e8bbde16328cc19b32b msgid "Below is an example of a parameter file for the example above. We encourage checking in working examples of parameter files for your tool. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." msgstr "" #: ../../src/topics/file-formats.md:39 -#: 5d530afa23f349a79f54d51d40724747 +#: aebee48b742c4145a600fd2daf8c75dc msgid "`sample.yml`" msgstr "" #: ../../src/topics/file-formats.md:45 -#: 16f965f86712483aa7f95dfa3f944a17 +#: 56ee4dcfff6141d5bef80eb96559876d msgid "___Note:___ To follow the example below, you need to download the example input file, *file-formats.bam*. The file is available from and can be downloaded e.g. via `wget`:" msgstr "" #: ../../src/topics/index.md:1 -#: dc629e2c90ed458b96107a6994676434 +#: 8d3a6d83e2e54c56995893c41590b7ff msgid "Topics" msgstr "" #: ../../src/topics/inputs.md:1 -#: cf2f077cf8044079a7005e6e508dcd8c +#: 5abcdebfa1cb401bb8892553be285fd3 msgid "Inputs" msgstr "" #: ../../src/topics/inputs.md:3 -#: 129e1d2a71894d28b009f4846754a75d +#: d3a55f71dc244026a97902de9ed819ea msgid "Essential Input Parameters" msgstr "" #: ../../src/topics/inputs.md:5 -#: d6791bbe575042b9a7282c69407dd907 +#: 96671c56523c4ea9992fb5dfcfa6490e msgid "The `inputs` of a tool is a list of input parameters that control how to run the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/inputs.md:9 -#: e8da87f8bb664334adf831995601f462 +#: bcc6246742cb46bfb185e415c4a3431a msgid "Available primitive types are *string*, *int*, *long*, *float*, *double*, and *null*; complex types are *array* and *record*; in addition there are special types *File*, *Directory* and *Any*." msgstr "" #: ../../src/topics/inputs.md:13 -#: de6c322618304207b6d1364d1ec2dc13 +#: 86dce36de687449c88fb5eb9d64eb045 msgid "The following example demonstrates some input parameters with different types and appearing on the command line in different ways." msgstr "" #: ../../src/topics/inputs.md:16 -#: 43bdcf6dc1b14030bff27fa53289c02c +#: cd9cea15f57b492ba4098237cd7c5bed msgid "First, create a file called `inp.cwl`, containing the following:" msgstr "" #: ../../src/topics/inputs.md:18 -#: 056510b42ea64717996ab49c307bda86 +#: 8bdb875b63104f699efe28ea0abb1e3d msgid "`inp.cwl`" msgstr "" #: ../../src/topics/inputs.md:24 -#: 6852f5dbd9094c99bb68f2a88f76c9bc +#: c6a0151a68494c0cb0176781e65e252e msgid "Create a file called `inp-job.yml`:" msgstr "" #: ../../src/topics/inputs.md:26 -#: f33b6800367248b7927d97ad7b4be5b5 +#: dc5e6b5e01d64226bd5dbbf3175fe010 msgid "`inp-job.yml`" msgstr "" #: ../../src/topics/inputs.md:33 -#: 8ad812d7e88f4cbba83228ffb1711576 +#: 36ab1d9edafc4831bb1bca5f123b04b0 msgid "You can use `cwltool` to create a template input object. That saves you from having to type all the input parameters in a input object file:" msgstr "" #: ../../src/topics/inputs.md:40 -#: cc680bbf091a46f8b4b3dbe6324c040a +#: 7dc630ea86464b1dba3a4e5079260b3b msgid "You can redirect the output to a file, i.e. `cwltool --make-template inp.cwl > inp-job.yml`, and then modify the default values with your desired input values." msgstr "" #: ../../src/topics/inputs.md:44 -#: 446ac81f078d46289a18f494748f482c +#: ae37901a8dbe48a59e27ab4e2e6e2d30 msgid "Notice that \"example_file\", as a `File` type, must be provided as an object with the fields `class: File` and `path`." msgstr "" #: ../../src/topics/inputs.md:47 -#: 3d6d958d111943f3a2139b4dbb7810db +#: 651e032007ea4a119d20c820bb61f86b msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." msgstr "" #: ../../src/topics/inputs.md:53 -#: ba0ec9157709430c822f4e91459288e2 +#: 0b056dde9e87428996e47870b12119da msgid "Now invoke `cwltool` with the tool description and the input object on the command line, using the command `cwltool inp.cwl inp-job.yml`. The following boxed text describes these two commands and the expected output from the command line:" msgstr "" #: ../../src/topics/inputs.md:64 -#: 2565f8fd4a15429e887aeb71eacdff1e +#: 628124a1670b4b058bb0fb6e495a099c msgid "The CWL reference runner (cwltool) and other runners create temporary directories with symbolic (\"soft\") links to your input files to ensure that the tools aren't accidentally accessing files that were not explicitly specified" msgstr "" #: ../../src/topics/inputs.md:70 -#: 659ed5c64fb546399b741553a347b8e8 +#: 10ca6321ce3e4b08ab6a5bb380b19c11 msgid "The field `inputBinding` is optional and indicates whether and how the input parameter should appear on the tool's command line. If `inputBinding` is missing, the parameter does not appear on the command line. Let's look at each example in detail." msgstr "" #: ../../src/topics/inputs.md:83 -#: 3d87e69d41374fbab23b26d36c1aee03 +#: ec2adb3912bc46e28891229e9e0d9a1c msgid "Boolean types are treated as a flag. If the input parameter \"example_flag\" is \"true\", then `prefix` will be added to the command line. If false, no flag is added." msgstr "" #: ../../src/topics/inputs.md:95 -#: 07bc81683e2c4ac68b379462bae95207 +#: a519be60726a44af9941fdce04735353 msgid "String types appear on the command line as literal values. The `prefix` is optional, if provided, it appears as a separate argument on the command line before the parameter . In the example above, this is rendered as `--example-string hello`." msgstr "" #: ../../src/topics/inputs.md:109 -#: 3e304da2150f448d9e39715ac5f5deaa +#: cb8fc8c4c79e467eac5fab4ca685201e msgid "Integer (and floating point) types appear on the command line with decimal text representation. When the option `separate` is false (the default value is true), the prefix and value are combined into a single argument. In the example above, this is rendered as `-i42`." msgstr "" #: ../../src/topics/inputs.md:124 -#: fd8a98686e3c4c609f79ae427f1558d3 +#: a26cc105716f47cb807174c9003153b0 msgid "File types appear on the command line as the path to the file. When the parameter type ends with a question mark `?` it indicates that the parameter is optional. In the example above, this is rendered as `--file=/tmp/random/path/whale.txt`. However, if the \"example_file\" parameter were not provided in the input, nothing would appear on the command line." msgstr "" #: ../../src/topics/inputs.md:131 -#: f1a2e1bbb1104a4fab5a7f04cac845c7 +#: cc159dd5fe5748caac838862f5b8c4d1 msgid "Input files are read-only. If you wish to update an input file, you must [first copy it to the output directory](staging-input-files.md)." msgstr "" #: ../../src/topics/inputs.md:134 -#: 6a7f0ccd227e4f90a8c8ca96744bda68 +#: 74f7a6b8f8f74dc2a970fdd6e63d8f80 msgid "The value of `position` is used to determine where parameter should appear on the command line. Positions are relative to one another, not absolute. As a result, positions do not have to be sequential, three parameters with positions 1, 3, 5 will result in the same command line as 1, 2, 3. More than one parameter can have the same position (ties are broken using the parameter name), and the position field itself is optional. The default position is 0." msgstr "" #: ../../src/topics/inputs.md:142 -#: 1f79d115d8a145189638c68c3095396c +#: 6812698e9ad84d3385de5e88e9dde0b3 msgid "The `baseCommand` field will always appear in the final command line before the parameters." msgstr "" #: ../../src/topics/inputs.md:146 -#: 6e1b3e2d90184e34925891099d2b5cc1 +#: 9654e65b1c0642dbb5d4f34edb211989 msgid "Array Inputs" msgstr "" #: ../../src/topics/inputs.md:148 -#: 4f6df7f13e42448eb4a53f03bc477b56 +#: d1f02be278754267893dfce5a940997d msgid "It is easy to add arrays of input parameters represented to the command line. There are two ways to specify an array parameter. First is to provide `type` field with `type: array` and `items` defining the valid data types that may appear in the array. Alternatively, brackets `[]` may be added after the type name to indicate that input parameter is array of that type." msgstr "" #: ../../src/topics/inputs.md:154 -#: dbc0b52627514ad0908969d0b4ddfdf4 +#: 01f30e38dfdd452dba3a996073936e16 msgid "`array-inputs.cwl`" msgstr "" #: ../../src/topics/inputs.md:160 -#: f173dd96ad124470a53573c86a8df203 +#: 787d4bfb093c4ad287b902084706b751 msgid "`array-inputs-job.yml`" msgstr "" #: ../../src/topics/inputs.md:166 #: ../../src/topics/outputs.md:82 #: ../../src/topics/outputs.md:105 -#: e0098a77080d4349b05ceb7735a5fdf5 -#: af25945b530048b685891b1de4e35e72 -#: cb07caa4ff0149b3ae832be53f8d76f6 +#: 588f0f7f967f4d69af27c9729d6d3119 +#: 02adef8ee8204842b5b4a0408f3bac33 +#: 9db68837918a4a349f32f15f12697a1d msgid "Now invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/inputs.md:178 -#: 2445d2c7c2794fd3ad8b6ed8b4a9440b +#: 75d59e395c66416cae9b352db5081516 msgid "The `inputBinding` can appear either on the outer array parameter definition or the inner array element definition, and these produce different behavior when constructing the command line, as shown above. In addition, the `itemSeparator` field, if provided, specifies that array values should be concatenated into a single argument separated by the item separator string." msgstr "" #: ../../src/topics/inputs.md:185 -#: 4459819ba75647d185986a3386939494 +#: 874c6f19abbf45d7ab7d30a378c4048d msgid "Note that the arrays of inputs are specified inside square brackets `[]` in `array-inputs-job.yml`. Arrays can also be expressed over multiple lines, where array values that are not defined with an associated key are marked by a leading `-`. This will be demonstrated in the next lesson and is discussed in more detail in the [YAML Guide](yaml-guide.md#arrays). You can specify arrays of arrays, arrays of records, and other complex types." msgstr "" #: ../../src/topics/inputs.md:191 -#: 8f163bd34ded4785b6e28c8e2147e0dd +#: 5d7d7a28cc5d4862803032aec78174d9 msgid "Inclusive and Exclusive Inputs" msgstr "" #: ../../src/topics/inputs.md:193 -#: 1799e11a7b9c4929a3d1379d7ea45d03 +#: dea0d4b681f94e73b13965dcfe75cf7d msgid "Sometimes an underlying tool has several arguments that must be provided together (they are dependent) or several arguments that cannot be provided together (they are exclusive). You can use records and type unions to group parameters together to describe these two conditions." msgstr "" #: ../../src/topics/inputs.md:198 -#: 9510c0b431a44b5e84e0b583de7c5446 +#: ddf598abf4f34aca9fffa045860fbf96 msgid "`record.cwl`" msgstr "" #: ../../src/topics/inputs.md:204 -#: efb4eb6f5e994b50a52fa2c707dad1ce +#: d52a8089920e45bd89d582533b50e3a1 msgid "`record-job1.yml`" msgstr "" #: ../../src/topics/inputs.md:215 -#: 34599c6f10ce4104be2359a1b37f91cb +#: 750474486a84482292eeba45f118287f msgid "In the first example, you can't provide `itemA` without also providing `itemB`." msgstr "" #: ../../src/topics/inputs.md:217 -#: 0663ea7918994d3f9c45c652a3ed12db +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b msgid "`record-job2.yml`" msgstr "" #: ../../src/topics/inputs.md:233 -#: a98dda6ca4b14edba467de638bba28fc +#: 1eb0e39bb6d04b8cab300f44a79f3add msgid "In the second example, `itemC` and `itemD` are exclusive, so only the first matching item (`itemC`) is added to the command line and remaining item (`itemD`) is ignored." msgstr "" #: ../../src/topics/inputs.md:236 -#: 10d0e9f8df8c47788703073b17529bc8 +#: bc21ee10bff843689cc98ac6630edcea msgid "`record-job3.yml`" msgstr "" #: ../../src/topics/inputs.md:252 -#: 9a0e1a130fba4d24a9168ca3e455cd23 +#: 4b2ab812f62c4f949dd25c8527f2411c msgid "In the third example, only `itemD` is provided, so it appears on the command line." msgstr "" #: ../../src/topics/inputs.md:255 -#: 992a8c801ceb4233acf56b6bff315188 +#: b771302d1bec4050a9417b080eef76c9 msgid "Exclusive Input Parameters with Expressions" msgstr "" #: ../../src/topics/inputs.md:257 -#: 9027d23fa7074b789c3b86ca5ea17fa4 +#: 2c3b884cb1c54521900cc90782e8a58d msgid "If you use exclusive input parameters combined with expressions, you need to be aware that the `inputs` JavaScript object will contain one of the exclusive input values. This means that you might need to use an **or** boolean operator to check which values are present." msgstr "" #: ../../src/topics/inputs.md:262 -#: 68b47710a8ea4b978428b42c627944e9 +#: a1073b6306044dffb414319ae01f68bb msgid "Let's use an example that contains an exclusive `file_format` input parameter that accepts `null` (i.e. no value provided), or any value from an enum." msgstr "" #: ../../src/topics/inputs.md:265 -#: d33e4cac65d14111a89c838c4d1759b9 +#: 4a31c733092142b1af834eab1747c224 msgid "`exclusive-parameter-expressions.cwl`" msgstr "" #: ../../src/topics/inputs.md:271 -#: 24cea1cf7d774b6ab56959f289cab39d +#: 9a1d92334685449386dfa3b3a899ed48 msgid "Note how the JavaScript expression uses the value of the exclusive input parameter without taking into consideration a `null` value. If you provide a valid value, such as “fasta” (one of the values of the enum), your command should execute successfully:" msgstr "" #: ../../src/topics/inputs.md:280 -#: b866867d6f8e4d3999b62a85e6884ebc +#: fb623af4c480411b8fde28d01c981411 msgid "However, if you do not provide any input value, then `file_format` will be evaluated to a `null` value, which does not match the expected type for the output field (a `string`), resulting in failure when running your workflow." msgstr "" #: ../../src/topics/inputs.md:289 -#: 80c49ed168b14d25b2f09b3b0186b44f +#: e98e165f6bba40809c90473d72f9d592 msgid "To correct it, you must remember to use an or operator in your JavaScript expression when using exclusive parameters, or any parameter that allows `null`. For example, the expression could be changed to `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." msgstr "" #: ../../src/topics/metadata-and-authorship.md:1 -#: 71628ebe908b4cd28dd1fa17e3d2e2fb +#: d33aa2353ad44fb885d3a1ee48263dc4 msgid "Metadata and Authorship" msgstr "" #: ../../src/topics/metadata-and-authorship.md:3 -#: f123ca244c23413c91405a4b84887525 +#: cd64d2d828834cbbb24ea5358caf5405 msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$namespaces` section of the document (e.g. edam: http://edamontology.org/) as described in the [Schema Salad specification][schema-salad]. Once you add the namespace prefix, you can access it anywhere in the document as shown below. Otherwise, one must use full URLs: `format: http://edamontology.org/format_2572`." msgstr "" #: ../../src/topics/metadata-and-authorship.md:13 -#: 23299ae1bec94b00a32a8af7eeac350f +#: 80af387fe3ff4e2da999903385bd602b msgid "For all developers, we recommend the following minimal metadata for your tool and workflows. This example includes metadata allowing others to cite your tool." msgstr "" #: ../../src/topics/metadata-and-authorship.md:16 -#: 2495a9f2032a47c188338cb81ba429eb +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 msgid "`metadata_example2.cwl`" msgstr "" #: ../../src/topics/metadata-and-authorship.md:28 -#: 3fd2f3cf7bdf44089df2ce3122534801 +#: d402bf528c7f4eb69aaaa275be2bf1d4 msgid "Extended Example" msgstr "" #: ../../src/topics/metadata-and-authorship.md:30 -#: d5a5b8b490b640439db92da949266e4e +#: cb9980db4e5f4c74b01c2dec6d5e92d0 msgid "For those that are highly motivated, it is also possible to annotate your tool with a much larger amount of metadata. This example includes EDAM ontology tags as keywords (allowing the grouping of related tools), hints at hardware requirements in order to use the tool, and a few more metadata fields." msgstr "" #: ../../src/topics/metadata-and-authorship.md:35 -#: 5935ed94331d4b2f8ce597f31edea843 +#: 2dfbd4d580044ed083992f3ceb1bc64e msgid "`metadata_example3.cwl`" msgstr "" #: ../../src/topics/operations.md:1 -#: 5feb559552194ba58da7206c601292fe +#: 8acf361cf77c4d45ba3f2e344146259f msgid "Operations" msgstr "" #: ../../src/topics/operations.md:3 -#: b7124ba4df9042baadc1641ee09545d6 +#: 83d3b9a0ed3148fda9ce72cd108cb9e1 msgid "An Operation is a type of CWL process, just like a workflow, a command-line tool, or an expression tool. It is a step of a workflow that specifies inputs and outputs, but it does not provide enough information to be executed." msgstr "" #: ../../src/topics/operations.md:7 -#: d34b698c62114041a64e0abce25ca935 +#: 5565c1b2d8a349169a305a9b26b4574d msgid "You can create operations to visualize a workflow during development, before you are ready to submit the workflow to a CWL runner:" msgstr "" #: ../../src/topics/operations.md:10 -#: cba2c31262bd450cbafc7ca77f4fb8fa +#: 49cf614893d8438299b3bca384eb40cf msgid "`operations.cwl`" msgstr "" #: ../../src/topics/operations.md:16 -#: b01be5f632104096b5af6193aab34d90 +#: 88160cef4cfa4add9020aa89511a5749 msgid "The `uppercase` step of the workflow is an operation. It can be used like a command line tool or an expression. You can also plot it with the CWL Viewer or `cwltool`:" msgstr "" #: ../../src/topics/operations.md:24 -#: 60a6a02c1367403db6df3ec10f75eb69 +#: 2f73a786b5d94dc0b23ed0cdd185afc8 msgid "The output of the command above can be rendered with a Graphviz renderer. The following image is rendered with the Sphinx Graphviz directive (this user guide is built with Sphinx):" msgstr "" #: ../../src/topics/operations.md:55 -#: 314ea7bc35154f41b2af5fa6683ca389 +#: 730ba1434a1445ae847ec6153b6a3b72 msgid "If you try running it with `cwltool`, the command will fail since `cwltool` does not have enough information to know how to execute it:" msgstr "" #: ../../src/topics/operations.md:58 -#: d81e679b13474f74bc5e1ce1e31c2bc6 +#: 98d9b8d867594543890af99e77e24edb msgid "`cwltool` does not know how to run operations" msgstr "" #: ../../src/topics/operations.md:66 -#: d7fb27131ee44bfc82f698ee44b2bae0 +#: a25d0b1e13324b40a6b8fcd227948c4f msgid "CWL runners may come up with ways to bind operations to concrete steps. A CWL runner could, for instance, use abstract operations with ID's that correspond to steps executed by a different workflow engine." msgstr "" #: ../../src/topics/outputs.md:1 -#: b8ef11eafd1d46e088f1277f4ac372bc +#: da077da5eb8a4ffebfde041fc16300de msgid "Outputs" msgstr "" #: ../../src/topics/outputs.md:3 -#: d2382ed1f644459594655d5b5b4d838a +#: 1b3016f0462f42deb42ddaa33f28bf3d msgid "Returning Output Files" msgstr "" #: ../../src/topics/outputs.md:5 -#: 6651632d977b44479b721174fffeda2d +#: d661df070e3040869da412d07a71f716 msgid "The `outputs` of a tool is a list of output parameters that should be returned after running the tool. Each parameter has an `id` for the name of parameter, and `type` describing what types of values are valid for that parameter." msgstr "" #: ../../src/topics/outputs.md:10 -#: bee5f532554241088764ac9e56abbe85 +#: a11585474d3849cca5467512ed964743 msgid "When a tool runs under CWL, the starting working directory is the designated output directory. The underlying tool or script must record its results in the form of files created in the output directory. The output parameters returned by the CWL tool are either the output files themselves, or come from examining the content of those files." msgstr "" #: ../../src/topics/outputs.md:16 -#: 0c7c506f38be421399073871f64e99b0 +#: 2682f9ca8e604a0c9986f7746fdec960 msgid "The following example demonstrates how to return a file that has been extracted from a tar file." msgstr "" #: ../../src/topics/outputs.md:19 -#: 8b60286e56cc42a8ab5f751a97adf771 +#: 7e3fa7baf0f549ec89457e7004ac9545 msgid "Passing mandatory arguments to the `baseCommand`" msgstr "" #: ../../src/topics/outputs.md:21 -#: fa0ad674f15348339a1eee771a6ba9e2 +#: 22447a560f6f4317bf67bd7c4336126c msgid "In previous examples, the `baseCommand` was just a string, with any arguments passed as CWL inputs. Instead of a single string we can use an _array of strings_. The first element is the command to run, and any subsequent elements are mandatory command line arguments" msgstr "" #: ../../src/topics/outputs.md:26 -#: 177b5f1b95a34fb9b2eb42f733d79ac8 +#: f1ee2e00b0cc4112b51c9df3a919b73f msgid "`tar.cwl`" msgstr "" #: ../../src/topics/outputs.md:32 -#: a08a6d8aca8e490482e127a8fd5e650e +#: ad8e1acb251246d2a47c39b20d4e483a msgid "`tar-job.yml`" msgstr "" #: ../../src/topics/outputs.md:38 -#: c2c60f68b1e045f88844076e191fda9b +#: dc200c6960ae4476a772645d021f14b8 msgid "Next, create a tar file for the example." msgstr "" #: ../../src/topics/outputs.md:45 -#: 6d939f62526e4e6d95acb57d72f60a84 +#: 52703d6b7f914097934bfad13663abeb msgid "And now invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/outputs.md:51 -#: c48edd9034364b81ad42540a98b51d91 +#: 5e1c79df657d4a6e84e055dd6b300a5d msgid "The field `outputBinding` describes how to set the value of each output parameter." msgstr "" #: ../../src/topics/outputs.md:62 -#: 9ebe0186a7124dfaa30e558e8f59653a +#: 329d2809dfae4f90bc638f5f03a47ee3 msgid "The `glob` field consists of the name of a file in the output directory. If you don't know name of the file in advance, you can use a wildcard pattern like `glob: '*.txt'`." msgstr "" #: ../../src/topics/outputs.md:65 -#: 9381b7d7c9904df0a5e16dac29c2e08f +#: 96df2d45e42441d49ce193ccbfab78a3 msgid "Capturing Standard Output" msgstr "" #: ../../src/topics/outputs.md:67 -#: 2aa9c6916e3546b7b92fa64bb83275d1 +#: c6bcf7c6a8774dd6be41cc775848c3b8 msgid "To capture a tool's standard output stream, add the `stdout` field with the name of the file where the output stream should go. Then add `type: stdout` on the corresponding output parameter." msgstr "" #: ../../src/topics/outputs.md:71 -#: 63afb7a597fc4e459b6a7dbd40bbf6ff +#: 9d86c03ab44841c785b924cc44727e31 msgid "`stdout.cwl`" msgstr "" #: ../../src/topics/outputs.md:89 -#: 7418915470f041c9af5bd39ea652de36 +#: 2fb58c2feaa84970bb5274c49f4b5b64 msgid "Array Outputs" msgstr "" #: ../../src/topics/outputs.md:91 -#: f82db001b58c4969b2d8bc1dcbd7cf8a +#: 9647019d8c37466886e7aab6f176634d msgid "You can also capture multiple output files into an array of files using `glob`." msgstr "" #: ../../src/topics/outputs.md:93 -#: 26d9f0b28d384617a8e490c1f8e26e52 +#: b9eaf21f5e014eefaae301c47dafd144 msgid "`array-outputs.cwl`" msgstr "" #: ../../src/topics/outputs.md:99 -#: cf46c971b31b4e10bf0fefb4cd028c2f +#: cffff6c43b4945daa3b2a49763bc50ae msgid "`array-outputs-job.yml`" msgstr "" #: ../../src/topics/outputs.md:112 -#: a4347983fb9945a4a2773af88e426dc9 +#: cc067051f22f433bbece08f60933e002 msgid "As described in the [YAML Guide](yaml-guide.md#arrays), the array of expected outputs is specified in `array-outputs-job.yml` with each entry marked by a leading `-`. This format can also be used in CWL descriptions to mark entries in arrays, as demonstrated in several of the upcoming sections." msgstr "" #: ../../src/topics/parameter-references.md:1 -#: c5489e0633114372b273098ee2c9ffd9 +#: a190a6440ec34898990cdac05d809f22 msgid "Parameter References" msgstr "" #: ../../src/topics/parameter-references.md:3 -#: 75de9fd63393429daf1ca10a85339aa7 +#: dbfe2c1123144316aa026374b0f353d3 msgid "In a previous example, we extracted a file using the \"tar\" program. However, that example was very limited because it assumed that the file we were interested in was called \"hello.txt\", and this was written into the `.cwl` file. This is not the best way to do this, as the \"hello.txt\" filename may vary or be dependent on the input file(s) used. To avoid this we can specify the name of the file we want in the job parameters file (`.yml`). In this example, you will see how to reference the value of input parameters dynamically from other fields, which will allow us to then specify the name of the file to extract." msgstr "" #: ../../src/topics/parameter-references.md:13 -#: 8b5d0ada32d645be9359f43a431f5f91 +#: 280f1a07d0ae41d7a4674504f832fcf0 msgid "`tar-param.cwl`" msgstr "" #: ../../src/topics/parameter-references.md:19 -#: 2ed93dc8778e44209194f41b9ad193d5 +#: 5c64d938862747cb9fb52515a656ce27 msgid "`tar-param-job.yml`" msgstr "" #: ../../src/topics/parameter-references.md:25 -#: a80dd6d9920540e9880514e04035af86 +#: 074cf5d912854d8c864607cc24b15302 msgid "Create your input files and invoke `cwltool` with the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/parameter-references.md:36 -#: 9de300f7b9da49f59d1c9fd96dec4a8b +#: 0290af3e3cbb4b32b0450c8771f3bf95 msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." msgstr "" #: ../../src/topics/parameter-references.md:47 -#: a61f52d3c1024c3692899e05fcea4bee +#: b54240bb94f746bba7511633aa969db0 msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." msgstr "" #: ../../src/topics/parameter-references.md:51 -#: dafc9ba578c14fd79d075160e6b7bd6b +#: 8b70a072aa87414c88e89a3e19af0a51 msgid "The value of the \"inputs\" variable is the input object provided when the CWL tool was invoked." msgstr "" #: ../../src/topics/parameter-references.md:54 -#: 28ca6cae42904559bcec98fb9d2b07cb +#: eea20f89c45f424a888178df53713b28 msgid "Note that because `File` parameters are objects, to get the path to an input file you must reference the path field on a file object; to reference the path to the tar file in the above example you would write `$(inputs.tarfile.path)`." msgstr "" #: ../../src/topics/parameter-references.md:59 -#: 616c9ff9fcae489285f0bbbc67f07d29 +#: cb4ea13f5db84c0da43df3f7f2478d78 msgid "Where are parameter references allowed?" msgstr "" #: ../../src/topics/parameter-references.md:61 -#: ac17acd83ddb43dc9fb7a5e595ab1153 +#: 6d3fb423e6c4434697cd113fb27e28ad msgid "You can only use parameter references in certain fields. These are:" msgstr "" #: ../../src/topics/parameter-references.md:63 -#: 156573324cde41ee8b3c47deabf43db8 +#: 7647e0229a924f988cf02b7812a55c06 msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" msgstr "" #: ../../src/topics/parameter-references.md:69 -#: c9725be01e8a401fb3ad9ff01339f81e +#: 9d663249666045618a0d3acddb85a9a9 msgid "From [CommandInputParameter](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:72 -#: 6797335256e2412cbbe7636507931455 +#: 5fed4984f6784347b4cbe0630b1dd2c2 msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" msgstr "" #: ../../src/topics/parameter-references.md:74 -#: 05a5f0fcb7454cb697e3d810d55fac26 +#: dbf6153cd02542a6a01c172803122b7f msgid "From [CommandOutputParamater](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:77 -#: 406e68280b5c4ee494632f94b635b7ad +#: b6250cf6fa8a4a0c94b33302e0decca5 msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" msgstr "" #: ../../src/topics/parameter-references.md:81 -#: 2d6e2a4ff391494591bbdf8dbcc4a6ae +#: fa6ca3bbc6784380a03a950a6f49a180 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [WorkflowOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#WorkflowOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:85 -#: e71a974b29624210a107fc2d097d4196 +#: b92b516e537a4773ad67b4af586e7a25 msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" msgstr "" #: ../../src/topics/parameter-references.md:89 -#: b59df98754e24654bfef0b1fe1d91660 +#: 467a701228504d06b971b79a59c69064 msgid "From [InputParameter](http://www.commonwl.org/v1.0/Workflow.html#InputParameter) and [ExpressionToolOutputParameter](http://www.commonwl.org/v1.0/Workflow.html#ExpressionToolOutputParameter)" msgstr "" #: ../../src/topics/parameter-references.md:92 -#: d2bccbff1ce646348fe38c776ad183e1 +#: 2634f989eb304009a8568d70ed42786c msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:101 -#: 943ba46512ce48fe8c5b62327734c503 +#: 5d8bed66282c408695292ea92a03b2c4 msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" msgstr "" #: ../../src/topics/parameter-references.md:103 -#: bbcd43d5af7d44108aeb65075a6bd2be +#: 958178d1fa8843aaa0541e2bb115cfd4 msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" msgstr "" #: ../../src/topics/parameter-references.md:107 -#: 834295755af841a78e466eea43864861 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" msgstr "" #: ../../src/topics/requirements-and-hints.md:5 -#: a6b626489bfa468e8f059ab3aa669201 +#: aac74f957774479a83aab4c6ff1390ae msgid "Requirements and Hints" msgstr "" #: ../../src/topics/specifying-software-requirements.md:1 -#: e1dbea105aa845c38cb1f90b43847271 +#: b75d29d1d55d44488338f9689f156855 msgid "Specifying Software Requirements" msgstr "" #: ../../src/topics/specifying-software-requirements.md:3 -#: e9640f47d40e45bca184eb30700df648 +#: 574d93d1d592458a985f259519c036cb msgid "Often, tool descriptions will be written for a specific version of a software. To make it easier for others to use your descriptions, you can include a `SoftwareRequirement` field in the `hints` section. This may also help to avoid confusion about which version of a tool the description was written for." msgstr "" #: ../../src/topics/specifying-software-requirements.md:13 -#: 0456efb3718b4356ad2b277ee16de967 +#: 82e48b3e3c3f451480cc0b6a529271f6 msgid "In this example, the software requirement being described is InterProScan version 5.21-60." msgstr "" #: ../../src/topics/specifying-software-requirements.md:25 -#: f7e97f926505407f8f8e9a427e055e43 +#: 02e40154eac74ecc98d0447d03475b44 msgid "Depending on your CWL runner, these hints may be used to check that the required software is installed and available before the job is run. To enable these checks with the reference implementation, use the [dependency resolvers configuration][dependencies]." msgstr "" #: ../../src/topics/specifying-software-requirements.md:29 -#: ec597ff8f6ee47bc815b069335869f1f +#: 8cb1c5d9b1a54c40924099494eb766c6 msgid "As well as a version number, a unique resource identifier (URI) for the tool is given in the form of an [RRID][rrid]. Resources with RRIDs can be looked up in the [SciCrunch][scicrunch] registry, which provides a portal for finding, tracking, and referring to scientific resources consistently. If you want to specify a tool as a `SoftwareRequirement`, search for the tool on SciCrunch and use the RRID that it has been assigned in the registry. (Follow this [Adding a Resource Tutorial][scicrunch-add-tool] to add a tool to SciCrunch). You can use this RRID to refer to the tool (via [identifiers.org][identifiers]) in the `specs` field of your requirement description. Other good choices, in order of preference, are to include the DOI for the main tool citation and the URL to the tool." msgstr "" #: ../../src/topics/staging-input-files.md:1 -#: 7467a7f6f26a459ba4ce83e4e6dfcc2b +#: b85eb83e05e845d7a179f1b1d74db444 msgid "Staging Input Files" msgstr "" #: ../../src/topics/staging-input-files.md:3 -#: 3ecdf98f7e4f4f869a6dd69e3fa2d0a9 +#: 35f97d37492b4c7ca3ad6cfc1e6fa366 msgid "Normally, input files are located in a read-only directory separate from the output directory. This causes problems if the underlying tool expects to write its output files alongside the input file in the same directory. You use `InitialWorkDirRequirement` to stage input files into the output directory. In this example, we use a JavaScript expression to extract the base name of the input file from its leading directory path." msgstr "" #: ../../src/topics/staging-input-files.md:9 -#: a03372581fa44f9b8e3e088a4099cdd9 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 msgid "`linkfile.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:1 -#: 36e082be73464be0ad5d0b681cc510da +#: 0f7508ce59754a7eb230dea6042244c6 msgid "Troubleshooting" msgstr "" #: ../../src/topics/troubleshooting.md:3 -#: 4464455b51ad4873ac13c4a63ee5fb54 +#: fbe0c65b444441f785d0054176d036a6 msgid "In this section you will find ways to troubleshoot when you have problems executing CWL. We focus on `cwltool` here but some of these techniques may apply to other CWL Runners." msgstr "" #: ../../src/topics/troubleshooting.md:6 -#: ed7ff0753d1743a995f4cfedd6e5dcc2 +#: 1b6b7a75cc754775bf9dd80c0941e8da msgid "Run `cwltool` with `cachedir`" msgstr "" #: ../../src/topics/troubleshooting.md:8 -#: 4c2dd10dd66446058477a52fb8d2c602 +#: 9a710602e00c4934ae3a3b471aa68458 msgid "You can use the `--cachedir` option when running a workflow to tell `cwltool` to cache intermediate files (files that are not input nor output files, but created while your workflow is running). By default, these files are created in a temporary directory but writing them to a separate directory makes accessing them easier." msgstr "" #: ../../src/topics/troubleshooting.md:14 -#: 978b6a5fd5fa425fa9a18d9f0e8788da +#: 21b5be7270a14f0987240c81d1ec879b msgid "In the following example `troubleshooting-wf1.cwl` we have two steps, `step_a` and `step_b`. The workflow is equivalent to `echo \"Hello World\" | rev`, which would print the message \"Hello World\" reversed, i.e. \"dlroW olleH\". However, the second step, `step_b`, **has a typo**, where instead of executing the `rev` command it tries to execute `revv`, which fails." msgstr "" #: ../../src/topics/troubleshooting.md:20 -#: 000c0d6ae8bf414d9293b9f13fd2e448 +#: 0490b1fab86749e49b473949c52bbe8b msgid "`troubleshooting-wf1.cwl`" msgstr "" #: ../../src/topics/troubleshooting.md:27 -#: 7e91b8811be14f8e80df39ac4c5bd316 +#: cfe9d8241fe84bd5b74042a5625d933f msgid "Let's execute this workflow with `/tmp/cachedir/` as the `--cachedir` value (`cwltool` will create the directory for you if it does not exist already):" msgstr "" #: ../../src/topics/troubleshooting.md:35 -#: d42799cc5bd4484bb6beb309a61e103e +#: 764d933cc4da446abd8dd8f913f05dac msgid "The workflow is in the `permanentFail` status due to `step_b` failing to execute the non-existent `revv` command. The `step_a` was executed successfully and its output has been cached in your `cachedir` location. You can inspect the intermediate files created:" msgstr "" #: ../../src/topics/troubleshooting.md:44 -#: 48bb0f6666ac48648c7d969608b3bd48 +#: c93efc6d4e004859981ee7f5fa28ed03 msgid "Each workflow step has received a unique ID (the long value that looks like a hash). The `${HASH}.status` files display the status of each step executed by the workflow. And the `step_a` output file `stdout.txt` is visible in the output of the command above." msgstr "" #: ../../src/topics/troubleshooting.md:48 -#: f8876044db184cbaaca56579d0c773df +#: 546601da44cb49bd9611b1c85807fd90 msgid "Now fix the typo so `step_b` executes `rev` (i.e. replace `revv` by `rev` in the `step_b`). After fixing the typo, when you execute `cwltool` with the same arguments as the previous time, note that now `cwltool` output contains information about pre-cached outputs for `step_a`, and about a new cache entry for the output of `step_b`. Also note that the status of `step_b` is now of success." msgstr "" #: ../../src/topics/troubleshooting.md:59 -#: a5a3d408dbe34cfda4dd0b2abe67e7d7 +#: 7e0bf00f8ce542b9b009cdcf1945a9e5 msgid "In this example the workflow step `step_a` was not re-evaluated as it had been cached, and there was no change in its execution or output. Furthermore, `cwltool` was able to recognize when it had to re-evaluate `step_b` after we fixed the executable name. This technique is useful for troubleshooting your CWL documents and also as a way to prevent `cwltool` to re-evaluate steps unnecessarily." msgstr "" #: ../../src/topics/using-containers.md:1 -#: 4c240a18c4e6441189489011242c1efd +#: eff5f28ca83c458a9b07faf7a81f7e91 msgid "Using Containers" msgstr "" #: ../../src/topics/using-containers.md:3 -#: e37e76ef376a4ee695e600998906ec1c +#: 2e634f3737d04d279ae78ceee4b0a664 msgid "Running Tools Inside Docker" msgstr "" #: ../../src/topics/using-containers.md:5 -#: 51a307b0ba7c4c1d89309ba8d2250471 +#: e07f33d01b804663a25ffb08aad74821 msgid "[Docker][docker] containers simplify software installation by providing a complete known-good runtime for software and its dependencies. However, containers are also purposefully isolated from the host system, so in order to run a tool inside a Docker container there is additional work to ensure that input files are available inside the container and output files can be recovered from the container. A CWL runner can perform this work automatically, allowing you to use Docker to simplify your software management while avoiding the complexity of invoking and managing Docker containers." msgstr "" #: ../../src/topics/using-containers.md:15 -#: 13cc38d72d34468fa4eb6d91f23ff105 +#: 7a644506619a4f08958ec7d4540cd557 msgid "One of the responsibilities of the CWL runner is to adjust the paths of input files to reflect the location where they appear inside the container." msgstr "" #: ../../src/topics/using-containers.md:18 -#: 42a48398d3ef4b03bd7395120f2cfb42 +#: b5195b7d8eaa419fb2b90cb33a57783a msgid "This example runs a simple Node.js script inside a Docker container which will then print \"Hello World\" to the standard output." msgstr "" #: ../../src/topics/using-containers.md:21 -#: d59387b433bc4ecfaf7e72026624db02 +#: 7921a837ee744c5aa9a5bda04b0c8db1 msgid "`docker.cwl`" msgstr "" #: ../../src/topics/using-containers.md:27 -#: d963418ccc0b4803bbc758d718ccb5aa +#: 387e9bc9381a4450af54aff77e4df6a2 msgid "`docker-job.yml`" msgstr "" #: ../../src/topics/using-containers.md:33 -#: a224d1510c9e46aab23d8bdc03c349dd +#: 2713594c937d4c528fc8d04d9e9819ed msgid "Before we run this, let's just break it down and see what some bits do. Most of this has been explained in previous sections, the only part that is really new is the `dockerRequirement` section." msgstr "" #: ../../src/topics/using-containers.md:44 -#: 0a82f8a45b0546aaac4c976dcc98014a +#: cf94c1424fc2413c85647fd1ee73d951 msgid "`baseCommand: node` tells CWL that we will be running this command using the Node Js runtime that is meant for Javascript files. We then need to specify some `hints` for how to find the container we want. In this case we list just our requirements for the docker container in `DockerRequirements`. The `dockerPull:` parameter takes the same value that you would pass to a `docker pull` command. That is, the name of the container image (you can even specify the tag, which is good idea for best practices when using containers for reproducible research). In this case we have used a container called `node:slim`." msgstr "" #: ../../src/topics/using-containers.md:52 -#: bc418a2a535e49359c4cd44b373bbe02 +#: dc0452107c604e29bdf32bb289fe5db8 msgid "Create a Javascript file named \"hello.js\" and invoke `cwltool` providing the tool description and the input object on the command line:" msgstr "" #: ../../src/topics/using-containers.md:55 -#: a799fba2322944cea00e413c08066536 +#: 1a5596243cec4c948d9b6bf0bb12fad0 msgid "`hello.js`" msgstr "" #: ../../src/topics/using-containers.md:69 -#: 35379c6b972940bd8451f10b74dd793e +#: 483181f498fc4d968b5fe6ef427709f7 msgid "Notice the CWL runner has constructed a Docker command line to run the script." msgstr "" #: ../../src/topics/using-containers.md:72 -#: 2d5265525ad544a0b64ad2cf07aacc26 +#: 7487485d6aa4458089a4b4bdf107ea64 msgid "In this example, the path to the script `hello.js` is `/home/me/cwl/user_guide/hello.js` outside the container but `/var/lib/cwl/job369354770_examples/hello.js` inside the container, as reflected in the invocation of the `node` command." msgstr "" #: ../../src/topics/workflows.md:1 -#: e2521b89596d42f8a87a3207fd6c32f2 +#: 7394e7690f934043af617436b40845f0 msgid "Workflows" msgstr "" #: ../../src/topics/workflows.md:3 -#: 3676f23b63e142cb8e5715ae07216a47 +#: b9ae9e9a896048caad7e6c38a5bc1bd1 msgid "A workflow is a CWL processing unit that executes command-line tools, expression tools, or workflows (sub-workflows) as steps. It must have `inputs`, `outputs`, and `steps` defined in the CWL document." msgstr "" #: ../../src/topics/workflows.md:13 -#: 00725aed13a440ca8b3c4f9155fbee99 +#: f228fb7953ea48ed99d89880205f4620 msgid "CWL workflow." msgstr "" #: ../../src/topics/workflows.md:41 -#: 2e38a4f9072b4ad9bbb74f943d22084d +#: 5870ac44e4c24b8daf5f06c49f95ce04 msgid "The CWL document `echo-uppercase.cwl` defines a workflow that runs the command-line tool, and the expression tool showed in the earlier examples." msgstr "" #: ../../src/topics/workflows.md:51 -#: 2b9f4035ea864b6db50c861a1819289d +#: a913c76d06164fa18718a8a6a7dcf0d6 msgid "`echo-uppercase.cwl`" msgstr "" #: ../../src/topics/workflows.md:81 -#: 28e9064780e7418a8e02a22f92e34404 +#: 93188ed43ee949cc98b3ea679ce14feb msgid "A command-line tool or expression tool can also be written directly in the same CWL document as the workflow. For example, we can rewrite the `echo-uppercase.cwl` workflow as a single file:" msgstr "" #: ../../src/topics/workflows.md:91 -#: 66ce14a10d2d4dc497d3ed71e11ed8b8 +#: 36618126a4df4326b236ebe2ea42cffa msgid "`echo-uppercase-single-file.cwl`" msgstr "" #: ../../src/topics/workflows.md:150 -#: 8dc00528c3d2426c8a3492a8191f1d81 +#: 1cc17ad26e9c474b895ba5cd20c8b66a msgid "Having separate files helps with modularity and code organization. But it can be helpful writing everything in a single file for development. There are other ways to combine multiple files into a single file (e.g. `cwltool --pack`) discussed further in other sections of this user guide." msgstr "" #: ../../src/topics/workflows.md:160 -#: f9ef5e258f7c4971a8543d1dfed711a8 +#: 24aca0bea4d94e3593b844cf0586cffe msgid "For a sub-workflows you need to enable the requirement `SubworkflowFeatureRequirement`. It is covered in another section of this user guide in more detail." msgstr "" #: ../../src/topics/workflows.md:165 -#: 324bc51071d743ea80124c23880ddc0a +#: 46cc4859856e4367a9e5e68eecd48b73 msgid "Writing Workflows" msgstr "" #: ../../src/topics/workflows.md:167 -#: d8c13e01976b43a1af34c11a7bc36897 +#: 9c56528acd5f49deb139e034dfbfac7c msgid "This workflow extracts a java source file from a tar file and then compiles it." msgstr "" #: ../../src/topics/workflows.md:170 -#: 43910a8ab4484e529a17df418b1aedbb +#: 55ab007d472f43388e4c77aae8f165e7 msgid "`1st-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:179 #: ../../src/topics/workflows.md:180 -#: eab3ac7490f24645bbf0babb20aa9df0 -#: 56917e39cfa34470a7a88b52b1f955d9 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 msgid "Visualization of 1st-workflow.cwl" msgstr "" #: ../../src/topics/workflows.md:180 -#: 7ad12d67e815400c94080804b9285629 +#: a2dd833fdca4443181648e41051a5232 msgid "[![Visualization of 1st-workflow.cwl](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)](https://view.commonwl.org/graph/png/github.com/common-workflow-language/user_guide/blob/a29e7eae0006660946fc705a310b37a21a7e1edc/_includes/cwl/21-1st-workflow/1st-workflow.cwl)" msgstr "" #: ../../src/topics/workflows.md:183 -#: 457d5a31c79143acae2683d95d27f7a3 +#: 7e40cc9f9e1341c195e843c009575b94 msgid "Use a YAML or a JSON object in a separate file to describe the input of a run:" msgstr "" #: ../../src/topics/workflows.md:185 -#: a2a73901bf634547900d08b9a1ac8889 +#: 26c51dcb76364ed780376aecb7cbacda msgid "`1st-workflow-job.yml`" msgstr "" #: ../../src/topics/workflows.md:191 -#: f347d80e62384b14acf6423675e5359a +#: 6fcf8ad3d1bd49afa4a105622437bd59 msgid "Next, create a sample Java file and add it to a tar file to use with the command-line tool." msgstr "" #: ../../src/topics/workflows.md:205 -#: 2a845a4f3f98428fb82f3ca7ce038a6e +#: 71cb81fa4511495b80422244849979e4 msgid "What's going on here? Let's break it down:" msgstr "" #: ../../src/topics/workflows.md:212 -#: e2007c74d5f449a882809d6b91c010bf +#: def35d6021394def80a53ae49a2cdbde msgid "The `cwlVersion` field indicates the version of the CWL spec used by the document. The `class` field indicates this document describes a workflow." msgstr "" #: ../../src/topics/workflows.md:221 -#: 7f5e53ee7cf94be2bff45ef64db28a24 +#: ea94a9a02cd44b9d8e06bfe16e6b8cc8 msgid "The `inputs` section describes the inputs of the workflow. This is a list of input parameters where each parameter consists of an identifier and a data type. These parameters can be used as sources for input to specific workflows steps." msgstr "" #: ../../src/topics/workflows.md:233 -#: a0d076b7b8b048478580c99ef0c8429f +#: c84d4450bc6a475dbf34e0b22cea9130 msgid "The `outputs` section describes the outputs of the workflow. This is a list of output parameters where each parameter consists of an identifier and a data type. The `outputSource` connects the output parameter `classfile` of the `compile` step to the workflow output parameter `compiled_class`." msgstr "" #: ../../src/topics/workflows.md:248 -#: 7fd926c18ad548e98845e9b5134dd6f2 +#: cca9665f6daa44b49233baf34ab9fcc7 msgid "The `steps` section describes the actual steps of the workflow. In this example, the first step extracts a file from a tar file, and the second step compiles the file from the first step using the java compiler. Workflow steps are not necessarily run in the order they are listed, instead the order is determined by the dependencies between steps (using `source`). In addition, workflow steps which do not depend on one another may run in parallel." msgstr "" #: ../../src/topics/workflows.md:256 -#: 789fbd47f8564cceb430ef3c0bc90e9b +#: 547edbf5fa424b8286cc21674ff159b0 msgid "The first step, `untar` runs `tar-param.cwl` (described previously in [Parameter References](parameter-references.md)). This tool has two input parameters, `tarfile` and `extractfile` and one output parameter `extracted_file`." msgstr "" #: ../../src/topics/workflows.md:261 -#: 45c4d0492d6143ca9cebe81e9b2cf3ae +#: 7ca248888b9d484cb544cd76ba538662 msgid "The ``in`` section of the workflow step connects these two input parameters to the inputs of the workflow, `tarball` and `name_of_file_to_extract` using `source`. This means that when the workflow step is executed, the values assigned to `tarball` and `name_of_file_to_extract` will be used for the parameters `tarfile` and `extractfile` in order to run the tool." msgstr "" #: ../../src/topics/workflows.md:267 -#: 73bd3da2af8545928d5ea71d0f7454f6 +#: ae6b240718104380b08db5552d7355ea msgid "The `out` section of the workflow step lists the output parameters that are expected from the tool." msgstr "" #: ../../src/topics/workflows.md:278 -#: 15ce3d2700424f0fbb280d602ccebcf6 +#: e5a8b7f84be64020b191099f3fad30ed msgid "The second step `compile` depends on the results from the first step by connecting the input parameter `src` to the output parameter of `untar` using `untar/extracted_file`. It runs `arguments.cwl` (described previously in [Additional Arguments and Parameters](additional-arguments-and-parameters.md)). The output of this step `classfile` is connected to the `outputs` section for the Workflow, described above." msgstr "" #: ../../src/topics/workflows.md:285 -#: af4268f19202436eb0a7e8c6bed5e386 +#: f0b04849253c4693904512ddd7f9ce84 msgid "Nested Workflows" msgstr "" #: ../../src/topics/workflows.md:287 -#: 94a4eadca6b949d79de2990a0150eee8 +#: 12a06d8358534102b202965d4258c18e msgid "Workflows are ways to combine multiple tools to perform a larger operations. We can also think of a workflow as being a tool itself; a CWL workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" msgstr "" #: ../../src/topics/workflows.md:297 -#: 09c1619e8cbd4febbb637f7e99ad5890 +#: 1658cac0de1b47e9b60f6d4a4ad9bb19 msgid "Here's an example workflow that uses our `1st-workflow.cwl` as a nested workflow:" msgstr "" #: ../../src/topics/workflows.md:300 -#: 677ea7a27eb64568ab3689142d6efe70 +#: 49ed137fe996452a8534c68d100db941 msgid "`nestedworkflows.cwl`" msgstr "" #: ../../src/topics/workflows.md:309 -#: 097e6d47f9394e62b80110700492783a +#: b7f93705e5b8416696be01850072e8c0 msgid "This two-step workflow starts with the `create-tar` step which is connected to the `compile` step in orange; `compile` is another workflow, diagrammed on the right. In purple we see the fixed string `\"Hello.java\"` being supplied as the `name_of_file_to_extract`." msgstr "" #: ../../src/topics/workflows.md:314 -#: e93affce8c104bf6977182047c1f1077 +#: e87045829b344089ab59dc27063ddd7a msgid "\"Visualization \"Visualization" msgstr "" #: ../../src/topics/workflows.md:322 -#: 06c9e04ba890473b851240a0fa9c3b12 +#: 42ef2f145b824d69b63abc1da175c216 msgid "A CWL `Workflow` can be used as a `step` just like a `CommandLineTool`, its CWL file is included with `run`. The workflow inputs (`tarball` and `name_of_file_to_extract`) and outputs (`compiled_class`) then can be mapped to become the step's input/outputs." msgstr "" #: ../../src/topics/workflows.md:336 -#: 0380dc1fe3aa48e4b62283b7b2a611d8 +#: c61cedf543664d388183e04b3939cc39 msgid "Our `1st-workflow.cwl` was parameterized with workflow inputs, so when running it we had to provide a job file to denote the tar file and `*.java` filename. This is generally best-practice, as it means it can be reused in multiple parent workflows, or even in multiple steps within the same workflow." msgstr "" #: ../../src/topics/workflows.md:341 -#: 49b251f7a313492ea60504b00109e526 +#: 9e39e3f1501c4fcaab3e8962e090f6be msgid "Here we use `default:` to hard-code `\"Hello.java\"` as the `name_of_file_to_extract` input, however our workflow also requires a tar file at `tarball`, which we will prepare in the `create-tar` step. At this point it is probably a good idea to refactor `1st-workflow.cwl` to have more specific input/output names, as those also appear in its usage as a tool." msgstr "" #: ../../src/topics/workflows.md:347 -#: 7ee55702d7dd4679a24ff052f6f0cbeb +#: 03e2f767c4da461982fc3c0f3ba94762 msgid "It is also possible to do a less generic approach and avoid external dependencies in the job file. So in this workflow we can generate a hard-coded `Hello.java` file using the previously mentioned `InitialWorkDirRequirement` requirement, before adding it to a tar file." msgstr "" #: ../../src/topics/workflows.md:366 -#: 85d7e2e270874aa6b9f477cec0f48154 +#: 3bea5822b8694e2aa32c446e1c54a045 msgid "In this case our step can assume `Hello.java` rather than be parameterized, so we can use hardcoded values `hello.tar` and `Hello.java` in a `baseCommand` and the resulting `outputs`:" msgstr "" #: ../../src/topics/workflows.md:383 -#: 570e94513c984c09ad6aa255f534216d +#: 426023bd6e3a471cbb30dbda3d6f9e57 msgid "Did you notice that we didn't split out the `tar --create` tool to a separate file, but rather embedded it within the CWL Workflow file? This is generally not best practice, as the tool then can't be reused. The reason for doing it in this case is because the command line is hard-coded with filenames that only make sense within this workflow." msgstr "" #: ../../src/topics/workflows.md:389 -#: a107258662fb4bd4a9a3d8754e34d1e9 +#: 0d498cd4caf54c15891ca1afe58e2727 msgid "In this example we had to prepare a tar file outside, but only because our inner workflow was designed to take that as an input. A better refactoring of the inner workflow would be to take a list of Java files to compile, which would simplify its usage as a tool step in other workflows." msgstr "" #: ../../src/topics/workflows.md:394 -#: fc1a6502d831458ab8371a575cea47e2 +#: b2d75045e02741b4850f5ff1243f7858 msgid "Nested workflows can be a powerful feature to generate higher-level functional and reusable workflow units - but just like for creating a CWL Tool description, care must be taken to improve its usability in multiple workflows." msgstr "" #: ../../src/topics/workflows.md:398 -#: 2d10806bf1ce4e26b92adda61efc0862 +#: cfa765264a27411ab914de569aa3dac4 msgid "Scattering Steps" msgstr "" #: ../../src/topics/workflows.md:400 -#: 046c5e134de94b629cc22d416f3c9182 +#: 35f8ee0a00274a5bbb8a80c0f1fcbad6 msgid "Now that we know how to write workflows, we can start utilizing the `ScatterFeatureRequirement`. This feature tells the runner that you wish to run a tool or workflow multiple times over a list of inputs. The workflow then takes the input(s) as an array and will run the specified step(s) on each element of the array as if it were a single input. This allows you to run the same workflow on multiple inputs without having to generate many different commands or input yaml files." msgstr "" #: ../../src/topics/workflows.md:411 -#: 52fa22d3277940049fbb589a3ea73433 +#: 5fa79c62049a447c8328ebf9db54ebf4 msgid "The most common reason a new user might want to use scatter is to perform the same analysis on different samples. Let's start with a simple workflow that calls our first example (`hello_world.cwl`) and takes an array of strings as input to the workflow:" msgstr "" #: ../../src/topics/workflows.md:415 -#: 6043beb96c2c49648011ec556aa9e986 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd msgid "`scatter-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:421 -#: 5ac4310515124e2986724425bed5651f +#: 3a67d77a2e7b4c0bb61cc3585ceae942 msgid "Aside from the `requirements` section including `ScatterFeatureRequirement`, what is going on here?" msgstr "" #: ../../src/topics/workflows.md:429 -#: 7958e91d5c2f4046aa9d2070a900f9ae +#: f1cb55fc59824cc18a95fd6dcb32cf4c msgid "First of all, notice that the main workflow level input here requires an array of strings." msgstr "" #: ../../src/topics/workflows.md:441 -#: 2db234d776fe4fd38bab07245dcb783a +#: d947c54933d64aad90df392a1cedd63f msgid "Here we've added a new field to the step `echo` called `scatter`. This field tells the runner that we'd like to scatter over this input for this particular step. Note that the input name listed after scatter is the one of the step's input, not a workflow level input." msgstr "" #: ../../src/topics/workflows.md:445 -#: 7cfb17230e284ee7b6e2a00efe8eeb74 +#: 651d35997332404186aa6d5711da4a3d msgid "For our first scatter, it's as simple as that! Since our tool doesn't collect any outputs, we still use `outputs: []` in our workflow, but if you expect that the final output of your workflow will now have multiple outputs to collect, be sure to update that to an array type as well!" msgstr "" #: ../../src/topics/workflows.md:450 -#: 4311ac98544e4fb0b2f4b24985710a01 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 msgid "Using the following input file:" msgstr "" #: ../../src/topics/workflows.md:452 -#: 780f9c72e6c34c39918642c7e2477355 +#: 842b926ae34542cb9023021f137b08be msgid "`scatter-job.yml`" msgstr "" #: ../../src/topics/workflows.md:458 -#: cc4a7316db644b438cbaa181ad9ef2d3 +#: b662c1a5a4424c8d8350a806356acc61 msgid "As a reminder, [`hello_world.cwl`](../introduction/quick-start.md) simply calls the command `echo` on a message. If we invoke `cwltool scatter-workflow.cwl scatter-job.yml` on the command line:" msgstr "" #: ../../src/topics/workflows.md:466 -#: dfc461a03fe8487794837904febb8b63 +#: 04d6babfd87343d7a5f13867ea02b65f msgid "You can see that the workflow calls echo multiple times on each element of our `message_array`. Ok, so how about if we want to scatter over two steps in a workflow?" msgstr "" #: ../../src/topics/workflows.md:469 -#: 1e83485b00b64dfaba897bd8d772e0f0 +#: 2eaacf1a90204a2b9bd621344560f2a1 msgid "Let's perform a simple echo like above, but capturing `stdout` by adding the following lines instead of `outputs: []`" msgstr "" #: ../../src/topics/workflows.md:472 -#: d0321d6805ec4d3abf3877d02a0a417f +#: 242993d42b164ee5abe7ca10d45856de msgid "`hello_world_to_stdout.cwl`" msgstr "" #: ../../src/topics/workflows.md:480 -#: d7d77e807b3048c7bdf89558f76804cb +#: 4a94e5f7e1bc4d628702140e4e51d6d3 msgid "And add a second step that uses `wc` to count the characters in each file. See the tool below:" msgstr "" #: ../../src/topics/workflows.md:483 -#: 8d9b8be147fc4a71922dde858842e543 +#: e61d93b848184c8e8e573928427b4d0a msgid "`wc-tool.cwl`" msgstr "" #: ../../src/topics/workflows.md:489 -#: 34b7705416a745a6a42e6d402c0757ed +#: e3a7182f00f440b8b5461da91194a64b msgid "Now, how do we incorporate scatter? Remember the scatter field is under each step:" msgstr "" #: ../../src/topics/workflows.md:491 -#: 257adcee9da64d5c987f3b64efd20ab0 +#: 99fa96caacaa45cb97aded9a24fcac6d msgid "`scatter-two-steps.cwl`" msgstr "" #: ../../src/topics/workflows.md:497 -#: fa6ed5d0c14f42f4aa3c5144648db22c +#: b5338f39e8c74ff28e139da68089a742 msgid "Here we have placed the scatter field under each step. This is fine for this example since it runs quickly, but if you're running many samples for a more complex workflow, you may wish to consider an alternative. Here we are running scatter on each step independently, but since the second step is not dependent on the first step completing all languages, we aren't using the scatter functionality efficiently. The second step expects an array as input from the first step, so it will wait until everything in step one is finished before doing anything. Pretend that `echo Hello World!` takes 1 minute to perform, `wc -c` on the output takes 3 minutes and that `echo Hallo welt!` takes 5 minutes to perform, and `wc` on that output takes 3 minutes. Even though `echo Hello World!` could finish in 4 minutes, it will actually finish in 8 minutes because the first step must wait on `echo Hallo welt!`. You can see how this might not scale well." msgstr "" #: ../../src/topics/workflows.md:509 -#: 333e8ce458d54de394526769f96d12d2 +#: f6d92156d67c4a339bcfd194cff897df msgid "Ok, so how do we scatter on steps that can proceed independent of other samples? Remember from [Nested Workflows](#nested-workflows), that we can make an entire workflow a single step in another workflow! Convert our two-step workflow to a single step subworkflow:" msgstr "" #: ../../src/topics/workflows.md:513 -#: b819e8a5df6e4fa495924095709669ef +#: 1c9e386922324ec8a59306572c19fb8b msgid "`scatter-nested-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:519 -#: f1955468a1364d44a930db77c9c4b495 +#: d80ab383eec9402faba997b548fe42eb msgid "Now the scatter acts on a single step, but that step consists of two steps so each step is performed in parallel." msgstr "" #: ../../src/topics/workflows.md:522 -#: 8c3b9b645a204d02b2c73a205e8ec296 +#: f7d2827d97db4bf4ab84b5d6621c3b48 msgid "Conditional Workflows" msgstr "" #: ../../src/topics/workflows.md:524 -#: 4d88b9c186cd4502adbf752e8a70b6ce +#: 49217c02f58c43ff9ec00f10da8d4e84 msgid "This workflow contains a conditional step and is executed based on the input. This allows workflows to skip additional steps based on input parameters given at the start of the program or by previous steps." msgstr "" #: ../../src/topics/workflows.md:527 -#: 9927673564024ba5833b5ac271737857 +#: 20b9f181420c401d8615c17a10027517 msgid "`conditional-workflow.cwl`" msgstr "" #: ../../src/topics/workflows.md:566 -#: 84f4ed7ce2004742b8db9087104a469a +#: 8dbd56473f8c40c0bb12a48be06117e3 msgid "The first thing you'll notice is that this workflow is only compatible for version 1.2 or greater of the CWL standards." msgstr "" #: ../../src/topics/workflows.md:573 -#: 2b5f9757adca4490a149c7f45e14fcb5 +#: 78d7f3ede2c746d482042adef050b2c4 msgid "The first step of the workflow (step1) contains two input properties and will execute foo.cwl when the conditions are met. The new property `when` is where the condition validation takes place. In this case only when `in1` from the workflow contains a value `< 1` this step will be executed." msgstr "" #: ../../src/topics/workflows.md:587 -#: 0418de720813442f81ecff293c9448b5 +#: cbbf93c70fe04ba7932ba25758ddc611 msgid "Using the following command `cwltool cond-wf-003.1.cwl --val 0` the value will pass the first conditional step and will therefore be executed and is shown in the log by `INFO [step step1] start` whereas the second step is skipped as indicated by `INFO [step step2] will be skipped`." msgstr "" #: ../../src/topics/workflows.md:607 -#: 524eec63be8248ae982939c975ef50a2 +#: cfa1c1fde4454df283f87cc54a9c59ec msgid "When a value of 3 is given the first conditional step will not be executed but the second step will `cwltool cond-wf-003.1.cwl --val 3`." msgstr "" #: ../../src/topics/workflows.md:627 -#: 5e99f9912cc549a7890e2934425eb943 +#: 1a8be2950cbb475bbb2617e005f0fac9 msgid "If no conditions are met for example when using `--val 2` the workflow will raise a permanentFail." msgstr "" #: ../../src/topics/yaml-guide.md:1 -#: b0121ee087d6424fbb0ea5957a7b0b8c +#: 5f09d4d897cf457d80b9a11b8c01747e msgid "YAML Guide" msgstr "" #: ../../src/topics/yaml-guide.md:6 -#: 49e9f6b3a06840289decf3f557860f87 +#: 5d83c56102e141cc978500f678dd0c1c msgid "[YAML][yaml] is a file format designed to be readable by both computers and humans. This guide introduces the features of YAML that are relevant when writing CWL descriptions and input parameter files." msgstr "" #: ../../src/topics/yaml-guide.md:13 -#: ed9eebec0b3d4b72ba65507d37757a37 +#: c38438fbf9a04e729ec2e3c962435289 msgid "You can skip this section if you are already comfortable with YAML." msgstr "" #: ../../src/topics/yaml-guide.md:16 -#: bf9b255a24a84f3ba989a223492b8f41 +#: fdb9cc750cec43ee962517e637dc5fea msgid "Contents" msgstr "" #: ../../src/topics/yaml-guide.md:18 -#: e79fa0b7f8b14810a3a20908ef92bc55 +#: 08da9cd8056b4ddd8f5150cc85ba72ee msgid "[Key-Value Pairs](#key-value-pairs)" msgstr "" #: ../../src/topics/yaml-guide.md:19 -#: 290e2035f903417cbecb5dc5f09d6ebe +#: b027fc234ed943bbb00d4c6bc03c040a msgid "[Comments](#comments)" msgstr "" #: ../../src/topics/yaml-guide.md:20 -#: d420730151534f1a89076588a3358f09 +#: b8befec0d8684638aaa616a659e0100c msgid "[Maps](#maps)" msgstr "" #: ../../src/topics/yaml-guide.md:21 -#: a6b5378bbe1e4bee9e37a765bddf75f7 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc msgid "[Arrays](#arrays)" msgstr "" #: ../../src/topics/yaml-guide.md:22 -#: 6e4d9465dc2b454d96b02d7ad1817795 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 msgid "[JSON Style](#json-style)" msgstr "" #: ../../src/topics/yaml-guide.md:24 -#: a649d4af5f434dac9395e013ec4836bb +#: 98056c5cfd5640ad9de0679360797cc7 msgid "Key-Value Pairs" msgstr "" #: ../../src/topics/yaml-guide.md:26 -#: 446190a298834b73bda068286e8490cf +#: cda73485875d4c8e9464679a20558616 msgid "Fundamentally, a file written in YAML consists of a set of _key-value pairs_. Each pair is written as `key: value`, where whitespace after the `:` is required. Key names in CWL files should not contain whitespace - [_camelCase_][camelCase] is used for multi-word key names that have special meaning in the CWL specification and underscored key names otherwise. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:42 -#: 2f35c012ff174721bffe66a3f58a804f +#: 98cae24919b74c088a5d89706aec581b msgid "The YAML above defines four keys - `first_name`, `last_name`, `age_years`, and `home` - with their four respective values. Values can be character strings, numeric (integer, floating point, or scientific representation), Boolean (`true` or `false`), or more complex nested types (see below)." msgstr "" #: ../../src/topics/yaml-guide.md:51 -#: 43127c98c9d94aedac61cee67929c1a6 +#: b4b0940b4b5743c09637b36b964202d0 msgid "Values may be wrapped in quotation marks, but be aware that this may change the way that they are interpreted i.e. `\"1234\"` will be treated as a character string , while `1234` will be treated as an integer. This distinction can be important, for example when describing parameters to a command: in CWL all parts of `baseCommand` must be strings so, if you want to specify a fixed numeric value to a command, make sure that you wrap that numeric value in quotes: `baseCommand: [echo, \"42\"]`." msgstr "" #: ../../src/topics/yaml-guide.md:61 -#: dc4fe561203c4c38a9caea5bd6eff2cd +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 msgid "Comments" msgstr "" #: ../../src/topics/yaml-guide.md:63 -#: f924e4896db2424d99ce8c9da14c599a +#: 9ca3554d771d45998e88aaede525b227 msgid "You may use `#` to add comments to your CWL and parameter files. Any characters to the right of ` #` will be ignored by the program interpreting the YAML. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:76 -#: bf7646f5f925485c842a6d34140e40b8 +#: 3fca839cede94cfd8e4f605c73ba699d msgid "If there is anything on the line before the comment, be sure to add at least one space before the `#`!" msgstr "" #: ../../src/topics/yaml-guide.md:79 -#: c483e61dec8949fa96bb893d422888a0 +#: da34c635707345b2a5e85a2fcd30bbaf msgid "Maps" msgstr "" #: ../../src/topics/yaml-guide.md:81 -#: 85fcb523d0e34a499eae04d304887f7b +#: 3ded0f125249485c921994b6e6b93ac9 msgid "When describing a tool or workflow with CWL, it is usually necessary to construct more complex, nested representations. Referred to as _maps_, these hierarchical structures are described in YAML by providing additional key-value pairs as the value of any key. These pairs (sometimes referred to as \"children\") are written on new lines under the key to which they belong (the \"parent\"), and should be indented with two spaces (⇥tab characters are not allowed). For example:" msgstr "" #: ../../src/topics/yaml-guide.md:104 -#: 83d47c8736a34f3cbf09e3997845e4f4 +#: 53ece35d309a4c8d99f1efb2122a7092 msgid "The YAML above illustrates how to build up complex nested object descriptions relatively quickly. The `inputs` map contains a single key, `example_flag`, which itself contains two keys, `type` and `inputBinding`, while one of these children, `inputBinding`, contains a further two key-value pairs (`position` and `prefix`). See the [Arrays](#arrays) section below for more information about providing multiple values/key-value pairs for a single key. For comparison with the example YAML above, here is a graphical representation of the `inputs` object it describes." msgstr "" #: ../../src/topics/yaml-guide.md:127 -#: c698fb3d37bc403e9aeb679b8fc0e15e +#: d74321b111d84ae7a515f2f17dd39e23 msgid "Arrays" msgstr "" #: ../../src/topics/yaml-guide.md:129 -#: ae8af2f0eeda4aec97201211dfa965c7 +#: 7fc0bdf2489a44f2a29e71b86f7c0055 msgid "In certain circumstances, it is necessary to provide multiple values or objects for a single key. As we've already seen in the [Maps](#maps) section above, more than one key-value pair can be mapped to a single key. However, it is also possible to define multiple values for a key without having to provide a unique key for each value. We can achieve this with an _array_, where each value is defined on its own line and preceded by `-`. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:146 -#: 2ee87aa465cd41fda16a61e242f8c9d0 +#: fd64dd818ec64bb6aa9a11586a5747f6 msgid "and a more complex example combining maps and arrays:" msgstr "" #: ../../src/topics/yaml-guide.md:167 -#: 0a6fd4469ff24b61b3ad001b09eead18 +#: 8c06e542dd4144fa83388d8142552c8d msgid "JSON Style" msgstr "" #: ../../src/topics/yaml-guide.md:169 -#: b96ba19bce9341d39c46054e1f10fe8f +#: 87bafb845c714b109874f6137b84462d msgid "YAML is based on [JavaScript Object Notation (JSON)][json]. Maps and arrays can also be defined in YAML using the native JSON syntax. For example:" msgstr "" #: ../../src/topics/yaml-guide.md:177 -#: 903f30af3d0c45cfb61063936a8097a7 +#: 5ab9ddf613a540a2b8228e37600cc5dc msgid "and:" msgstr "" #: ../../src/topics/yaml-guide.md:184 -#: ede8db7c0a58432e8a1c416e937a06d2 +#: fcd05b1ef31a4046946a2399c7fc5575 msgid "Native JSON can be useful in indicating where a field is intentionally left empty (such as `[]` for an empty array), as well as where it makes more sense for the values to be located on the same line (For example, when providing option flags and their values in a shell command). However, as the second example above shows, it can severely affect the readability of a YAML file, and should be used sparingly." msgstr "" #: ../../src/topics/yaml-guide.md:194 -#: c8b53615476a4a1fbef2420d93bac94e +#: f4b8fc8236044fada420def13a02813d msgid "Reference" msgstr "" #: ../../src/topics/yaml-guide.md:196 -#: ea03cb5525cc491f9feb5c4780b38fee +#: 859368c1f25c4a4aad57abfd046c63f5 msgid "The [Learn YAML in Y Minutes][yaml-y-mins] reference was very helpful for us while we wrote this guide, though it also covers features that are not valid in CWL." msgstr "" #: ../../src/tutorials.md:1 -#: 92fd3a5e31714eab859dd630af2e78cf +#: 2203c93f02ac4514a43508ecb98dfcc5 msgid "Tutorials" msgstr "" #: ../../src/tutorials.md:5 -#: de660ecdb5b44c97a0e519d00b232497 +#: 5d92464923c245818c070fbef102be89 msgid "This is a list of tutorials provided by the CWL community. Use the `Edit this page` link in the menu if you would like to add another tutorial to the list." msgstr "" #: ../../src/tutorials.md:7 -#: 5afc1e1288e74ed0985e61e5164479c7 +#: 8a5cd557dab5456bb41cdc24af73b50c msgid "Beginner Tutorials" msgstr "" #: ../../src/tutorials.md:9 -#: 862dc7ac81e54b1fb3d4c2f961b8810e +#: 13d7e2e92e96432787c712cf6a595424 msgid "[Introduction to Workflows with Common Workflow Language: For Contributors.](https://carpentries-incubator.github.io/cwl-novice-tutorial/)" msgstr "" #: ../../src/tutorials.md:11 -#: e2c94c0e1c7048d38cd7aa2c465a859d +#: 0abdd85c9b964a4e89ba3d80a6c78d6f msgid "Advanced Tutorials" msgstr "" #: ../../src/tutorials.md:13 -#: b63253780f51467a95207d820d13ac39 +#: 3cbf1f69a5514fd3bee90e68b201190f msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" msgstr "" #: ../../src/tutorials.md:15 -#: 6d06ca7ed5df4560aaed286f4fe33928 +#: 68c97a7065634d02956f3f5c1d4eeb9f msgid "Bioinformatics Tutorials" msgstr "" #: ../../src/tutorials.md:17 -#: 5448df4a6a8f431d80e269bcd480e19e +#: a67c7e0eaf4e4d27b3e5db303333a088 msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" msgstr "" diff --git a/src/LICENSE.md b/src/LICENSE.md new file mode 100644 index 00000000..84798e58 --- /dev/null +++ b/src/LICENSE.md @@ -0,0 +1,2 @@ +```{include} ../LICENSE.md +``` diff --git a/src/LICENSE.rst b/src/LICENSE.rst deleted file mode 100644 index 68c5792f..00000000 --- a/src/LICENSE.rst +++ /dev/null @@ -1 +0,0 @@ -.. include:: ../LICENSE.rst diff --git a/src/conf.py b/src/conf.py index 921ced1e..bcfe20a8 100644 --- a/src/conf.py +++ b/src/conf.py @@ -238,3 +238,85 @@ gettext_uuid = True gettext_compact = "user_guide" locale_dirs = ['../locales/'] + + +# Patched MyST parser +# from __future__ import annotations + +from docutils import nodes +from docutils.parsers.rst import Parser as RstParser +from sphinx.parsers import Parser as SphinxParser +from sphinx.util import logging + +from myst_parser.config.main import ( + MdParserConfig, + TopmatterReadError, + merge_file_level, + read_topmatter, +) +from myst_parser.mdit_to_docutils.sphinx_ import SphinxRenderer, create_warning +from myst_parser.parsers.mdit import create_md_parser + +SPHINX_LOGGER = logging.getLogger(__name__) + +class MystParser(SphinxParser): + """Sphinx parser for Markedly Structured Text (MyST).""" + + supported: tuple[str, ...] = ("md", "markdown", "myst") + """Aliases this parser supports.""" + + settings_spec = RstParser.settings_spec + """Runtime settings specification. + Defines runtime settings and associated command-line options, as used by + `docutils.frontend.OptionParser`. This is a concatenation of tuples of: + - Option group title (string or `None` which implies no group, just a list + of single options). + - Description (string or `None`). + - A sequence of option tuples + """ + + config_section = "myst parser" + config_section_dependencies = ("parsers",) + translate_section_name = None + + def parse(self, inputstring: str, document: nodes.document) -> None: + """Parse source text. + :param inputstring: The source string to parse + :param document: The root docutils node to add AST elements to + """ + # get the global config + config: MdParserConfig = document.settings.env.myst_config + + # update the global config with the file-level config + try: + topmatter = read_topmatter(inputstring) + except TopmatterReadError: + pass # this will be reported during the render + else: + if topmatter: + warning = lambda wtype, msg: create_warning( # noqa: E731 + document, msg, line=1, append_to=document, subtype=wtype + ) + config = merge_file_level(config, topmatter, warning) + + parser = create_md_parser(config, SphinxRenderer) + # TODO: In the first pass, the call above will use MarkdownIt over the whole document, + # populating the ``.md_env`` correctly. Over the next passes, from transforms as + # ``sphinx.transforms.i18n.Locale`` it will create a blank new document, as well + # as a new MarkdownIT parser but using just the Docutils document that is being + # translated. As a result of this, the translation has no reference-links, and it + # gives you the translation without resolving the links. Here we just re-use the + # ``md_env`` dictionary that contains the ``.references`` populated in the first + # pass, fixing i18n with MyST Parser. + env = {} if not hasattr(document.settings, 'md_env') else document.settings.md_env + parser.options["document"] = document + parser.render(inputstring, env) + document.settings.md_env = parser.renderer.md_env + + +def setup(app): + """Sphinx setup callback.""" + + # TODO: Here we replace the MySTParser (that replaces the Sphinx default parser...), + # with our patched version above. + app.add_source_parser(MystParser, override=True) diff --git a/src/index.md b/src/index.md index e1a0c0cb..8e10fa54 100644 --- a/src/index.md +++ b/src/index.md @@ -35,7 +35,7 @@ introduction/index.md topics/index.md tutorials.md faq.md -LICENSE.rst +LICENSE.md ``` [repo]: https://github.com/common-workflow-language/user_guide/issues