diff --git a/locales/ja/LC_MESSAGES/user_guide.po b/locales/ja/LC_MESSAGES/user_guide.po index ce4d41ef..2aa1d64d 100644 --- a/locales/ja/LC_MESSAGES/user_guide.po +++ b/locales/ja/LC_MESSAGES/user_guide.po @@ -9,15 +9,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2023-12-16 02:08+0000\n" +"PO-Revision-Date: 2024-01-31 06:01+0000\n" "Last-Translator: Manabu ISHII \n" +"Language-Team: Japanese \n" "Language: ja\n" -"Language-Team: Japanese \n" -"Plural-Forms: nplurals=1; plural=0;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" +"X-Generator: Weblate 5.4-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -923,6 +924,7 @@ msgid "Windows" msgstr "Windows" #: ../../src/introduction/prerequisites.md:29 aeeb990abbbd42cca122c342054be29c +#, fuzzy msgid "" "If you are using Windows, you will have to install the Windows Subsystem " "for Linux 2 as documented in the [`cwltool` documentation for Microsoft " @@ -930,6 +932,11 @@ msgid "" "language/cwltool/blob/main/README.rst#ms-windows-users). Your operating " "system also needs internet access and a recent version of Python (3.6+)." msgstr "" +"Windowsを使用している場合は、[`cwltool` documentation for Microsoft Windows " +"users](https://github.com/common-workflow-language/cwltool/blob/main/README." +"rst#ms-windows-users)に記載されているように、Windows Subsystem for Linux 2を" +"インストールする必要があります。インターネットアクセスとPythonの最新バージョ" +"ン(3.6+)も必要です。" #: ../../src/introduction/prerequisites.md:34 21d1f29fb15745c480194eae6acdd031 #, fuzzy @@ -953,6 +960,8 @@ msgid "" "`cwltool` can be installed with `pip`, `apt`, or `conda`. We recommend " "using a virtual environment like `venv` or `conda`." msgstr "" +"`cwltool` は `pip`、`apt` または `conda` でインストールできます。`venv` や " +"`conda` のような仮想環境を使用することを推奨します。" #: ../../src/introduction/prerequisites.md:48 1edf8b8438334ae29dc406dbfd711228 #, fuzzy @@ -1000,8 +1009,9 @@ msgid "Running `true.cwl` with `cwltool`." msgstr "`cwltool` を使って `true.cwl` を実行します。" #: ../../src/introduction/prerequisites.md:78 d2dc809318be49cc996d892e93ad84ac +#, fuzzy msgid "Generic ``cwl-runner`` alias" -msgstr "" +msgstr "一般的な ``cwl-runner`` エイリアス" #: ../../src/introduction/prerequisites.md:80 9809c2e262924ef286b0bd62e0b00995 msgid "" @@ -1453,6 +1463,7 @@ msgstr "ここでは、`arguments` フィールドを使用して、特定の入 #: ../../src/topics/additional-arguments-and-parameters.md:43 #: dc9fa5f2cbb147b1853c4042c54010f3 +#, fuzzy msgid "" "This example references a runtime parameter. Runtime parameters provide " "information about the hardware or software environment when the tool is " @@ -1462,6 +1473,13 @@ msgid "" "`$(runtime.outdirSize)`, and `$(runtime.tmpdirSize)`. See the [Runtime " "Environment][runtime] section of the CWL specification for details." msgstr "" +"この例では、ランタイムパラメータを参照しています。 ランタイムパラメータは、" +"ツールが実際に実行されたときのハードウェアまたはソフトウェア環境に関する情報" +"を提供します。 ` $(runtime.outdir)` " +"パラメータは、指定された出力ディレクトリへのパスです。 その他、`$(runtime." +"tmpdir)`,`$(runtime.ram)`,`$(runtime.cores)`,`$(runtime." +"outdirSize)`,`$(runtime.tmpdirSize)` などがあります。 詳細はCWL仕様書の[" +"Runtime Environment][runtime]の項を参照してください。" #: ../../src/topics/best-practices.md:1 964bf8276dd04b65887448e1386e63fe msgid "Best Practices" @@ -1485,6 +1503,7 @@ msgstr "" "Direcotry` を適宜使用します。" #: ../../src/topics/best-practices.md:11 ae127b776eed4894af8cb680377703e0 +#, fuzzy msgid "" "A CWL document (in conjunction with any external components like " "`Dockerfile`s) is software code. Workflow developers should be aware that" @@ -1499,8 +1518,20 @@ msgid "" "license that allows for re-use by anyone, e.g. [Apache 2.0][apache-" "license]." msgstr "" +"CWL 定義（`Dockerfile`のような外部コンポーネントと合わせて）は、ソフトウェア" +"コードです。ワークフロー開発者は、ソフトウェアライセンスに関する通常の規則が" +"このCWL定義に適用されることを認識する必要があります。例えば、ワークフローが一" +"般に共有される場合、将来のユーザーがどのような条件でワークフローを実行、修正" +"、および/または他のワークフローと組み合わせることができるかを理解するために、" +"ライセンス条項は明確でなければなりません。このような理由から、CWL定義にライセ" +"ンスフィールドを含めることを検討してください。このガイドの著者は、独自のライ" +"センスを作成するのではなく、既存のライセンスを選択することをお勧めします（ラ" +"イセンスの選択について詳しくは、以下のリンクを参照してください）。そして、私" +"たちの推奨する実践は、誰でも再利用できるライセンスを選択することです。例えば " +"[Apache 2.0][apache-license]です。" #: ../../src/topics/best-practices.md:20 384eb620dc31468e8c3f5f33a3436200 +#, fuzzy msgid "" "If possible, the license should be specified with its corresponding [SPDX" " identifier][spdx]. Construct the metadata field for the license by " @@ -1509,6 +1540,11 @@ msgid "" "example snippet below for guidance. For non-standard licenses without an " "SPDX identifier, provide a URL to the license." msgstr "" +"可能であれば、ライセンスは対応する [SPDX 識別子][spdx] " +"と共に指定されるべきです。`https://spdx.org/licenses/[SPDX-ID]` (`SPDX-ID` " +"は、上記のリンク先の識別子のリストから選択) という形式の URL を指定して、ライ" +"センスのメタデータフィールドを構築します。以下の例を参照してください。SPDX識" +"別子のない非標準ライセンスの場合は、そのライセンスへのURLを指定します。" #: ../../src/topics/best-practices.md:26 e8259b43fa6944eda73eae381db6b97b msgid "" @@ -1719,12 +1755,17 @@ msgid "Network Access" msgstr "ネットワークアクセス" #: ../../src/topics/command-line-tool.md:69 201712f3ceee4d4ea56ab96d3fef97b0 +#, fuzzy msgid "" "This indicates whether a process requires outgoing IPv4/IPv6 network " "access. Starting with CWL v1.1, programs are not granted network access " "by default, so you must include the requirement for network access in the" " specification of your tool." msgstr "" +"これは、プロセスが送信先としてIPv4/" +"IPv6ネットワーク・アクセスを必要とするかどうかを示します。 CWL v1.1以降、プロ" +"グラムにはデフォルトでネットワーク・アクセス権が付与されないため、ツール定義" +"にネットワーク・アクセスの要件を含める必要があります。" #: ../../src/topics/command-line-tool.md:84 3282a357799f4a72a6b8bace206144c4 #, fuzzy @@ -1814,6 +1855,7 @@ msgstr "" #: ../../src/topics/creating-files-at-runtime.md:40 #: 9aeea5a6a4244bc7a1626e0cb7351068 +#, fuzzy 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," @@ -1823,6 +1865,13 @@ msgid "" "means that you are using a multiline string (without it, we would need to" " write the whole script on one line)." msgstr "" +"`InitialWorkDirRequirement` は`listing` を必要とします。`listing` は YAML " +"配列なので、配列の各要素の最初の行に`-` が必要です。この場合、要素は 1 " +"つだけです。`entryname:` は任意の値を指定できますが、`baseCommand` " +"で指定したものと一致していなければなりません。最後の部分は`entry:` " +"で、この後に`|-` が続きます。これは YAML の引用構文で、" +"複数行の文字列を使用していることを意味します (これがなければ、" +"スクリプト全体を 1 行で記述する必要があります)." #: ../../src/topics/creating-files-at-runtime.md:51 #: 867239e9ad3d4187a2703662a0ca3976 @@ -1848,6 +1897,7 @@ msgid "Custom Types" msgstr "カスタムタイプ" #: ../../src/topics/custom-types.md:3 e0275ddda8f84207a58d10c17ca99a45 +#, fuzzy 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 " @@ -1855,6 +1905,10 @@ msgid "" "for additional customisation/configuration of a tool/analysis without the" " need to fiddle with the CWL description directly." msgstr "" +"CWL定義で使用・再利用するために、独自のカスタム型を書きたい場合があります。こ" +"のようなカスタムタイプを使用することで、同じタイプを使用する複数の記述の間の" +"冗長性を減らし、また、CWL記述を直接いじらずに、ツールや分析のカスタマイズや設" +"定を追加できるようになります。" #: ../../src/topics/custom-types.md:9 8367e38e5e7c4a298d1d87b9001aaddc msgid "" @@ -1871,6 +1925,7 @@ msgid "`custom-types.yml`" msgstr "`custom-types.yml`" #: ../../src/topics/custom-types.md:24 56b8912a1ea84f28adeb8beaf92ab563 +#, fuzzy msgid "" "___Note:___ To follow the example below, you need to [download the " "example input file](https://github.com/common-workflow-" @@ -1878,6 +1933,10 @@ msgid "" "types/rich_sparse_otu_table.biom), *rich_sparse_otu_table.biom* e.g. via " "`wget`:" msgstr "" +"___注意:___ 以下の例に行うには、`wget`などで*rich_sparse_otu_table." +"biom*という入力ファイルを[ダウンロード](https://github.com/" +"common-workflow-language/user_guide/blob/main/src/_includes/cwl/custom-types/" +"rich_sparse_otu_table.biom)する必要があります：" #: ../../src/topics/custom-types.md:30 a48539920c4944898918bc90b2d4e3c9 msgid "" @@ -1917,6 +1976,7 @@ msgstr "" " で定義されており、例として`custom-types.cwl` の定義にあるように、インポートされます：" #: ../../src/topics/custom-types.md:76 dce43b138ba24b22bfa9fa5692a17009 +#, fuzzy msgid "" "Note also that the author of this CWL description has also included " "[`ResourceRequirement`](https://w3id.org/cwl/CommandLineTool.html#ResourceRequirement)s," @@ -1926,6 +1986,13 @@ msgid "" "These features are discussed further in other chapters of this user " "guide." msgstr "" +"また、この CWL 定義には、[`ResourceRequirement`](https://w3id.org/cwl/" +"CommandLineTool." +"html#ResourceRequirement)も含まれていることに注意してください。これは、" +"ツールが正常に動作するために必要な最小限の RAM の量とコアの数、さらにその定義" +"に書かれたソフトウェアのバージョンの詳細やその他の有用なメタデータを指定する" +"ものです。これらの機能については、このユーザーガイドの他の章で詳しく説明する" +"。" #: ../../src/topics/environment-variables.md:1 19737f89f2994815969fa4a88346f49a msgid "Environment Variables" @@ -2511,6 +2578,11 @@ msgid "" " tool with others. You can browse existing [IANA file format " "listings][IANA] and [EDAM file format listings][EDAM] on their websites." msgstr "" +"ファイルフォーマットについては、既存のオントロジーを参照すること（例ではEDAM" +"）、所属機関のローカルオントロジーを参照すること、またはツールを他者と共有す" +"る前に迅速に開発するために最初はファイルフォーマットを追加しないことを推奨し" +"ています。既存の[IANAファイルフォーマット一覧][IANA]と[EDAMファイルフォーマッ" +"ト一覧][EDAM]は、それぞれのウェブサイトで参照することができます。" #: ../../src/topics/file-formats.md:14 81c441846fc249c58607bacf97095eb8 msgid "" @@ -2675,6 +2747,7 @@ msgid "" msgstr "CWLリファレンスランナー（cwltool）と他のランナーは、ツールが明示的に指定されていないファイルに誤ってアクセスしないように、入力ファイルへの（\"ソフト\"）シンボリックリンクを持つ一時ディレクトリを作成します。" #: ../../src/topics/inputs.md:70 5bdf77c45346445d8f93353c1e73f768 +#, fuzzy msgid "" "The field " "[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_binding)" @@ -2683,6 +2756,10 @@ msgid "" "parameter does not appear on the command line. Let's look at each " "example in detail." msgstr "" +"フィールド[`inputBinding`](https://w3id.org/cwl/CommandLineTool.html#Input_bi" +"nding)はオプションであり、入力パラメータをツールのコマンドラインに表示するか" +"どうか、またどのように表示するかを指定します。`inputBinding`がない場合、パラ" +"メータはコマンドラインに表示されません。 それぞれの例を詳しく見てみましょう。" #: ../../src/topics/inputs.md:83 d783fe52e86f4feda33ea0eecb622603 msgid "" @@ -2705,14 +2782,19 @@ msgstr "" " hello` と与えられます。" #: ../../src/topics/inputs.md:109 b106eed01c1744a792368f91f547e553 +#, fuzzy 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 "" +"整数型（および浮動小数点型）はコマンドラインに10進数のテキスト表現で表示され" +"ます。 `separate`オプションがfalseの場合（デフォルト値はtrue）、prefixと値は1" +"つの引数にまとめられます。 上の例では `-i42` として表示されます。" #: ../../src/topics/inputs.md:124 1c70336741a842a5b16b687642d1d9b4 +#, fuzzy 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 " @@ -2721,6 +2803,11 @@ msgid "" "parameter were not provided in the input, nothing would appear on the " "command line." msgstr "" +"ファイル型は、コマンドライン上にファイルへのパスとして表示されます。 パラメ" +"ータの型の末尾にクエスチョンマーク`?`がある場合、これは、パラメータがオプショ" +"ンであることを表します。 上記の例では、`--file=/tmp/random/path/whale.txt` " +"と表示されます。 ただし、入力パラメータに \"example_file\" " +"パラメータを指定しなかった場合、コマンドラインには何も表示されません。" #: ../../src/topics/inputs.md:131 9294c07c672b414f9c3895ed70b9b4ee msgid "" @@ -2752,6 +2839,7 @@ msgid "Array Inputs" msgstr "配列入力" #: ../../src/topics/inputs.md:148 b11a5c7a13b345939e4ae15e1e2c0786 +#, fuzzy 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 " @@ -2760,6 +2848,11 @@ msgid "" " be added after the type name to indicate that input parameter is array " "of that type." msgstr "" +"コマンドラインに表現される入力パラメータの配列を簡単に追加することができます" +"。配列パラメータを指定するには、2つの方法があります。1つ目の方法は、`type` " +"に`type: array` と`items` を指定して、配列に現れる可能性のある有効なデータ型" +"を定義する方法です。2つ目の方法は、入力パラメータがその型の配列であることを示" +"すために、型名の後に`[]` という括弧を付けることもできます。" #: ../../src/topics/inputs.md:154 aa00bcfc6c0f4085ae52621a2f4ae8d9 msgid "`array-inputs.cwl`" @@ -2787,8 +2880,13 @@ msgid "" "values should be concatenated into a single argument separated by the " "item separator string." msgstr "" +"`inputBinding` は、外側の配列パラメータ定義と内側の配列要素定義のいずれかに記" +"述することができ、上図のようにコマンドラインを構築する際に異なる挙動を示しま" +"す。また、`itemSeparator` フィールドがあれば、配列の値を項目区切り文字列で区" +"切って1つの引数に連結することを指定することができます。" #: ../../src/topics/inputs.md:185 bb31c6784ea843ec88f185523cfa25df +#, fuzzy msgid "" "Note that the arrays of inputs are specified inside square brackets `[]` " "in `array-inputs-job.yml`. Arrays can also be expressed over multiple " @@ -2798,6 +2896,11 @@ msgid "" "guide.md#arrays). You can specify arrays of arrays, arrays of records, " "and other complex types." msgstr "" +"なお、入力の配列は角括弧の中で指定します `array-inputs-job.yml`の`[]`です.配" +"列は複数行に渡って表現することも可能で、関連するキーで定義されていない配列の" +"値は、先頭の`-` でマークされます。これは次のレッスンで実演され、[YAML Guide" +"](yaml-guide.md#arrays) でより詳細に説明されています。配列の配列、レコードの" +"配列、その他の複雑な型を指定することができます。" #: ../../src/topics/inputs.md:191 53817379078548b2aeb6195cae9cbab7 #, fuzzy @@ -2805,12 +2908,17 @@ msgid "Inclusive and Exclusive Inputs" msgstr "包括的入力と排他的入力" #: ../../src/topics/inputs.md:193 e163c0cfe9694a85b2e42682f42970a5 +#, fuzzy 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 "" +"基本的なツールには、一緒に提供しなければならない複数の引数（依存関係あり）や" +"、一緒に提供できない複数の引数（排他関係あり）があることがあります。 record" +"とユニオン型を使ってパラメータをグループ化し、この2つの条件を定義することがで" +"きます。" #: ../../src/topics/inputs.md:198 84e1ab25511c49d1baabb1f80f247b49 msgid "`record.cwl`" @@ -3027,10 +3135,12 @@ msgid "" msgstr "上記のコマンドの出力は、Graphvizレンダラーでレンダリングすることができます。以下の画像は、SphinxのGraphvizディレクティブでレンダリングしたものです（このユーザーガイドはSphinxで構築されています）：" #: ../../src/topics/operations.md:56 c07e3ff02ac14ffb89bcbd1b30f3f3fd +#, fuzzy msgid "" "The operation file will fail to run with `cwltool` because `cwltool` " "lacks the necessary information to execute it:" -msgstr "" +msgstr "操作ファイルを `cwltool` で実行しようとすると、`cwltool` " +"が実行に必要な情報を持っていないため、失敗します：" #: ../../src/topics/operations.md:59 e184470550e645f6b9ce658af7e65ecf msgid "`cwltool` does not know how to run operations" @@ -3198,6 +3308,7 @@ msgid "Parameter References" msgstr "パラメータリファレンス" #: ../../src/topics/parameter-references.md:3 f5c0592ca28c46c2a89943f4f6f69a27 +#, fuzzy 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 " @@ -3209,6 +3320,15 @@ msgid "" "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 "" +"前の例では、\"tar \"プログラムを使用してファイルを抽出しました" +"。しかし、その例は非常に限定的なものでした。というのも、" +"私たちが興味を持っているファイルは\"hello.txt\"と呼ばれ、これが`.cwl` ファイ" +"ルに書き込まれていると仮定していたからです。これは最良の方法ではありません。" +"なぜなら、\"hello.txt \"というファイル名は" +"、使用する入力ファイルによって異なるか、または依存する可能性があるからです。" +" これを避けるために、ジョブパラメーターファイル(`.yml`)で必要なファイル名を" +"指定することができます。この例では、入力パラメーターの値を他のフィールドから" +"動的に参照し、抽出するファイル名を指定する方法を説明します。" #: ../../src/topics/parameter-references.md:13 50db8add9b1942d986e581b8d21c2ee4 msgid "`tar-param.cwl`" @@ -3393,6 +3513,7 @@ msgstr "ソフトウェア要求事項の指定" #: ../../src/topics/specifying-software-requirements.md:3 #: e708866921ea49d69d3c2a32d63ea468 +#, fuzzy 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 " @@ -3401,6 +3522,12 @@ msgid "" " field in the `hints` section. This may also help to avoid confusion " "about which version of a tool the description was written for." msgstr "" +"多くの場合、ツール定義はソフトウェアの特定のバージョン用に書かれます。他の人" +"があなたの説明を使いやすくするために、`hints` セクションに " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#SoftwareRequirement) フィールドを含めることができます。これは、ツール定" +"義がどのツールのどのバージョン用に書かれたかについての混乱を避けるのにも役立" +"ちます。" #: ../../src/topics/specifying-software-requirements.md:13 #: 6f722d6fd54f485fa964076c8d08938b @@ -3418,6 +3545,10 @@ msgid "" "enable these checks with the reference implementation, use the " "[dependency resolvers configuration][dependencies]." msgstr "" +"CWLランナーによっては、これらのヒントを使用して、ジョブの実行前に必要なソフト" +"ウェアがインストールされ、利用可能であることをチェックすることができます。リ" +"ファレンス実装でこれらのチェックを有効にするには、[依存性解決のための設定][de" +"pendencies] を使用します。" #: ../../src/topics/specifying-software-requirements.md:29 #: 1a8b8aadf1c64e87b8b670e288bc14bc @@ -3442,6 +3573,7 @@ msgid "Staging Input Files" msgstr "入力ファイルのステージング" #: ../../src/topics/staging-input-files.md:3 ac2ef1fced5f4044861761a11c35e78a +#, fuzzy msgid "" "Normally, input files are located in a read-only directory separate from " "the output directory. This causes problems if the underlying tool " @@ -3452,6 +3584,13 @@ msgid "" "a JavaScript expression to extract the base name of the input file from " "its leading directory path." msgstr "" +"通常、入力ファイルは出力ディレクトリとは別の読み取り専用ディレクトリに置かれ" +"ます。 これは、ツールが同じディレクトリに入力ファイルと一緒に出力ファイルを書" +"き込むことを期待している場合に問題を引き起こします。 入力ファイルを出力ディレ" +"クトリにステージング（配置のこと）するには、[`InitialWorkDirRequirement`](htt" +"ps://w3id.org/cwl/CommandLineTool.html#InitialWorkDirRequirement)を使用します" +"。この例では、JavaScript式を使用して、先頭のディレクトリパスから入力ファイル" +"のベース名を抽出しています。" #: ../../src/topics/staging-input-files.md:9 d8ca16f5321e486ebe8ea9f9752b3737 msgid "`linkfile.cwl`" @@ -3482,6 +3621,11 @@ msgid "" "these files are created in a temporary directory but writing them to a " "separate directory makes accessing them easier." msgstr "" +"ワークフロー実行時に`--cachedir` オプションを使用すると、`cwltool` に中間ファ" +"イル（入力ファイルでも出力ファイルでもないが、ワークフロー実行中に作成される" +"ファイル）をキャッシュするよう指示することができます。デフォルトでは、これら" +"のファイルは一時ディレクトリに作成されますが、別のディレクトリに書き込むこと" +"でアクセスが容易になります。" #: ../../src/topics/troubleshooting.md:14 36ec60b80c714357a4274217274136ff msgid "" @@ -3492,6 +3636,13 @@ msgid "" " where instead of executing the `rev` command it tries to execute `revv`," " which fails." msgstr "" +"次の例では、`troubleshooting-wf1.cwl` ` step_a` と`step_b` " +"という2つのステップを用意しています。このワークフローは、`echo \"Hello " +"World\" | rev` と同等で、\"Hello World\" というメッセージを反転して、" +"すなわち \"dlroW olleH\" " +"と表示します。しかし、2番目のステップである`step_b`,**にはタイプミス** " +"があり、`rev` コマンドを実行する代わりに`revv` " +"を実行しようとし、失敗しています。" #: ../../src/topics/troubleshooting.md:20 6f34038054ac4f4fa0b0ad9cbc3ecdc7 msgid "`troubleshooting-wf1.cwl`" @@ -3508,22 +3659,33 @@ msgstr "" "は、ディレクトリがまだ存在しない場合、新規作成します）：" #: ../../src/topics/troubleshooting.md:35 8654b7f2f4464d13be4b47729e1f07e5 +#, fuzzy 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 "" +"`step_b` が存在しない `revv` コマンドの実行に失敗したため、ワークフローは " +"`permanentFail` ステータスになっています。`step_a` は正常に実行され、" +"その出力は `cachedir` " +"にキャッシュされました。作成された中間ファイルを確認することができます：" #: ../../src/topics/troubleshooting.md:44 04e80f7ce14d4d73bc5d290dcf01bcdb +#, fuzzy msgid "" "Each workflow step has received a unique ID (the long value that looks " "like a hash). The `${HASH}.status` files display the status of each step " "executed by the workflow. And the `step_a` output file `stdout.txt` is " "visible in the output of the command above." msgstr "" +"各ワークフローのステップには、一意のID（ハッシュのような長い値）が付与されて" +"います。`${HASH}.status` ファイルは、ワークフローによって実行された各ステップ" +"のステータスを表示します。そして、`step_a` 出力ファイル`stdout.txt` " +"は、上記のコマンドの出力で確認できます。" #: ../../src/topics/troubleshooting.md:48 719917cb0fd849f5a328671df8726189 +#, fuzzy 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" @@ -3532,8 +3694,16 @@ msgid "" "new cache entry for the output of `step_b`. Also note that the status of " "`step_b` is now of success." msgstr "" +"`step_b` が`rev` を実行するように、タイプミスを修正します（すなわち、`step_b`" +" の`revv` を`rev` " +"で置き換えます）。タイプミスを修正した後、前回と同じ引数で`cwltool` " +"を実行すると、`cwltool` の出力に、`step_a` " +"の出力が事前にキャッシュされていることと、`step_b` " +"の出力の新しいキャッシュ・エントリーがあることがわかります。また、`step_b` " +"のステータスは、現在、成功であることに注目してください。" #: ../../src/topics/troubleshooting.md:59 2a9dbb3ad7564f5aa103349c45ee7925 +#, fuzzy 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. " @@ -3542,6 +3712,11 @@ msgid "" " troubleshooting your CWL documents and also as a way to prevent " "`cwltool` to re-evaluate steps unnecessarily." msgstr "" +"この例では、ワークフローのステップ`step_a` はキャッシュされていたため再実行さ" +"れず、その実行や出力に変化はありませんでした。さらに、`cwltool` " +"は、実行ファイル名を修正した後、`step_b` を再実行する必要があることがわかりま" +"した。このテクニックは、CWL文書のトラブルシューティングに役立つだけでなく、`c" +"wltool` が不必要にステップを再実行するのを防ぐ方法としても有効です。" #: ../../src/topics/using-containers.md:1 7439fe097aa4459ba1e4c0e28fc59b9a msgid "Using Containers" @@ -3690,19 +3865,28 @@ msgid "`echo-uppercase-single-file.cwl`" msgstr "`echo-uppercase-single-file.cwl`" #: ../../src/topics/workflows.md:150 5a9a1dd6ed1f4ca6803f1d235c4fd392 +#, fuzzy 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 "" +"ファイルを分けることは、モジュール化やコードの整理に役立ちます。しかし、開発" +"のためにすべてを1つのファイルに書いておくと便利なことがあります。複数のファイ" +"ルを1つのファイルにまとめる方法は他にもあります（例：`cwltool --pack` " +"）このユーザーガイドの他のセクションで詳しく説明します。" #: ../../src/topics/workflows.md:160 277ed30d4b3a4156a4523e8d10e6ce60 +#, fuzzy 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 "" +"サブワークフローでは、Requirement、`SubworkflowFeatureRequirement` を有効にす" +"る必要があります。このユーザーガイドの別のセクションで、より詳しく説明してい" +"ます。" #: ../../src/topics/workflows.md:165 82818ab17aa4403eb982fd81a14a5865 msgid "Writing Workflows" @@ -3914,6 +4098,7 @@ msgstr "" "）と出力（`compiled_class` ）は、ステップの入力/出力になるようにマッピングすることができます。" #: ../../src/topics/workflows.md:336 d621821d2c1b403cb7415b381dd883f6 +#, fuzzy 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 " @@ -3921,8 +4106,13 @@ msgid "" " reused in multiple parent workflows, or even in multiple steps within " "the same workflow." msgstr "" +"`1st-workflow.cwl` はワークフロー入力でパラメータ化されているため、" +"実行時には tar ファイルと`*.java` ファイル名を示すジョブファイルを提供する必" +"要がありました。これは、複数の親ワークフローや、同じワークフロー内の複数のス" +"テップで再利用できることを意味するため、一般的にベストプラクティスです。" #: ../../src/topics/workflows.md:341 358c612f175241f7bf148a04d75e00c9 +#, fuzzy 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" @@ -3931,6 +4121,11 @@ msgid "" "have more specific input/output names, as those also appear in its usage " "as a tool." msgstr "" +"ここでは、`default:` を使って、`\"Hello.java\"` を`name_of_file_to_extract` " +"input として固定しています。しかし、このワークフローでは`tarball` の tar " +"ファイルも必要です。これは`create-tar` ステップで用意します。この時点で" +"、`1st-workflow.cwl` 、より具体的な入力/出力名を持つようにリファクタリングす" +"るのがよいでしょう。これらは、ツールとしての使用法にも現れるからです。" #: ../../src/topics/workflows.md:347 c6297c120e004ae8b52d5b519fbc04d2 #, fuzzy @@ -4358,6 +4553,7 @@ msgid "Arrays" msgstr "配列" #: ../../src/topics/yaml-guide.md:129 5aca9a90fb6149529ed717992746a2f3 +#, fuzzy 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) " @@ -4367,6 +4563,12 @@ msgid "" "this with an _array_, where each value is defined on its own line and " "preceded by `-`. For example:" msgstr "" +"ある状況下では、1つのキーに対して複数の値やオブジェクトを提供する必要がありま" +"す。上記の[Maps](#maps)のセクションですでに見たように、1つのキーに複数のキー" +"と値のペアをマッピングすることができます。しかし、各値にユニークなキーを用意" +"しなくても、キーに対して複数の値を定義することも可能です。この場合、_array_ " +"を用いて、各値を独自の行で定義し、その前に`-` " +"を置くことで実現できます。例えば、次のようになります：" #: ../../src/topics/yaml-guide.md:146 d1c9e72e004b4fb4a6efb7748a15ab6f #, fuzzy @@ -4629,4 +4831,3 @@ msgstr "[CWLでrnaseq](https://arvados.github.io/rnaseq-cwl-training/)" #~ " file from its leading directory " #~ "path." #~ msgstr "" - diff --git a/locales/zgh/LC_MESSAGES/sphinx.po b/locales/zgh/LC_MESSAGES/sphinx.po new file mode 100644 index 00000000..fa449b56 --- /dev/null +++ b/locales/zgh/LC_MESSAGES/sphinx.po @@ -0,0 +1,27 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: YEAR-MO-DA HO:MI+ZONE\n" +"Last-Translator: Automatically generated\n" +"Language-Team: none\n" +"Language: zgh\n" +"MIME-Version: 1.0\n" +"Content-Type: text/plain; charset=UTF-8\n" +"Content-Transfer-Encoding: 8bit\n" + +#: ../../src/_templates/sidebar-nav-bs.html:1 +#: d65b012160e9455eb4d2628279fffc42 +msgid "Main navigation" +msgstr "" + +#: ../../src/_templates/sidebar-nav-bs.html:3 +#: 4b3441eb77f448daa60718b7bfa862db +msgid "Section Navigation" +msgstr "" diff --git a/locales/zgh/LC_MESSAGES/user_guide.po b/locales/zgh/LC_MESSAGES/user_guide.po new file mode 100644 index 00000000..702fb704 --- /dev/null +++ b/locales/zgh/LC_MESSAGES/user_guide.po @@ -0,0 +1,3125 @@ +# SOME DESCRIPTIVE TITLE. +# Copyright (C) 2013, CWL Project Team +# This file is distributed under the same license as the Common Workflow Language User Guide package. +# FIRST AUTHOR , YEAR. +# +msgid "" +msgstr "" +"Project-Id-Version: Common Workflow Language User Guide\n" +"Report-Msgid-Bugs-To: \n" +"POT-Creation-Date: 2023-01-25 14:33+0100\n" +"PO-Revision-Date: 2023-12-24 21:09+0000\n" +"Last-Translator: ⵣⵓⵀⵉⵔ ⴰⵎⴰⵣⵉⵖ ZOUHIR DEHBI \n" +"Language-Team: Tamazight (Standard Moroccan) \n" +"Language: zgh\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 5.4-dev\n" + +#: ../../LICENSE.md:2 +#: 4e203044f0464fd5a3256430391dde12 +msgid "Licenses" +msgstr "ⵜⵓⵔⴰⴳⵉⵏ" + +#: ../../LICENSE.md:4 +#: 79a9837f877147fa8e3931968aae7fb5 +msgid "Instructional Material" +msgstr "" + +#: ../../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.md:12 +#: 98f18f72afa043f9a79aa9b5fc8bdf22 +msgid "You are free:" +msgstr "" + +#: ../../LICENSE.md:14 +#: 466be810dd8d4a838e0edb5869f2c4eb +msgid "to **Share**---copy and redistribute the material in any medium or format" +msgstr "" + +#: ../../LICENSE.md:15 +#: 18a3a0aec35743848c97bc178f9c94ff +msgid "to **Adapt**---remix, transform, and build upon the material" +msgstr "" + +#: ../../LICENSE.md:17 +#: b746b1e4dca14de1a8e18036b7602a73 +msgid "for any purpose, even commercially." +msgstr "" + +#: ../../LICENSE.md:19 +#: 6021e65292a149d5b15e14491f3eb05e +msgid "The licensor cannot revoke these freedoms as long as you follow the license terms:" +msgstr "" + +#: ../../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.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.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.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.md:44 +#: a091addc2dea4830a06bb72ead56c5ea +msgid "Software" +msgstr "" + +#: ../../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.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 +#: 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 +#: 0d3267f84f4e4aedb1e9fce00b4ea4bc +#: 436cfca6f857469bbff7c652df32160f +msgid "This page has moved" +msgstr "" + +#: ../../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 +#: e2ed894d325a4f50a5e2dc69da5531a1 +msgid "FAQ" +msgstr "" + +#: ../../src/faq.md:11 +#: 61edb787dab04ca2ad3ed07616d878a0 +msgid "Non \"`File`\" Types Using `evalFrom`" +msgstr "" + +#: ../../src/faq.md:41 +#: d5321589e7ed4f0db3c630cc39800791 +msgid "Rename an Input File" +msgstr "" + +#: ../../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 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 +#: 1c6b8a4194a14611b4061b1540c3807f +msgid "Rename an Output File" +msgstr "" + +#: ../../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 +#: 7225a993d281421b95c8e3df2846a0e3 +msgid "Referencing a Local Script" +msgstr "" + +#: ../../src/faq.md:84 +#: 7ef1dbb81993473f948d9c6f3c64b381 +msgid "There are two ways to reference a local script:" +msgstr "" + +#: ../../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 +#: 1a8cc75ea6174b9297871b2e58971077 +msgid "Start with adding a _shebang_ at the top of your file:" +msgstr "" + +#: ../../src/faq.md:95 +#: a7d84f740a714ec588503ee084fbbc34 +msgid "After that, make the script executable with the command `chmod +x scriptname.sh`" +msgstr "" + +#: ../../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 +#: 95f5dbbd21084a318413b9528fb867be +msgid "Now you can use `baseCommand: scriptname.sh` to run the script directly." +msgstr "" + +#: ../../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 +#: 8d86baa239364f799d4f9d5ea2b0e314 +msgid "The second method involves including an input of `type: File` in the script itself:" +msgstr "" + +#: ../../src/faq.md:135 +#: f2c109998c76434893ff16b17fdb2bd0 +msgid "In CWL, everything must be directly stated." +msgstr "" + +#: ../../src/faq.md:138 +#: c2c752b86bf94d6fb3751f4dd81bc7a7 +msgid "Setting `self`-based Input Bindings for Optional Inputs" +msgstr "" + +#: ../../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 +#: ce6db54bd0f54839a5beb948530a21f0 +msgid "Model a \"one-or-the-other\" Parameter" +msgstr "" + +#: ../../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 +#: d53fb28dcad04e7788cba9e280a2343c +msgid "Connect a Solo Value to an Input that Expects an Array of that Type" +msgstr "" + +#: ../../src/faq.md:190 +#: 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 +#: 941077158ec54ae19bfa2e2ad6662da1 +msgid "merge_nested" +msgstr "" + +#: ../../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 +#: a1d57e15656548128a76a8b975c564c9 +msgid "Which means \"create a list with exactly these sources as elements\"" +msgstr "" + +#: ../../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 `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 +#: 3da4dcb043eb4423a53a14182949d9cd +msgid "Optional Inputs 💯" +msgstr "" + +#: ../../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 +#: a854006054ce4ffe94bbfa73bdbecbf2 +msgid "" +msgstr "" + +#: ../../src/faq.md:248 +#: f80eb714e9df417fbba555b5dd5f4d8c +msgid "Enum Inputs ⚜️" +msgstr "" + +#: ../../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 form style. It does the same thing as the question mark on the other inputs.**" +msgstr "" + +#: ../../src/faq.md:267 +#: ad1c26711ccd4efd8fdb25f9293d33fd +msgid "" +msgstr "" + +#: ../../src/faq.md:268 +#: 49e2095b51f84f609f5d4bc088ad9745 +msgid "Record Inputs 📀" +msgstr "" + +#: ../../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 +#: f96c9257e3734b8aa0cc5e065f74f944 +msgid "Setting Mutually Exclusive Parameters" +msgstr "" + +#: ../../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 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 +#: b53dc77466b24a67b52b8aadf4fab724 +msgid "Setting Booleans" +msgstr "" + +#: ../../src/faq.md:344 +#: cf4e7f3977ae4f9b877072c2b1c4b533 +msgid "These can be set by using the default field" +msgstr "" + +#: ../../src/faq.md:349 +#: 99b37739ef18443ca7c0e715a131e0c7 +msgid "Concatenating Strings in Inputs" +msgstr "" + +#: ../../src/faq.md:351 +#: 9b00b5a55ee941e1adbfe89e133791e3 +msgid "The valueFrom field must be used instead of default." +msgstr "" + +#: ../../src/faq.md:359 +#: 07922147f7ab487ba2a1e7c43c9f410c +msgid "`cwltool` Errors due to Filenames with Space Characters Inside" +msgstr "" + +#: ../../src/faq.md:361 +#: 7a11806f0c7045b48fe58a271f814797 +msgid "`cwltool` does not allow some characters in filenames by default." +msgstr "" + +#: ../../src/faq.md:363 +#: fdaec25650ab4b0fb1c527610e24ae5a +msgid "For example, the filename `a space is here.txt` includes 3 space characters." +msgstr "" + +#: ../../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 +#: cc7752e9989e4a6d957682f479d6fc60 +msgid "CWL Parameter Reference Error due to Hyphen in Input Identifier" +msgstr "" + +#: ../../src/faq.md:375 +#: 6db1ebd2d6c74ceca889662cd7df5cd5 +msgid "If `cwltool --validate` returns valid" +msgstr "" + +#: ../../src/faq.md:384 +#: 3de2513c7d7b4569ba63f7e6d29137b7 +msgid "But executing it causes an error like:" +msgstr "" + +#: ../../src/faq.md:396 +#: ae3a9188706649e28f97bc4ec34c0821 +msgid "The file is here" +msgstr "" + +#: ../../src/faq.md:410 +#: e1ac97ab6ad3449b8c54933d25257f73 +msgid "Problem caused by `-` (hyphen character)." +msgstr "" + +#: ../../src/faq.md:423 +#: f6c402f7f6974edbbb5582c8e22f3869 +msgid "To fix this error, change `-` (hyphen) to `_` (underscore)" +msgstr "" + +#: ../../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 +#: 06a4f6ffc2da4d43b453d4784b42efd3 +msgid "Use CWL and cwltool with Singularity" +msgstr "" + +#: ../../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 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 +#: 2d498470524d47f18f9936ace6acebb0 +msgid "Debug JavaScript Expressions" +msgstr "" + +#: ../../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 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 +#: 2754519265eb426b940bbbd2b8d64e1e +msgid "Common Workflow Language User Guide" +msgstr "" + +#: ../../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 +#: 132d40fee3b84469afa80d5ff613bf77 +msgid "Contributions and Feedback are Welcome!" +msgstr "" + +#: ../../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 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 +#: 6d269e8d70184034bcb56385a6ca198f +msgid "Navigating the User Guide" +msgstr "" + +#: ../../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 subsections of the [Topics](/topics/index.md) have detailed information about the most common topics for CWL." +msgstr "" + +#: ../../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 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 +#: ee6b82bd86264e4bb1e8e4065b1e6b9c +msgid "Table of Contents" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:1 +#: e208c8a7506e41dcac9a403c5d2850c1 +msgid "Basic Concepts" +msgstr "" + +#: ../../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 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 +#: 984e6676b9d04c7092bc492f195dfb91 +msgid "The CWL Specification" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: b3df1607e9d242d78b22dc44335fbe2d +msgid "Implementations" +msgstr "" + +#: ../../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. 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 +#: 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 +#: 2482c84831fc4dfab629e7bfcfb41cbf +msgid "CWL specification, implementations, and other tools." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:105 +#: a5ebc727fb3443f78e81d6b7ed5ac750 +msgid "Processes and Requirements" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:107 +#: 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 +#: 8c9772f96caf4169924d22eb929a4f0f +msgid "A command-line tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:113 +#: 4fac209a62114798b79e4810f7a0148b +msgid "An expression tool." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:114 +#: b97ba368fd664caab0494e2392795697 +msgid "An operation." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:115 +#: 903a6796e3304a19ad885b2428b0e80f +msgid "A workflow." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:118 +#: 6e352ac1f8e144c392ac5adf18c28298 +msgid "The processing units available in the CWL objects model." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:119 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: cc6cd8cb81564cadb8e6a4c49423b7f7 +msgid "`InlineJavascriptWorkflow` - enables JavaScript in expressions." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:142 +#: 2d9f53b6ed5041dbb6c0b54835897856 +msgid "`SubworkflowFeatureRequirement` - enables nested workflows." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:143 +#: 907674a4ecff4826a2b880e28fc38f33 +msgid "`InitialWorkDirRequirement` - controls staging files in the input directory." +msgstr "" + +#: ../../src/introduction/basic-concepts.md:145 +#: 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 +#: 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 +#: c4c3315c96714e81b364f8cc003b87e6 +msgid "FAIR Workflows" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:157 +#: 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 +#: 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 +#: 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 +#: 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 +#: 65c24244713741e196da08cb9ba237b2 +#: f059896039524095b4deb65d693f8ddf +#: 3439764fab0e49d2bcb7c9fbae556e65 +msgid "Learn More" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:180 +#: 9d5100c7d0a040aea1020bf633ad17de +msgid "Semantic Versioning - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:181 +#: 36eb4b3b966640af90faa55db3789cb6 +msgid "The CWL Specification page in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:182 +#: 2ccb956baa6b4376a04ad9fcc4654631 +msgid "The current CWL specification on GitHub: {{ ''.format(cwl_version_text) }}" +msgstr "" + +#: ../../src/introduction/basic-concepts.md:183 +#: 72889b830c514afe9a7cb1e64b5666a0 +msgid "The list of Implementations in the CWL website: " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:184 +#: e29bd7f973544600be589c3b3f84cf63 +msgid "PROV-O: The PROV Ontology - " +msgstr "" + +#: ../../src/introduction/basic-concepts.md:185 +#: c377a7f5dbe645cebbb6c7eccf831a0b +msgid "CWL Operations are covered in the [Operations](../topics/operations.md) section of this user guide." +msgstr "" + +#: ../../src/introduction/index.md:1 +#: 1769a0cbf4de4d77879c1f202cd11af9 +msgid "Introduction" +msgstr "" + +#: ../../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 +#: f01faaf1b253407cbbc2f353c24774f3 +msgid "Prerequisites" +msgstr "" + +#: ../../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 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 +#: b5a0607096814c0aa577f977c3b57c54 +msgid "CWL Implementations" +msgstr "" + +#: ../../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 engines. We have a better explanation in the [Implementations](basic-concepts.md#implementations) section." +msgstr "" + +#: ../../src/introduction/prerequisites.md:19 +#: cbbcce4c2a96471b8b0ae3593ad59de4 +msgid "Operating System" +msgstr "" + +#: ../../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 +#: dbaa4bae22fe4d05b18d7351967ddbc3 +msgid "Linux" +msgstr "" + +#: ../../src/introduction/prerequisites.md:25 +#: c05187af85be41b782678b79627f8fbf +msgid "macOS" +msgstr "" + +#: ../../src/introduction/prerequisites.md:26 +#: beb6cf4d7c154eb9b6d7fe024a318ed7 +msgid "Windows" +msgstr "" + +#: ../../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) (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 +#: 56d78c95daa54135b6aa9b2bfdc34d01 +msgid "CWL Runner" +msgstr "" + +#: ../../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 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 +#: 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 +#: 0a0f0e5151ab4c498b4f8a12c016f28d +msgid "Installing `cwltool` with `pip` and `venv`." +msgstr "" + +#: ../../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 +#: 5eced7e4cd084e8a806b1d3b12d0c000 +msgid "Let's use a simple CWL tool description `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:67 +#: 040c019b6e844eda8c8c2b210852516b +msgid "`true.cwl`" +msgstr "" + +#: ../../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 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 +#: cdef47fca304479c9a9df75afc0afb35 +msgid "Validating `true.cwl` with `cwltool`." +msgstr "" + +#: ../../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 +#: 24d7be55d3994f0b82c38da47918e0c9 +msgid "Running `true.cwl` with `cwltool`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:91 +#: 39d6ceecb54a4a7fb5dff4a7cae1bfe7 +msgid "Cwl-runner Python Module" +msgstr "" + +#: ../../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 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 +#: 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 +#: 71ebe91d4bda473abe87578929433212 +msgid "Installing `cwl-runner` alias for cwltool with `pip`." +msgstr "" + +#: ../../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 +#: b9cc5a843a0f49daad56e9303657bdd5 +msgid "Validating `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../src/introduction/prerequisites.md:120 +#: 34ab40437ab646488ba3ee86cd7fe071 +msgid "Running `true.cwl` with `cwl-runner`." +msgstr "" + +#: ../../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 new file: `true_shebang.cwl`, and include a special first line, a *shebang*:" +msgstr "" + +#: ../../src/introduction/prerequisites.md:129 +#: f74dd9bd4ff84bf48f3f8e8c8d6fb51a +msgid "`true_shebang.cwl`" +msgstr "" + +#: ../../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 +#: bf8be77af6154326b28442c5d2e2b852 +msgid "Making `true.cwl` executable." +msgstr "" + +#: ../../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 +#: 7c4f45b3e7b549e186126693aa4a3d4f +msgid "Running `true_shebang.cwl` with a shebang." +msgstr "" + +#: ../../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 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 +#: eec6c07455384630809ff1c532bfe7d4 +msgid "Text Editor" +msgstr "" + +#: ../../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 +#: 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 +#: 1f07135156254f74a6b043bf33d00cc3 +msgid "Visual Studio Code with the Benten (CWL) plugin - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:172 +#: de344f356b1c466d9131cdbd4d7353a3 +msgid "cwl-plugin for IntelliJ - " +msgstr "" + +#: ../../src/introduction/prerequisites.md:174 +#: 3f9324ede11441f58d93875867034cf0 +msgid "The CWL community also maintains a list of editors and viewers: " +msgstr "" + +#: ../../src/introduction/prerequisites.md:177 +#: 6ce8b81560e341c580d316d69202b268 +msgid "Docker" +msgstr "" + +#: ../../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 documentation to install it for your operating system: ." +msgstr "" + +#: ../../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 examples, and to clarify the differences between the execution models with and without containers." +msgstr "" + +#: ../../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 +#: 9390b03889de44638141d705e0ef8322 +msgid "The [Implementations](basic-concepts.md#implementations) topic in the next section, Basic Concepts." +msgstr "" + +#: ../../src/introduction/prerequisites.md:199 +#: 12042e411482458f8c35a2491f9433e0 +msgid "The Python `venv` module: " +msgstr "" + +#: ../../src/introduction/quick-start.md:1 +#: cdd4196f9aa34beba115901ec97913b6 +msgid "Quick Start" +msgstr "" + +#: ../../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 +#: 280936bb2a22469799b2c9e9ba22adee +msgid "“Hello World”" +msgstr "" + +#: ../../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 +#: 9e51962a7e5c47248f3e20703ae101eb +msgid "`hello_world.cwl`" +msgstr "" + +#: ../../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 +#: 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 +#: 498a43362a4749f3b8b433709d34a1d5 +msgid "Installing a CWL Runner" +msgstr "" + +#: ../../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 the latest version of the specification: {{ cwl_version }}. You can install `cwltool` using `pip`:" +msgstr "" + +#: ../../src/introduction/quick-start.md:39 +#: 81481f5b82e4488398f87f0a169bd359 +msgid "Installing `cwltool` with `pip`." +msgstr "" + +#: ../../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 `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 +#: c12cf89f8b9a421ebd05330326e219b3 +msgid "Running \"Hello World\"" +msgstr "" + +#: ../../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 +#: ce04027dfcfe4b7b91ea3c2136b18b23 +msgid "Running `hello_world.cwl` with `cwltool`." +msgstr "" + +#: ../../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 +#: 6d0b679efab24813a7a3b709ade940d1 +msgid "Running `hello_world.cwl` with `cwltool` passing an input parameter." +msgstr "" + +#: ../../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 corresponding values. The Inputs Objects file can be written in JSON or YAML. For example:" +msgstr "" + +#: ../../src/introduction/quick-start.md:74 +#: 1a44a545434b448aa956005deeed90a8 +msgid "`hello_world-job.json`" +msgstr "" + +#: ../../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 +#: d4cdbe870a6f4a68b542ca719d989062 +msgid "Passing an Inputs Object file to `cwltool`." +msgstr "" + +#: ../../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 it is not a requirement. You can choose any name for your workflows and Inputs Object files." +msgstr "" + +#: ../../src/introduction/quick-start.md:96 +#: 5535b98e8b1342f09f003ec6db2b44b1 +msgid "Continue reading the next sections of this User Guide!" +msgstr "" + +#: ../../src/introduction/quick-start.md:97 +#: 77e43c7117fd4c52b140f0dd52cc3963 +msgid "[List of CWL Implementations](https://www.commonwl.org/implementations)." +msgstr "" + +#: ../../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 +#: 176d8d47830f4031bb95dc231ebf1303 +msgid "[Common Workflow Language at Wikipedia](https://en.wikipedia.org/wiki/Common_Workflow_Language)." +msgstr "" + +#: ../../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 +#: d039a9d6461c44628d4660c00d9ce6ff +msgid "The {{'[CWL Specification VERSION](https://www.commonwl.org/VERSION)'.replace('VERSION', cwl_version_text) }}." +msgstr "" + +#: ../../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 +#: 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 +#: 9c87c76c690948ac8e18088a0fffe679 +msgid "Additional Arguments and Parameters" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:3 +#: 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 +#: 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 +#: a74935dc31664e979ca8f90a6a4ba53c +msgid "`arguments.cwl`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:19 +#: ../../src/topics/staging-input-files.md:15 +#: 0a8065edd8af4eaea08989a1060ce48f +#: f357755f6dcb4971bade8636064f8dd1 +msgid "`arguments-job.yml`" +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:24 +#: 6359191b4f684d5aa3602e4aaf394883 +msgid "Next, create a sample Java file to use with the command-line tool." +msgstr "" + +#: ../../src/topics/additional-arguments-and-parameters.md:30 +#: 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 +#: 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 +#: 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 +#: 612c4a66c36a43d4ac5d74c1757d6845 +msgid "Best Practices" +msgstr "" + +#: ../../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 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 +#: 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 +#: 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 +#: 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 +#: b651f80f47b4442fbf29454a233697fc +msgid "Useful reading: \"[A Quick Guide to Software Licensing for the Scientist-Programmer][sci-license]\"" +msgstr "" + +#: ../../src/topics/best-practices.md:28 +#: 263a127a77cf4c41af76854f22f1f260 +msgid "_Example of metadata field for license with SPDX identifier:_" +msgstr "" + +#: ../../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 +#: 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 +#: e24cb13d98014e558b6a6946758359e0 +msgid "In tool descriptions, list dependencies using short name(s) under `SoftwareRequirement`." +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 1ac4c3d8c3e44bd1af3fc5df70051926 +msgid "Custom types should be defined with one external YAML per type definition for re-use." +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 3f4e98f6bfa141feba8c4b120e3d03e8 +msgid "Command Line Tool" +msgstr "" + +#: ../../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`, `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 +#: 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 +#: abb83f0097654a43bd78639d3dbb2bc8 +msgid "CWL command-line tool." +msgstr "" + +#: ../../src/topics/command-line-tool.md:50 +#: 3b1a9ae3412f4d6e96a39b9a16934232 +msgid "`echo.cwl`" +msgstr "" + +#: ../../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 +#: 1849b8f3ae1c4a84ae59a78ffd6b371e +msgid "Network Access" +msgstr "" + +#: ../../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 +#: 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 +#: a2a0f0eb0f404eb3aaf19cfd3cdb559b +msgid "Creating Files at Runtime" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:3 +#: 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 +#: 2df3a3a9094d4b79b1d5dd99195f3bff +msgid "To generate such files, we can use the `InitialWorkDirRequirement`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:9 +#: d3f74c3b094a427fbec831afab657d50 +msgid "`createfile.cwl`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:15 +#: cfffc518ba6e4ed1a80762ed6f7d25df +msgid "Any [expressions](../topics/expressions.md) like `$(inputs.message)` are expanded by the CWL engine before creating the file. Here, insert the value at the input `message`." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:20 +#: 9454a330b9324744b89448f2694b1b03 +msgid "The _CWL expressions_ are independent of any _shell variables_ used later during command line tool invocation. That means that any genuine need for the character `$` 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 +#: 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 +#: 2d2ef4769b2347e79db827655f1bcdeb +#: 2699fbc4376148af91b7a5a6cdac467c +#: ca03defa3ad14cf698171cb09e3055c1 +msgid "`echo-job.yml`" +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:35 +#: 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 +#: 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 +#: 1741804e33aa43ce88b4320c11ae5973 +msgid "See the [YAML Guide](../topics/yaml-guide.md#maps) for more about the formatting." +msgstr "" + +#: ../../src/topics/creating-files-at-runtime.md:54 +#: ../../src/topics/environment-variables.md:18 +#: ../../src/topics/file-formats.md:52 +#: ../../src/topics/staging-input-files.md:20 +#: ../../src/topics/workflows.md:198 +#: 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 +#: cb34fd4c8cb04053ada491a227651048 +msgid "Custom Types" +msgstr "" + +#: ../../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 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 +#: 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 +#: ef5f35acb97f4ddfad7b688712f53484 +msgid "`custom-types.cwl`" +msgstr "" + +#: ../../src/topics/custom-types.md:18 +#: 7015dfa99a6f4cfb87ebf0ed61e8043c +msgid "`custom-types.yml`" +msgstr "" + +#: ../../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-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 +#: 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 +#: 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 +#: b0a4df0fd3ca42338cff4689235dcf4e +msgid "The contents of the YAML file describing the custom type are given below:" +msgstr "" + +#: ../../src/topics/custom-types.md:55 +#: fecfbb44456640d8ba05e519bf2ff564 +msgid "`biom-convert-table.yaml`" +msgstr "" + +#: ../../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 `requirements:SchemaDefRequirement`, as below in the example `custom-types.cwl` description:" +msgstr "" + +#: ../../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 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 +#: 59014808cbef4c02aaef03129d8a29b0 +msgid "Environment Variables" +msgstr "" + +#: ../../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 +#: bfdebb32440a4034beb42135e38884e8 +msgid "`env.cwl`" +msgstr "" + +#: ../../src/topics/expression-tool.md:1 +#: 777d4a52f7554eff84db2df6d4d0f729 +msgid "Expression Tool" +msgstr "" + +#: ../../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 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 +#: 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 +#: b63e6f5a2e89431c8fc7d04f47fd69fe +msgid "CWL expression tool." +msgstr "" + +#: ../../src/topics/expression-tool.md:48 +#: 39727e9058f24b62b8746a46d3f812c2 +msgid "`uppercase.cwl`" +msgstr "" + +#: ../../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 +#: c8d648b765ec499a8e9c464590838492 +msgid "Expressions" +msgstr "" + +#: ../../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 legal you can provide a fragment of Javascript that will be evaluated by the CWL runner." +msgstr "" + +#: ../../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 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 +#: 7fdbfd1c937b4991bf4a2fa26ea310e4 +msgid "`expression.cwl`" +msgstr "" + +#: ../../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 +#: e833649b951841c49397796f996d29f3 +msgid "`empty.yml`" +msgstr "" + +#: ../../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 +#: ebf399ea4d5f47b9be03e24f04c69f2d +msgid "We can then run `expression.cwl`:" +msgstr "" + +#: ../../src/topics/expressions.md:37 +#: 65e0cdd505b944caa40f65e612cdddfc +msgid "Running `expression.cwl`" +msgstr "" + +#: ../../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 +#: 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 +#: d957f55a6377422c9834f85d45e35009 +msgid "Where are JavaScript expressions allowed?" +msgstr "" + +#: ../../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 +#: 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 +#: 1acb064f7a4a482aa0174bdc847c6382 +#: 0222780b98ac48e89b1b4f57c9df8590 +msgid "`arguments`" +msgstr "" + +#: ../../src/topics/expressions.md:68 +#: ../../src/topics/expressions.md:76 +#: ../../src/topics/expressions.md:89 +#: ../../src/topics/parameter-references.md:65 +#: ../../src/topics/parameter-references.md:73 +#: ../../src/topics/parameter-references.md:86 +#: ef2b8433778a40408f179c3e6f0cf99e +#: 224732683a9c41f3ba1b778851e745a8 +#: 17b10d1e91b24dc582df98fcd2ac850e +#: ffd3ca1f97cf4d3a892ef4f4b04771e4 +#: e4e68011dc5f42e4918c747afa7d764b +#: d44e3cfa661840eb851782e24caf1b68 +msgid "`valueFrom`" +msgstr "" + +#: ../../src/topics/expressions.md:69 +#: ../../src/topics/parameter-references.md:66 +#: 0bddedfe40e841f7878e09792531e6bf +#: 17ac6d2c703b466f9720b7489209a2ff +msgid "`stdin`" +msgstr "" + +#: ../../src/topics/expressions.md:70 +#: ../../src/topics/parameter-references.md:67 +#: 58a6510ef69a4c51a4ea348cd98ef0d2 +#: a11d0de5ac6a4a6d9afe0e34823e3b45 +msgid "`stdout`" +msgstr "" + +#: ../../src/topics/expressions.md:71 +#: ../../src/topics/parameter-references.md:68 +#: 2437656e20354d63bede1b98d5348e2c +#: 37392218309d4baebe62fc38bf50efe9 +msgid "`stderr`" +msgstr "" + +#: ../../src/topics/expressions.md:72 +#: 8210b36347a749889450529ecdf4ff0e +msgid "From [CommandInputParameter](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandInputParameter)" +msgstr "" + +#: ../../src/topics/expressions.md:73 +#: ../../src/topics/expressions.md:78 +#: ../../src/topics/expressions.md:85 +#: ../../src/topics/expressions.md:93 +#: ../../src/topics/parameter-references.md:70 +#: ../../src/topics/parameter-references.md:75 +#: ../../src/topics/parameter-references.md:82 +#: ../../src/topics/parameter-references.md:90 +#: d0a92a3792b549e9b5ddce4667d168d2 +#: 801729c7c71b4109824b035437e69bf9 +#: 1bc510d525f0414e88692e356e67fbbc +#: d2e246ae56a24e4abdd6b7d9812a86e2 +#: b1446bab2732412e91f721a08067b0bd +#: e89dbeb22f41430ca39c923d9fdf68cb +#: bd61499b71e64164878dea08d6d7141e +#: ed875a006df64f9e8a55fa5e9fa87404 +msgid "`format`" +msgstr "" + +#: ../../src/topics/expressions.md:74 +#: ../../src/topics/expressions.md:79 +#: ../../src/topics/expressions.md:86 +#: ../../src/topics/expressions.md:94 +#: ../../src/topics/parameter-references.md:71 +#: ../../src/topics/parameter-references.md:76 +#: ../../src/topics/parameter-references.md:83 +#: ../../src/topics/parameter-references.md:91 +#: 8a1748579de14f0888d5ee9023e37c2d +#: f760465a49d64d4c8468ad9c4fea62b1 +#: 28b6b5ffa7524374aaa9525ebfafb762 +#: d11f6a19ddf34cf19ec856bacf998e29 +#: bcb7cd10cb5947bb9d85c040f57f954f +#: da5188d3bedc4997a35bdf417f2f643c +#: cd7a0190511d4613b09600a3b1e9d55f +#: 47def3b078e2402182039be0227090ae +msgid "`secondaryFiles`" +msgstr "" + +#: ../../src/topics/expressions.md:75 +#: 23088850ad02459696f6bbd385109aac +msgid "From [`inputBinding`](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../src/topics/expressions.md:77 +#: f02257a822ad46ac93c5981531cc85d5 +msgid "From [CommandOutputParamater](https://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputParameter)" +msgstr "" + +#: ../../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 +#: 582b03ac742745a89f4dfc86b7404db2 +#: d193ce0123db4535a4f0b11405ad0322 +msgid "`glob`" +msgstr "" + +#: ../../src/topics/expressions.md:82 +#: ../../src/topics/parameter-references.md:79 +#: d555a3d991e344a5a8e1289168d7c6d1 +#: 44b3f123c9b04a308c1161b742a7b34b +msgid "`outputEval`" +msgstr "" + +#: ../../src/topics/expressions.md:83 +#: ../../src/topics/parameter-references.md:80 +#: e9fa9430535c424fa3e8be5d460d2ba4 +#: 0e306cc923974d1db83fdfb45105a11c +msgid "From `Workflow`" +msgstr "" + +#: ../../src/topics/expressions.md:84 +#: 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 +#: b0290d1a477b48119e17cf1fed9d6dff +#: 446f1190af7a40a0913ff04ce7aa938c +msgid "From `steps`" +msgstr "" + +#: ../../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 +#: 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 +#: c2a92d3eca7f4ee39cec649170eeea53 +#: 3c939769ede94602a67fc50c435741cf +msgid "`expression`" +msgstr "" + +#: ../../src/topics/expressions.md:92 +#: 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 +#: 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 +#: 4b73495cf18a4d908525292b6f23c419 +#: d0eec6969d174b258e0f010800884cc6 +msgid "`coresMin`" +msgstr "" + +#: ../../src/topics/expressions.md:97 +#: ../../src/topics/parameter-references.md:94 +#: 718ceee9973240ec9c100977bbcc8921 +#: 2b25152f6df5494a8632f3ce631c20d8 +msgid "`coresMax`" +msgstr "" + +#: ../../src/topics/expressions.md:98 +#: ../../src/topics/parameter-references.md:95 +#: c07ab08eb75d4528949c56a3d7c12b28 +#: 846cd427ae25410eae7c920b237edcb0 +msgid "`ramMin`" +msgstr "" + +#: ../../src/topics/expressions.md:99 +#: ../../src/topics/parameter-references.md:96 +#: 594bc5b7e5be4be9b5e1f6b2502e3bd3 +#: b885e108dced4981a445e5fa0a044394 +msgid "`ramMax`" +msgstr "" + +#: ../../src/topics/expressions.md:100 +#: ../../src/topics/parameter-references.md:97 +#: 700c57ccd5e347be86702c83a8af24b3 +#: e9f5306ae6ea49bbb6801dcce9be2d67 +msgid "`tmpdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:101 +#: ../../src/topics/parameter-references.md:98 +#: 509a5e2ec52d413eb57754d359f133e4 +#: 58bf8016f5f04c26b645025f405e2288 +msgid "`tmpdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:102 +#: ../../src/topics/parameter-references.md:99 +#: 5a60ab5ee19446f8a6f49ab8583101a9 +#: 7c817029d55b4700ae8e84be4d0f0ca0 +msgid "`outdirMin`" +msgstr "" + +#: ../../src/topics/expressions.md:103 +#: ../../src/topics/parameter-references.md:100 +#: 1f39f016524a459895ed03c72d74932b +#: e3b76f42c924489f9a0bcf5a7b636d23 +msgid "`outdirMax`" +msgstr "" + +#: ../../src/topics/expressions.md:104 +#: 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 +#: 9359ef94c41249ea8e76fe629926054e +#: a258554d462f4f5f83ece28d5b2fc584 +msgid "`listing`" +msgstr "" + +#: ../../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 +#: effc0208cf4f4551958db6e526c0528b +#: 9d4889c8cec24351a7a9e3c547e331b6 +msgid "`entry`" +msgstr "" + +#: ../../src/topics/expressions.md:108 +#: ../../src/topics/parameter-references.md:105 +#: be6c1e85c7b6495d8086c262daad20e7 +#: af4f7f232a9d42388c0ba1cfc7c2cdf7 +msgid "`entryname`" +msgstr "" + +#: ../../src/topics/expressions.md:109 +#: ../../src/topics/parameter-references.md:106 +#: 2183ac54ae10428388649daa57b6a7f4 +#: 6abeba392b0444b19f92a19f178a4682 +msgid "From `EnvVarRequirement`" +msgstr "" + +#: ../../src/topics/expressions.md:110 +#: 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 +#: 107b54b832df4d408d1315bdba05b4dd +#: 949c376120d8441796ec9c89364f8851 +msgid "`envValue`" +msgstr "" + +#: ../../src/topics/expressions.md:116 +#: 10d36a1adfd04144b401c993b12b4094 +msgid "Using External Libraries and Inline JavaScript Code with `expressionLib`" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 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 +#: 49d0fda2fc144e0b8b7c92afc1d8945e +msgid "`hello-world-expressionlib-inline.cwl`" +msgstr "" + +#: ../../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 +#: 26c74b11bb1849cea0763bb74ec43e42 +msgid "Running `hello-world-expressionlib-inline.cwl`." +msgstr "" + +#: ../../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 +#: ed590f9e6f4f425da886b110295c45db +msgid "`custom-functions.js`" +msgstr "" + +#: ../../src/topics/expressions.md:164 +#: 093235307d6f47d4858e559b780ef5e5 +msgid "`hello-world-expressionlib-external.cwl`" +msgstr "" + +#: ../../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 +#: 973a9b257b1a4f0dbd4444d4f11dadd7 +msgid "Running `hello-world-expressionlib-external.cwl`." +msgstr "" + +#: ../../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 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 +#: c4098489fbb049789f022cd3e5c3d49b +msgid "`hello-world-expressionlib.cwl`" +msgstr "" + +#: ../../src/topics/expressions.md:193 +#: 5979e4ae5c424276bdbc47f69b379d0f +msgid "Running `hello-world-expressionlib.cwl`." +msgstr "" + +#: ../../src/topics/expressions.md:200 +#: fd4579a3c9844492b314b5c3c1775fc7 +msgid "The `$include` statement can be used to include a file from the local disk or from a remote location. It works with both relative and absolute paths. Read the [text about `$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 +#: 3f038e7371f84ed9b4547358dfb55a11 +msgid "File Formats" +msgstr "" + +#: ../../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 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 +#: 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 +#: 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 +#: 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 +#: 0535d5de416b4ea3b2f5996583deecc1 +msgid "`metadata_example.cwl`" +msgstr "" + +#: ../../src/topics/file-formats.md:26 +#: ../../src/topics/metadata-and-authorship.md:22 +#: f558bcf2a993482195cd418b37761809 +#: fb47f73c38cf4ec59bd3021866a631f8 +msgid "The equivalent of this CWL description in command line format is:" +msgstr "" + +#: ../../src/topics/file-formats.md:32 +#: 74b28c1b09c6429b82e462e4ec61808e +msgid "Sample Parameter Files" +msgstr "" + +#: ../../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. This allows others to quickly work with your tool, starting from a \"known good\" parameterization." +msgstr "" + +#: ../../src/topics/file-formats.md:39 +#: aebee48b742c4145a600fd2daf8c75dc +msgid "`sample.yml`" +msgstr "" + +#: ../../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 and can be downloaded e.g. via `wget`:" +msgstr "" + +#: ../../src/topics/index.md:1 +#: 8d3a6d83e2e54c56995893c41590b7ff +msgid "Topics" +msgstr "" + +#: ../../src/topics/inputs.md:1 +#: 5abcdebfa1cb401bb8892553be285fd3 +msgid "Inputs" +msgstr "" + +#: ../../src/topics/inputs.md:3 +#: d3a55f71dc244026a97902de9ed819ea +msgid "Essential Input Parameters" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: cd9cea15f57b492ba4098237cd7c5bed +msgid "First, create a file called `inp.cwl`, containing the following:" +msgstr "" + +#: ../../src/topics/inputs.md:18 +#: 8bdb875b63104f699efe28ea0abb1e3d +msgid "`inp.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:24 +#: c6a0151a68494c0cb0176781e65e252e +msgid "Create a file called `inp-job.yml`:" +msgstr "" + +#: ../../src/topics/inputs.md:26 +#: dc5e6b5e01d64226bd5dbbf3175fe010 +msgid "`inp-job.yml`" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 651e032007ea4a119d20c820bb61f86b +msgid "Next, create a whale.txt using [touch] by typing `touch whale.txt` on the command line." +msgstr "" + +#: ../../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 following boxed text describes these two commands and the expected output from the command line:" +msgstr "" + +#: ../../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 that the tools aren't accidentally accessing files that were not explicitly specified" +msgstr "" + +#: ../../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 `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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 6812698e9ad84d3385de5e88e9dde0b3 +msgid "The `baseCommand` field will always appear in the final command line before the parameters." +msgstr "" + +#: ../../src/topics/inputs.md:146 +#: 9654e65b1c0642dbb5d4f34edb211989 +msgid "Array Inputs" +msgstr "" + +#: ../../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 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 +#: 01f30e38dfdd452dba3a996073936e16 +msgid "`array-inputs.cwl`" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 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 +#: 5d7d7a28cc5d4862803032aec78174d9 +msgid "Inclusive and Exclusive Inputs" +msgstr "" + +#: ../../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 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 +#: ddf598abf4f34aca9fffa045860fbf96 +msgid "`record.cwl`" +msgstr "" + +#: ../../src/topics/inputs.md:204 +#: d52a8089920e45bd89d582533b50e3a1 +msgid "`record-job1.yml`" +msgstr "" + +#: ../../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 +#: 9a5cf1d76fc84c1f9b0d123a3a2a480b +msgid "`record-job2.yml`" +msgstr "" + +#: ../../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 +#: bc21ee10bff843689cc98ac6630edcea +msgid "`record-job3.yml`" +msgstr "" + +#: ../../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 +#: b771302d1bec4050a9417b080eef76c9 +msgid "Exclusive Input Parameters with Expressions" +msgstr "" + +#: ../../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 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 +#: 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 +#: 4a31c733092142b1af834eab1747c224 +msgid "`exclusive-parameter-expressions.cwl`" +msgstr "" + +#: ../../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 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 +#: 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 +#: 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 `$(inputs.file_format || 'auto')`, to have a default value if none was provided in the command line or job input file." +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:1 +#: d33aa2353ad44fb885d3a1ee48263dc4 +msgid "Metadata and Authorship" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:3 +#: cd64d2d828834cbbb24ea5358caf5405 +msgid "Implementation extensions not required for correct execution (for example, fields related to GUI presentation) and metadata about the tool or workflow itself (for example, authorship for use in citations) may be provided as additional fields on any object. Such extensions fields (e.g. `format: edam:format_2572`) can use a namespace prefix listed in the `$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 +#: 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 +#: 0d5200bbbfdc43e6a78b4e4c3096ebd7 +msgid "`metadata_example2.cwl`" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:28 +#: d402bf528c7f4eb69aaaa275be2bf1d4 +msgid "Extended Example" +msgstr "" + +#: ../../src/topics/metadata-and-authorship.md:30 +#: 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 +#: 2dfbd4d580044ed083992f3ceb1bc64e +msgid "`metadata_example3.cwl`" +msgstr "" + +#: ../../src/topics/operations.md:1 +#: 8acf361cf77c4d45ba3f2e344146259f +msgid "Operations" +msgstr "" + +#: ../../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 specifies inputs and outputs, but it does not provide enough information to be executed." +msgstr "" + +#: ../../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 +#: 49cf614893d8438299b3bca384eb40cf +msgid "`operations.cwl`" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 98d9b8d867594543890af99e77e24edb +msgid "`cwltool` does not know how to run operations" +msgstr "" + +#: ../../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 +#: da077da5eb8a4ffebfde041fc16300de +msgid "Outputs" +msgstr "" + +#: ../../src/topics/outputs.md:3 +#: 1b3016f0462f42deb42ddaa33f28bf3d +msgid "Returning Output Files" +msgstr "" + +#: ../../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 of parameter, and `type` describing what types of values are valid for that parameter." +msgstr "" + +#: ../../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 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 +#: 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 +#: 7e3fa7baf0f549ec89457e7004ac9545 +msgid "Passing mandatory arguments to the `baseCommand`" +msgstr "" + +#: ../../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 _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 +#: f1ee2e00b0cc4112b51c9df3a919b73f +msgid "`tar.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:32 +#: ad8e1acb251246d2a47c39b20d4e483a +msgid "`tar-job.yml`" +msgstr "" + +#: ../../src/topics/outputs.md:38 +#: dc200c6960ae4476a772645d021f14b8 +msgid "Next, create a tar file for the example." +msgstr "" + +#: ../../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 +#: 5e1c79df657d4a6e84e055dd6b300a5d +msgid "The field `outputBinding` describes how to set the value of each output parameter." +msgstr "" + +#: ../../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 +#: 96df2d45e42441d49ce193ccbfab78a3 +msgid "Capturing Standard Output" +msgstr "" + +#: ../../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 +#: 9d86c03ab44841c785b924cc44727e31 +msgid "`stdout.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:89 +#: 2fb58c2feaa84970bb5274c49f4b5b64 +msgid "Array Outputs" +msgstr "" + +#: ../../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 +#: b9eaf21f5e014eefaae301c47dafd144 +msgid "`array-outputs.cwl`" +msgstr "" + +#: ../../src/topics/outputs.md:99 +#: cffff6c43b4945daa3b2a49763bc50ae +msgid "`array-outputs-job.yml`" +msgstr "" + +#: ../../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 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 +#: a190a6440ec34898990cdac05d809f22 +msgid "Parameter References" +msgstr "" + +#: ../../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 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 +#: 280f1a07d0ae41d7a4674504f832fcf0 +msgid "`tar-param.cwl`" +msgstr "" + +#: ../../src/topics/parameter-references.md:19 +#: 5c64d938862747cb9fb52515a656ce27 +msgid "`tar-param-job.yml`" +msgstr "" + +#: ../../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 +#: 0290af3e3cbb4b32b0450c8771f3bf95 +msgid "Certain fields permit parameter references which are enclosed in `$(...)`. These are evaluated and replaced with value being referenced." +msgstr "" + +#: ../../src/topics/parameter-references.md:47 +#: b54240bb94f746bba7511633aa969db0 +msgid "References are written using a subset of Javascript syntax. In this example, `$(inputs.extractfile)`, `$(inputs[\"extractfile\"])`, and `$(inputs['extractfile'])` are equivalent." +msgstr "" + +#: ../../src/topics/parameter-references.md:51 +#: 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 +#: 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 +#: cb4ea13f5db84c0da43df3f7f2478d78 +msgid "Where are parameter references allowed?" +msgstr "" + +#: ../../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 +#: 7647e0229a924f988cf02b7812a55c06 +msgid "From [`CommandLineTool`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineTool)" +msgstr "" + +#: ../../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 +#: 5fed4984f6784347b4cbe0630b1dd2c2 +msgid "From [`inputBinding`](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandLineBinding)" +msgstr "" + +#: ../../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 +#: b6250cf6fa8a4a0c94b33302e0decca5 +msgid "From [CommandOutputBinding](http://www.commonwl.org/v1.0/CommandLineTool.html#CommandOutputBinding)" +msgstr "" + +#: ../../src/topics/parameter-references.md:81 +#: 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 +#: b92b516e537a4773ad67b4af586e7a25 +msgid "From [WorkflowStepInput](http://www.commonwl.org/v1.0/Workflow.html#WorkflowStepInput)" +msgstr "" + +#: ../../src/topics/parameter-references.md:89 +#: 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 +#: 2634f989eb304009a8568d70ed42786c +msgid "From [`ResourceRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#ResourceRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:101 +#: 5d8bed66282c408695292ea92a03b2c4 +msgid "From [`InitialWorkDirRequirement`](http://www.commonwl.org/v1.0/CommandLineTool.html#InitialWorkDirRequirement)" +msgstr "" + +#: ../../src/topics/parameter-references.md:103 +#: 958178d1fa8843aaa0541e2bb115cfd4 +msgid "in [Dirent](http://www.commonwl.org/v1.0/CommandLineTool.html#Dirent)" +msgstr "" + +#: ../../src/topics/parameter-references.md:107 +#: 9a6b311ded8d4e43ae635b1b927dbdf2 +msgid "From [EnvironmentDef](http://www.commonwl.org/v1.0/CommandLineTool.html#EnvironmentDef)" +msgstr "" + +#: ../../src/topics/requirements-and-hints.md:5 +#: aac74f957774479a83aab4c6ff1390ae +msgid "Requirements and Hints" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:1 +#: b75d29d1d55d44488338f9689f156855 +msgid "Specifying Software Requirements" +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:3 +#: 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 +#: 82e48b3e3c3f451480cc0b6a529271f6 +msgid "In this example, the software requirement being described is InterProScan version 5.21-60." +msgstr "" + +#: ../../src/topics/specifying-software-requirements.md:25 +#: 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 +#: 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 +#: b85eb83e05e845d7a179f1b1d74db444 +msgid "Staging Input Files" +msgstr "" + +#: ../../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 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 +#: c8159d0cb2ab452a9ce8e8d2adbaaa94 +msgid "`linkfile.cwl`" +msgstr "" + +#: ../../src/topics/troubleshooting.md:1 +#: 0f7508ce59754a7eb230dea6042244c6 +msgid "Troubleshooting" +msgstr "" + +#: ../../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 +#: 1b6b7a75cc754775bf9dd80c0941e8da +msgid "Run `cwltool` with `cachedir`" +msgstr "" + +#: ../../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 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 +#: 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 +#: 0490b1fab86749e49b473949c52bbe8b +msgid "`troubleshooting-wf1.cwl`" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 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 +#: 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 +#: eff5f28ca83c458a9b07faf7a81f7e91 +msgid "Using Containers" +msgstr "" + +#: ../../src/topics/using-containers.md:3 +#: 2e634f3737d04d279ae78ceee4b0a664 +msgid "Running Tools Inside Docker" +msgstr "" + +#: ../../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, 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 +#: 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 +#: 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 +#: 7921a837ee744c5aa9a5bda04b0c8db1 +msgid "`docker.cwl`" +msgstr "" + +#: ../../src/topics/using-containers.md:27 +#: 387e9bc9381a4450af54aff77e4df6a2 +msgid "`docker-job.yml`" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 1a5596243cec4c948d9b6bf0bb12fad0 +msgid "`hello.js`" +msgstr "" + +#: ../../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 +#: 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 +#: 7394e7690f934043af617436b40845f0 +msgid "Workflows" +msgstr "" + +#: ../../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 +#: f228fb7953ea48ed99d89880205f4620 +msgid "CWL workflow." +msgstr "" + +#: ../../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 +#: a913c76d06164fa18718a8a6a7dcf0d6 +msgid "`echo-uppercase.cwl`" +msgstr "" + +#: ../../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 +#: 36618126a4df4326b236ebe2ea42cffa +msgid "`echo-uppercase-single-file.cwl`" +msgstr "" + +#: ../../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. 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 +#: 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 +#: 46cc4859856e4367a9e5e68eecd48b73 +msgid "Writing Workflows" +msgstr "" + +#: ../../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 +#: 55ab007d472f43388e4c77aae8f165e7 +msgid "`1st-workflow.cwl`" +msgstr "" + +#: ../../src/topics/workflows.md:179 +#: ../../src/topics/workflows.md:180 +#: 23af7bd2facf4043b2b1c4373fce15fa +#: 307b6618a92948fca4203ccb497c77e6 +msgid "Visualization of 1st-workflow.cwl" +msgstr "" + +#: ../../src/topics/workflows.md:180 +#: 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 +#: 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 +#: 26c51dcb76364ed780376aecb7cbacda +msgid "`1st-workflow-job.yml`" +msgstr "" + +#: ../../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 +#: 71cb81fa4511495b80422244849979e4 +msgid "What's going on here? Let's break it down:" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: f0b04849253c4693904512ddd7f9ce84 +msgid "Nested Workflows" +msgstr "" + +#: ../../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 workflow can be used as a step in another CWL workflow, if the workflow engine supports the `SubworkflowFeatureRequirement`:" +msgstr "" + +#: ../../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 +#: 49ed137fe996452a8534c68d100db941 +msgid "`nestedworkflows.cwl`" +msgstr "" + +#: ../../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, 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 +#: e87045829b344089ab59dc27063ddd7a +msgid "\"Visualization \"Visualization" +msgstr "" + +#: ../../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 `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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 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 +#: cfa765264a27411ab914de569aa3dac4 +msgid "Scattering Steps" +msgstr "" + +#: ../../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 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 +#: 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 +#: 1e1f4d85fc5f49b5aac5c5b00f77d6fd +msgid "`scatter-workflow.cwl`" +msgstr "" + +#: ../../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 +#: f1cb55fc59824cc18a95fd6dcb32cf4c +msgid "First of all, notice that the main workflow level input here requires an array of strings." +msgstr "" + +#: ../../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 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 +#: 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 +#: 61642a1a4eaa49eaa1fc2ffa7fc99bf2 +msgid "Using the following input file:" +msgstr "" + +#: ../../src/topics/workflows.md:452 +#: 842b926ae34542cb9023021f137b08be +msgid "`scatter-job.yml`" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 242993d42b164ee5abe7ca10d45856de +msgid "`hello_world_to_stdout.cwl`" +msgstr "" + +#: ../../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 +#: e61d93b848184c8e8e573928427b4d0a +msgid "`wc-tool.cwl`" +msgstr "" + +#: ../../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 +#: 99fa96caacaa45cb97aded9a24fcac6d +msgid "`scatter-two-steps.cwl`" +msgstr "" + +#: ../../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 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 +#: 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 +#: 1c9e386922324ec8a59306572c19fb8b +msgid "`scatter-nested-workflow.cwl`" +msgstr "" + +#: ../../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 +#: f7d2827d97db4bf4ab84b5d6621c3b48 +msgid "Conditional Workflows" +msgstr "" + +#: ../../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 +#: 20b9f181420c401d8615c17a10027517 +msgid "`conditional-workflow.cwl`" +msgstr "" + +#: ../../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 +#: 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 +#: 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 +#: 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 +#: 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 +#: 5f09d4d897cf457d80b9a11b8c01747e +msgid "YAML Guide" +msgstr "" + +#: ../../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 +#: c38438fbf9a04e729ec2e3c962435289 +msgid "You can skip this section if you are already comfortable with YAML." +msgstr "" + +#: ../../src/topics/yaml-guide.md:16 +#: fdb9cc750cec43ee962517e637dc5fea +msgid "Contents" +msgstr "" + +#: ../../src/topics/yaml-guide.md:18 +#: 08da9cd8056b4ddd8f5150cc85ba72ee +msgid "[Key-Value Pairs](#key-value-pairs)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:19 +#: b027fc234ed943bbb00d4c6bc03c040a +msgid "[Comments](#comments)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:20 +#: b8befec0d8684638aaa616a659e0100c +msgid "[Maps](#maps)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:21 +#: 4ea28c6f8faf4cc1a5b29fdcf34c5fdc +msgid "[Arrays](#arrays)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:22 +#: 36db4f26b5194e9da5c6a1ed8cb0ad04 +msgid "[JSON Style](#json-style)" +msgstr "" + +#: ../../src/topics/yaml-guide.md:24 +#: 98056c5cfd5640ad9de0679360797cc7 +msgid "Key-Value Pairs" +msgstr "" + +#: ../../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 `:` 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 +#: 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 +#: 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 +#: dcdaadc7dfff4ebc9fef0d5d05b34cc1 +msgid "Comments" +msgstr "" + +#: ../../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 +#: 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 +#: da34c635707345b2a5e85a2fcd30bbaf +msgid "Maps" +msgstr "" + +#: ../../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_, 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 +#: 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 +#: d74321b111d84ae7a515f2f17dd39e23 +msgid "Arrays" +msgstr "" + +#: ../../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) 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 +#: fd64dd818ec64bb6aa9a11586a5747f6 +msgid "and a more complex example combining maps and arrays:" +msgstr "" + +#: ../../src/topics/yaml-guide.md:167 +#: 8c06e542dd4144fa83388d8142552c8d +msgid "JSON Style" +msgstr "" + +#: ../../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 +#: 5ab9ddf613a540a2b8228e37600cc5dc +msgid "and:" +msgstr "" + +#: ../../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 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 +#: f4b8fc8236044fada420def13a02813d +msgid "Reference" +msgstr "" + +#: ../../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 +#: 2203c93f02ac4514a43508ecb98dfcc5 +msgid "Tutorials" +msgstr "" + +#: ../../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 +#: 8a5cd557dab5456bb41cdc24af73b50c +msgid "Beginner Tutorials" +msgstr "" + +#: ../../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 +#: 0abdd85c9b964a4e89ba3d80a6c78d6f +msgid "Advanced Tutorials" +msgstr "" + +#: ../../src/tutorials.md:13 +#: 3cbf1f69a5514fd3bee90e68b201190f +msgid "[Typescript in CWL](https://github.com/umccr/cwl-ica/wiki/TypeScript)" +msgstr "" + +#: ../../src/tutorials.md:15 +#: 68c97a7065634d02956f3f5c1d4eeb9f +msgid "Bioinformatics Tutorials" +msgstr "" + +#: ../../src/tutorials.md:17 +#: a67c7e0eaf4e4d27b3e5db303333a088 +msgid "[rnaseq with CWL](https://arvados.github.io/rnaseq-cwl-training/)" +msgstr "" diff --git a/locales/zh_Hans/LC_MESSAGES/user_guide.po b/locales/zh_Hans/LC_MESSAGES/user_guide.po index e55e61c3..e0316d50 100644 --- a/locales/zh_Hans/LC_MESSAGES/user_guide.po +++ b/locales/zh_Hans/LC_MESSAGES/user_guide.po @@ -9,15 +9,16 @@ msgstr "" "Project-Id-Version: Common Workflow Language User Guide\n" "Report-Msgid-Bugs-To: \n" "POT-Creation-Date: 2023-12-16 11:48+0100\n" -"PO-Revision-Date: 2023-07-05 09:51+0000\n" -"Last-Translator: Michael Crusoe \n" +"PO-Revision-Date: 2024-01-27 01:01+0000\n" +"Last-Translator: Zoë Ma \n" +"Language-Team: Chinese (Simplified) \n" "Language: zh_Hans\n" -"Language-Team: Chinese (Simplified) " -"\n" -"Plural-Forms: nplurals=1; plural=0;\n" "MIME-Version: 1.0\n" "Content-Type: text/plain; charset=utf-8\n" "Content-Transfer-Encoding: 8bit\n" +"Plural-Forms: nplurals=1; plural=0;\n" +"X-Generator: Weblate 5.4-dev\n" "Generated-By: Babel 2.12.1\n" #: ../../LICENSE.md:2 a48279b2231348eea3f7a3b74a6362ac @@ -3397,12 +3398,11 @@ msgid "" "enable these checks with the reference implementation, use the " "[dependency resolvers configuration][dependencies]." msgstr "" -"您的 CWL " -"运行程序有可能支持在运行作业之前，根据提示检查所需软件是否已安装就绪。如果要让参考实现启用这些检查，请使用[依赖项解析配置][dependencies]。" +"您的 CWL 运行程序有可能支持在运行作业前根据提示检查所需软件是否已安装就绪。如" +"果要让参考实现启用此类检查，请使用[依赖项解析配置][dependencies]。" #: ../../src/topics/specifying-software-requirements.md:29 #: 1a8b8aadf1c64e87b8b670e288bc14bc -#, fuzzy 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" @@ -3418,11 +3418,15 @@ msgid "" "preference, are to include the DOI for the main tool citation and the URL" " to the tool." msgstr "" -"除了版本号之外，该工具的唯一资源标识符 (URI) 以 [RRID][rrid] 的形式给出。可以在 [SciCrunch][scicrunch]" -" 注册表中查找具有 RRID 的资源，该注册表提供了一个用于查找、跟踪和一致引用科学资源的门户。如果要将工具指定为 " -"`SoftwareRequirement`，请在 SciCrunch 上搜索该工具并使用在注册表中分配的 RRID。 （按照 [添加资源教程" -"][scicrunch-add-tool] 将工具添加到 SciCrunch）。您可以使用此 RRID 在需求描述的 `specs` " -"字段中引用该工具（通过 [identifiers.org][identifiers]）。其他不错的选择（按优先顺序）包括主要工具引用的 DOI " +"此处我们不仅给出了工具的版本号，还以 [RRID][rrid] " +"的形式给出了该工具的统一资源标识符 (URI) 。查找以 RRID 标识的资源可以使用 " +"[SciCrunch][scicrunch] " +"注册表。该信息门户网站可供查询、跟踪和一致引用科学资源。如果要将工具指定为 " +"[`SoftwareRequirement`](https://w3id.org/cwl/CommandLineTool." +"html#SoftwareRequirement)，请在 SciCrunch 上搜索该工具并使用在注册表中分配的 " +"RRID。 （按照 [添加资源教程][scicrunch-add-tool] 将工具添加到 SciCrunch）。" +"您可以使用此 RRID 在需求描述的 `specs` 字段中引用该工具（通过 [identifiers." +"org][identifiers]）。其他不错的选择（按优先顺序）包括主要工具引用的 DOI " "和工具的 URL。" #: ../../src/topics/staging-input-files.md:1 d10c792550e8498c8ee384d3093da306 @@ -4374,4 +4378,3 @@ msgstr "" #~ " only part that is really new " #~ "is the `dockerRequirement` section." #~ msgstr "" -