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changelog.txt
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changelog.txt
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NEXTFLOW CHANGE-LOG
===================
21.01.1-edge - 15 Jan 2021
- Plugins stability improvements [8d849ec9] [bf093826]
- Charliecloud improvements [2242411a]
- Fix issue of FS discovery with dyn plugin loading [bf5e86df]
- Fix crash on startup when mem reported < 0 [095236b8]
- Fix and stability [e4b8afb5]
- Fix launcher on Java11 [c6b78034]
- Add plugins custom version manager (4 days ago) <Paolo Di Tommaso>
- Improve NF version checking [d33ea642]
- Bump plugins minor upgrade [f91bc21e]
21.01.0-edge - 04 Jan 2021
- Merge plugins feature [d959bfdb]
- Prevent twice access remote scm file [b2798556]
- Fix DAG edges not connected correctly #1486 [cece1161]
- Fix k8s executor must provide cpu resource requests #1570 [6896e923]
- Fix http/ftp read buffer size [a2886baf]
- Add support for OAuth Bearer auth [5823c280]
- Add support for basic auth for http/s file provider [6027fcba]
- Add User-Agent info to httpfs requests [222637de]
- Update CPU and RAM for containers (#1833) [ccf5c8ba]
- Move test containes to quay.io [7db053eb] [773be707] [c10a7f53]
20.12.0-edge - 12 Dec 2020
- Add support for charliecloud container engine #1809
- Fix glitch on K8s task progress update [668434f6]
- Upgrade to groovy 3.0.7 [27056035]
20.11.0-edge - 16 Nov 2020
- Fix Allow nextflow to handle http protocol for Singularity images #1791
- Fix params-file overrides config parameters [b03efcac]
- Fix println failing test #1621 [8c6f0f97] [9d2e5850]
- Let output env variables be optional (#1740) [3fca3655]
- Add stub-run feature #1774 [3de45c22] [e2d6d55b]
- Add overwrite option to trace/time/report/dag features #813 [a0615474]
- Allow nested CLI params #1182 [19ab8a8f] [df6204e3]
- Allow setting google projectId in nextflow config [223b5d6c]
- Make binDir accessible from the executor scope [1405a28f]
20.10.0 - 1 Nov 2020
- Add warning for AWS Batch mem request lower than 4 GB [e9240fc9]
- Fix issue with docker images tagged by SHA #1777
- Add support for Bitbucket tags and branches retrivial [5083066e]
- Add support for Tower client bearer authentication [532282ae]
- Fix Skip FS lock when Conda dir exist #1771
- Add support for Java 15 [b1f48884]
- Fix build with Gradle 6.7 [8d7227f0]
20.09.1-edge - 15 Oct Sep 2020
- Prevent USR1 signal to stop jobs #1753
- Add -main-script cli option [702ff64c]
- Improve Singularity image file caching #1706 [dd92772b]
- Fix unexpected default GLS action flags #1749
- Patch unpexpected error on tower serialization [f922324a]
20.09.0-edge - 23 Sep 2020
- Fix invalid error message on missing process #1719 [fc607f11]
- Deduplicate GS file + parallel up/downloads [29d37083]
- Deduplicate S3 file uploads [0b65d61f]
- Fix issue on GS path composition [276f0ed3]
- Add NXF_PARAMS_FILE env var [2e3c9232]
- Allow configurable container mounts [8dc0adf4]
- Refactor common Bash helper functions [22a0ff34] [502309b7]
- Fix race condition creating FTP file system #1725
- Fix invalid checkWarn method invocation [ba052a02]
- Move makeDigest into build.gradle file [a2b5de8f]
- Add variable NXF_CONFIG_FILE [83365aa3]
- Patch use of GString for fromSra apiKey option [a8b81ada]
- Use repository URL instead of Git clone URL [75a04d90]
- Fix Invalid exception capture for missing config [ce427924]
- Fix podman issue on duplicate mounts [661a40e9]
- Fix FromSra illegal character error [5a86d180]
- Fix Allow custom SCM file location #1657 [a90e66e3]
20.08.1-edge - 2 Sep 2020
- Add variable NXF_CONFIG_FILE [d15edcb8]
20.08.0-edge - 24 Aug 2020
- Merge Groovy3 runtime and support for Java 12/13/14
- Use repository URL instead of Git clone URL [102f8b01]
- Fix Invalid exception capture for missing config [8c7accca]
- Fix podman issue on duplicate mounts #1710 [d0cc38de]
- Fix FromSra illegal character error #1700 [a45decfb]
- Fix Allow custom SCM file location #1657 [7c27f895]
- Fix dynamic executors loading [7b9ce82f]
- Fix missing newline on cmd log stdout/err #1705 [1416a388]
- Fix k8s timeline start #1687 [24dff871]
- Remove unneeded parentheses from stdout declaration [dc029c04]
- Merge execution logs command docs [577ec744]
- Passing exact memory to TES executor in GiB #1696 [c8a15545]
- Improve docs replacing suscribe{println it} with view() [f84ccb6f] [cb2d607d]
- Use current environment Bash #1598 #1614 [e70ef87a]
- Include GA4GH support into the standalone binary (make pack) #1666 [e2175d45]
- Update Bitbucket docs [b9b57f83]
- Clone/Pull submodules recursively #1615 [5f20ab6a]
- Bump nf-ignite to version 1.1.0
20.07.1 - 24 Jul 2020
- see 20.07.0 and 20.07.0-RC1
20.07.0 - (skipped)
- Allow unqualified stdin/stdout defintions with DSL2 [bcdcaab6]
20.07.0-RC1 - 21 Jul 2020
- Add Dsl2 enable flag [08238109]
- Add check on invalid scope syntax definition [23c92021]
- Add channel as alias for Channel [05c358c9]
- Add DSL2 deprecation + clean up syntax [1b4b1307]
- Add DOI field to NF manifest #1676 [ec6ee223]
- Improve join duplicate detection [33eb9ef5]
- Improve mix operator error message [8074d714]
- Remove invalid log message [48b1b9f1]
- Fix hidden error message on fail fast run [3b4b377c]
- Disallow upwrapped includes + hard deprecation [19130f87]
- Suppress trap for SIGUSR1 signal #1656 [ca5bcf46]
- Improve error reporting on invalid task id [3921de1a]
20.06.0-edge - 5 Jul 2020
- Add more debug logging for AWS helper [2a62fdf7]
- Add join options failOnDuplicate and failOnMismatch [387366aa]
- Add strict mode flag [4ba5ac18]
- Add support for selecting minimum CPU platform on GCP (#1633) [afc4375d]
- Add missing trace fields to docs [bf2e1637]
- Fix Invalid GLS path composition in staging directories #1654 [e33fff98]
- Fix for feature 1647 that allows non gpu k8s accelerator resources. (#1649) [c1efa29d]
- Fix Issue accessing S3 bucket #1596 [ffc6f843]
- Fix Update getDomain method in ProviderConfig to support local repositories - #1492 (#1624) [651501ac]
20.05.0-edge - 31 May 2020
- Add support for NXF_LOG_NAME env var [cf496615]
- Add exception specialiation for ambiguous repo [a34b1d2a]
- Add support for tower_workflow_id env var [53188126]
- Add config profile names accessor [2784cdb8]
- Add support for Google Cloud buckets with Requester Pays set #1466 [bc9db8d8]
- Add Git tag and branch retrieval [7c97f23f]
- Fix PublishDir error caused by duplicates output files [5f3b69c1]
- Fix weird issue on config resolution [0d0fef4b]
- Fix resolution of malformed configs [fe213e41]
- Fix K8s labels and annotation normalization [6434b9d] #1577 #1584
- Fix minor git path provider ending slash [9888be29]
- Fix bugs in GA4GH TES support (#1589) [26708335]
20.04.1-edge - 19 Apr 2020
- Fix AWS auth with temporary security token [6a7b11b8]
20.04.0-edge - 13 Apr 2020
- Add SGE hr status handling (#1558) [f4db0049]
- Add moduleDir, projectDir and launchDir vars [7832a697] [576a5694]
- Add executor display name rendering [74c90ca9]
- Add ability to pipe custom fun [DSL2] [80bb6485]
- Add Aws Batch container image validation [e73951fa]
- Recognizes more UGE states (#1536) [4dacebbf]
- Prevent invalid process tag values [f2da1357]
- Report Tower backend error cause on failure [da8ac8f5]
- Fix Config cmd should resolve remote projects #889 [c2e0ac0b]
- Fix issue applying branch/multiMap to value channel [e69f39fa]
- Fix Kill signal is not propagated for Singularity container #1561
- Fix docs typos [d7261d2e]
- Fix Minor docs update #1545
- Revert "Bump jline 2.14.9" [ef7040cb]
- Deprecate validExitStatus directive #1564
- Improve error message [DSL2] [f8a0ee1c]
- Add sluper parse method for Path [a54fd03d]
- Report error message when accessing invalid out #1553 [83bd009c]
- Remove deprecated $ config syntax [0a31f9df]
- Remove deprecated workflow publish [DSL2] [1bd7b4a4]
- Remove support for workflow 'get' [d9b91149]
- Remove deprecated process output getter [013a323b]
- Remove deprecated out cardinal getters [414fae94]
- Remove deprecated gpu directive [f48b2c24]
- Minor executor logging [7f94299b]
- Minor improvement createDirIfNotExists API [34211675]
- Bump groovy 2.5.11
20.03.0-edge - 28 Mar 2020
- Add support for GLS private addr #1545 [a481b42b]
- Add AWS batch job def normalise function [79239f05]
- Fix Escape Singularity env variables #1535 [b651a371]
- Add Local executor file system check [ffc92926]
- Add Launch Id to Tower client [d768d2d1]
- Add workflow progress on completion [aea41f37]
- Remove deprecated onFlowStart method [14f12b5f]
- Minor method visibility change [43bc9697]
- Minor log change [130a963b]
- Fix docs broken link [0a1ec9a9]
- Fix typo CVS -> CSV #1500 [d89281c3]
20.02.0-edge - 29 Feb 2020
- Fix Unable to create AWS helper class warn #1504
- Fix Ansi log flickers when variable-length tags are used #1288
- Fix Directive maxForks may cause execution to hang #1432
- Fix Missing tag in ansi log #1503
- Fix PBSPRO res req should always include cpus #1510
- Deprecate workflow publish 7f315a63
20.01.0 - 12 Feb 2020
- Fix ansi logging and line count [4f5c7187]
- Fix Division by 0 in launcher script with Biocontainers #1488
- Fix Run name validation to 80 chars max #1491
- Add GitHub badge to README
- Add Bash version to issue template [78928546]
- Bump jline 2.14.9 [5df2b27e]
20.01.0-rc1 - 6 Feb 2020
- Add ability to extend module params #1484 [17c6acca]
- Add dsl2 command line opt [1cf544d5]
- Add GLS executor docs [574f2098] [7ce2597a]
- Add HTCondor detail on data sharing #1473 [f0af66de]
- Allow aliased process to inherit config settings [DSL2] [1c447e85]
- Allow module inclusion to inherit context params #1484
- Allow multiple inclusion from the same module [DSL2] [a9ae36f9]
- Fix Script template fails to render list of files #1478 [2e97bbbc]
- Fix process name validation when using legacy script [1543365c]
- Fix Early detection Dsl2 declaration #1468 [93a642aa]
- Fix Missing script validation checks #1468 [5d0cf145]
- Revert "Disable ansi log on non-tty env #1417" [98e6758b]
- Minor changes gradle build [619385f1]
- Minor AWS Batch api refactor [c20abc11]
- Improve foreign file detection [50508684]
- Improve GLS location validation [5b89ab50]
- Removed unused module flag [cf19cc9c]
- Update dsl2 docs [5c57c3a8]
20.01.0-edge - 20 Jan 2020
- Add Prevent negative progress stats [87cdddc6]
- Add More cloud tests [7a5dd828]
- Add support for UGE throttled jobs (Tr) #1461 [20408e4b]
- Add progress stats to tower client [781116a4] [138cf0b0]
- Add experimental Podman containers support (#1451) 026866cd
- Add support for Gexf format for DAG rendering [28bfe0ee]
- Improve ansi logging for multilines output [1ce978c3] [004e23eb]
- Improve progress stats and ansi log [0212ba16]
- Improve api to enable wr executor #1148 [21088ad3]
- Update tower trace client requests [138cf0b0]
- Enhance progress execution stats & tracking [a30e2b9a]
- Unexpected output when using Google Storage as work dir #1452
- Fix typos and minor changes [fb2f954f]
- Fix Operator splitFastq fails with PE option and DSL2 enabled #1390
- Fix Container entrypoint when using GLS executor #1291
- Fix GLS file unstaging #1406 [e67ef3be]
- Fix GLS unstage for file patterns #1406
- Fix Scratch directive does not work #1280 [644e9ac7] [6c7291fa]
- Fix Resume fails due to LevelDB exception #1358 [28fa3a6c]
- Fix Conda env activation #1195 [e3919275]
- Fix java command in launch script #1436 [f28b015f]
- Rename variable java to JAVA_BIN [086377d8]
- Removed unused compile deps [686bcd98]
- Bump capsule-maven 1.0.3.2 and fix broken env [004684e3]
- Bump capsule-maven 1.0.3.1 and seqera repo [62964eed]
19.12.0-edge - 20 Dec 2019
- Add GLS assigned zone discovery #1406
- Add Google Life sciences (GLS) executor improvements #1406 [ead29c11] [8228e9b4]
- Add GLS bootDiskSize support #1331 [f118798c] [af8fe16d]
- Add GLS job debugging #1351
- Fix NPE when file pattern is missing [1cbb6e49]
- Fix AWS cloud parsing for NVEe storage and tests
- Fix Disable ansi log on non-tty env #1417
- Fix Allow Singularity image path with blank #1368
- Fix Shell template invalid caching #1422
- Fix Task vars ordering may invalidate cache #1408
- Fix Join operator not matching gstrings #1394
- Fix sigpipe error caused by runner script #1332
- Fix Google Storage bucket with underscore is not recognized #1069 [85cd0cde]
- Fix fromFilePairs can't take list of paths #1405 [c00f5669]
- Refactor onFlowInit to onFlowCreate event [c477eeaf]
- Improve err msg when input files are remove from output [5d5744a8]
- Upgrade to Gradle 6.0.1 [e0c1a3ac]
19.11.0-edge - 2 Dec 2019
- Increase tasks.module to 255 [7332c606]
- Fix Allow the output of process env variables #69 [1c1befc7]
- Fix docs rounding issue #1350 [af824fc7]
- Fix Join operation incorrectly represented in DAG #1346 [9d83ed51]
- Fix Tiny typo in docs #1361
- Fix lost trace/report/timeline file name
- Fix invalid class exception [4308d6a4]
- Fix Invalid dynamic resolution of stageIn/OutMode directive #1374
- Fix No such property stackTraceDepth error #1387 [49450f67] [f5342e71]
- Fix Singularity env variables are not accessible #1386 [036af4a6]
- Fix PublishDir should not create dir when disabled #1381
- Fix Process hangs for non zero exit status #1344
- Fix Output stdout does not support emit attribute #1373
- Fix False positive warning when importing module #1349
- Fix HTCondor queue status command #1353 [a1addc8f]
- Fix Escape file names with blanks #1392
- Fix broken docs tutorial #1366
- Patch Duration unit cannot be a negative number #1384
- Handle ProviderMismatchException in CacheHelper (#1382) [cc584368] [3523f174]
- Introduce workflow take in place of get [DSL2] [e8cbbf08]
- Disable ansi log when using dockerized run [86bc2ada]
- Minor logging change [238b0e6c] [f5342e71] [b707882f] [ce97f073]
- Add multiMap in place of fork operator [afd671c8]
- Add Show Tower init response message as warning
- Add output path includeInputs docs [2ce7e861]
- Add metrics fields check #1360 [5b7f42e9] [caf9f137]
- Add console command to cli help #1347
- Add OAR executor #1343
- Add graphiviz to Docker image #1370
- Removed unused property [9c65426a]
19.10.0 - 21 Oct 2019
- Merge Use a delete function that doesn't follow symlinks #1337
- Merge Allow multiple mounts for the same K8s claim name [1d288a3d] #1284
- Make Google Pipelines logging less verbose [6edd9954]
- Merge Shifterimg workaround for ensuring image pulls #1327
- Merge Add ENDPOINT support for China regions #1323 [636cbfb5]
- Add limit on max field lengths sent by Tower [4d5cabc2]
- Add retry ability to Tower client for 500 class errors [c7f70fc5]
- Add support for Java 12 #1082 [b86b2da0]
- Add BitBucket Server provider [6af6a902] #1297 #1309
- Add support for AWS temporary security credentials #934
- Fix Broken container environment when enabling metrics #1289
- Improve resource not found error message [02cf0a55]
- Remove route operator #991
19.09.0-edge - 16 Sep 2019
- Add `of` and `fromList` channel factories [cc60b305]
- Add nf-tower init request [120ed8ba]
- Add support for accelerator directive #997 [624c8e83]
- Add support for native shifterimg for shifter engine (#1292) [a106712e]
- Add nf-tower subproject [285e09ce]
- Add sticky log marker [f9a3c9da]
- Add support for config resolution [4754abc6]
- Add enable option to publishDir [7b9c2d2f]
- Fix race condition on task workdir creation [5bc323a0]
- Fix issue when fetching aws profile from env #1248 [ba30b97c]
- Fix minor issue when reporting invalid entry error msg [814d6728]
- Fix non determinist test failure [a9289e9e]
- Throw error cause on InovationTargetException [9e1467d0]
- Remove verbos logs on readExitFile check [a5a6a1fc]
- Revert "Patch capsule error message" [ac4ac073]
- Patch for inconsistent cached task id #1301 [7bfd0008]
- Improve flow execution events [335b76d1]
19.08.1-edge - 26 Aug 2019
- Add Process named output channels #1290 [DSL] [6a756fd2]
- Add workflow publish directive [DSL2] [287a095e]
- Add stageAs option to input path [DSL2] [9b5f55f6]
- Add workflow entry option [DSL2] [f29e3e04]
- Add extension to module file name instead of simpleName [DSL2] [71a60365]
- Add support AWS temporary session token support [15ac3938]
- Add support for GCP disk resource [72bb9c41]
- Add fork operator #1281 [DSL2] [6f89833a]
- Add branch operator #1202 [706a182a] [DSL2]
- Add workflow definition and composition #1276 [13f43291] [DSL2]
- Add projectName to workflow metadata [55be0762]
- Add support for tower [1255f702]
- Add support for timezoned timestamp to metadata [6f4a2e28]
- Add task pending event [d2d66698]]
- Add support for path in/out qualifier [DSL2] #1201 [5552b38a]
- Add set chainable operator #1262 [2651a099]
- Fix name generator uniq check [0bbf7015]
- Fix execution report nested processes aggregation [e4fad827]
- Fix nested process names config resolution [ccd8e833]
- Fix missing deprecation [8af85189]
- Fix broken div structure in html report [3e055a7a]
- Fix set operator for multi-channel #1262 [eab39378] [DSL2]
- Fix typo in the `delete` file docs [38fa2dca]
- Fix test #1276 [cc03d76b]
- Fix classpath resolving when launched from foreign path [04024fe6]
- Fix console cmd throws runtime exception #1273 [2f78d943]
- Fix process names validation fails for included modules #1175 [75b96aa8] [DSL2]
- Fix issue with `set` as operator #1262
- Fix misleading name when throwing multiple in/out channel [e7c8cdb9]
- Fix Combine operation incorrectly represented in DAG #1268 [6e86e28a]
- Fix docs collectFile `size` vs `skip` option [8cfb5a64]
- Fix K8s TaskHandler updates its status correctly to 'RUNNING' (#1256) [a1457a1c]
- Remove potential sensitive environment vars #1075 [a413b967]
- Enable use AWS profiles other than `default` (#1248) [d7434773]
- Relax deprecation messages #1269 [454e78f1] [fd11f8d8]
- Defer process start and channel emission [DSL2] [f5eef256]
- Rename ChannelFactory helper to CH [4b5b3c7e]
- Improve modules error checking and reporting [aa650b9e] [DSL2]
- Increase build test max heap size [daca896e]
- Upgrade Gradle to version 5.5.1 [027cb16b]
- Enforce process execution in `workflow` scope` [DSL2] [bca15a91] [0a582240]
- Replace InterruptedException with TimeoutException in GCP test [a6d3c24c]
- Explicitly check whether module path does not end with .nf (#1254) [8253608a]
- Minor improvement AWS Batch docs [bd56ea44]
- Upgrade Groovy to version 2.5.8 [36dffa18]
- Enhance execution report [ab5f8d98]
- Enhance simple http client [2e0f5c2b]
- Refactor resource metrics collector [fec86ed2]
- Refactor observers plugin system [9dab8f08]
- Replace input/output set type with tuple [DSL2] #1207 [5e19f72f]
- Convert any simple object to a value channel [DSL2] [86b0469d]
- Improve logging [5adc2c09]
19.07.0 - 27 Jul 2019
- Add support for K8s annotations #1240 [8eeb7f9f]
- Add support for Moab resource manager #1224 [3ba51a19]
- Add Pbs Pro execution documentation [1d39ab31]
- Add code of conduct document
- Fix missing LFS executor register invocation #1234 [b1b7ab1]
- Fix "invalid pod status" when running scrips with the kubernetes executor #1242 [11caac68]
- Revert Fix Environment activation fails with recent versions of Conda #1195 [98c0d1f8]
- (includes changes from `19.07.0-edge`, `19.05.0-edge` and `19.05.0-edge`)
19.07.0-edge - 9 Jul 2019
- Fix Remote input file download slowdown submission rate #1206 [b710e21e]
- Fix serial publishDir uploads #856 [14774854]
- Fix Trace file option is not honoured #1217
- Fix Custom lib path is not added to the classpath #1213
- Fix Discovery executor tracing error [3e26c146]
- Add megabyte unit to Slurm memory requirement #1216 [efabdd2f]
- Add support for GCP dynamic machine type #1198 [5c2c7665]
- Add setCredentialsProvider for submodules #1205 [e2460414]
- Improve google pipelines docs [aed407ed]
- Improve FileTransfer await termination log #1206 [cb968da7]
- Allow trace logging for `com.upplication.s3fs` package [d71b94e1]
- Upgrade s3fs lib to version 1.0.6 #856
19.06.0-edge - 21 Jun 2019
- Fix Nextflow indefinitely waiting for killed jobs #981
- Fix Suppress Unknown hashing type logging message #1178 [a005b1b0]
- Fix a typo in AWS docs (#1171)
- Fix Invalid response cause Google pipelines exec to crash #1163
- Fix kuberun doesn't delete config maps #1165
- Fix Disable ansi logging when using kuberun command #1161
- Fix comparable test with groovy 2.5.8 [3d1c0833]
- Fix Unexpected config selector warning #1167 [52e70e31]
- Fix Kuberun should honour `-bg` (background) option #1159 [4b160b7b]
- Add S3 download retry (#1164)
- Upgrade BitBucket provider with API 2.0 [feeddcda]
- Print ansi summary for exec > 60 secs [53c94270]
- Remove deprecated countText operator #983
- Demote warmup into to debug level [c7d08337]
- Demote barrier logging to trace level [5b7234a1]
19.05.0-edge - 20 May 2019
- Add Aws Batch maxParallelTransfers config #1107 [26d37556]
- Add NXF_ANSI_SUMMARY var to disable log summary [d4b9cc44]
- Add support for AWS user volumes and jobRoleArn [651eeadd]
- Add Support for LSF per task resource reserve mode #1071
- Fix Env variable with blanks is not resolved correctly in containers #1146
- Fix method isDynamic visibility [f241781b]
- Fix WebLogObserver data leak on completion #1010
- Fix unit test execution [622d97d4]
- Fix Quiet cli option is not honoured [e656e4b0]
- Fix Log messages don't show in the console #1129 [95f4dd7b]
- Fix nextflow build timestamp json rendering [af6584c9]
- Fix Launcher should return non-zero exit when fail to step env #1126
- Update get started docs [68f53367]
- Update aws sdk to version 1.11.542
- Update created label in timestamp [e8945e8b]
- Update readme IDE version
- Refactor AWS cli path option [ad9af0dd]
- Improve Dsl-2 error reporting [4e2621ff]
- Improve CI tests scripts [febeb530]
- Improve docs for config profiles [8cf95a5d]
- Syntax enhancement aka DSL-2 #984 [651af95a]
- Print summary only the run takes > 3mins [cd459713]
- Render last tag along with the process name #1144 [8cf8cc44]
- Sync build scripts [a5689217]
- Provide scm credentials when fetching information about remote branches #1135 [808847b5]
- Code cleanup [2322fbcf]
19.04.0-edge - 24 Apr 2019
- Add Experimental support for gpu resources #997
- Fix LSF executor should use mem setting in lsf.config #1124
- Fix Unable to list S3 bucket content #1121
19.04.0 - 15 Apr 2019
- Added support for NCBI_API_KEY variable [e4d9b62c]
- Added warning message when using untested Java version [35acd1cb]
- Added parameter and workflow metadata to weblog payload #1077
- Added warning on publish with a null var [7d58bfb7] [95c219fb]
- Fixed Echo directive when Ansi log is enabled #1112 #996
- Fixed Do not mount inputs when `stageInMode == copy` #1105
- Fixed `splitCsv` operator fails to parse values containing commas #1102
- Fixed missing return type for Date.format method
- Fixed Channel operations `toList` followed by `merge` hang execution #1083
- Avoid printing execution summary when no processes are computed #996
- Improved error reporting for null publishDir [0b9b52f0]
19.03.0-edge - 14 Mar 2019
- Fix Nextflow hangs submitting jobs to AWS Batch #1024
- Fix process builder incomplete output [2fe1052c]
- Fix Grid executor reports invalid queue status #1045
- Fix Script execute permission is lost in container #1060
- Fix K8s serviceAccount is not honoured #1049
- Fix K8s kuberun login path #1072
- Fix K8s imagePullSecret and imagePullPolicy #1062
- Fix Google Storage docs #1023
- Fix Env variable NXF_CONDA_CACHEDIR is ignored #1051
- Fix failing task due to legacy sleep command [3e150b56]
- Fix SplitText operator should accept a closure parameter #1021
- Add Channel.fromSRA factory method #1070
- Add voluntary/involuntary context switches to metrics #1047
- Add noHttps option to singularity config #1041)
- Add docker-daemon Singularity support #1043 [dfef1391]
- Use peak_vmem and peak_rss as default output in the trace file instead of rss and vmem #1020
- Improve ansi log rendering #996 [33038a18]
19.02.0-edge - 6 Feb 2019
- Added foreign files caching ability #686
- Added Ansi logging as default console output
- Added Gitea source code provider [ae04fc37]
- Fixed Join operator returns invalid remainder values #1015
- Fixed Invalid trigger of integration tests [7aa5908a]
- Fixed memory allocation for SGE executor [29353c90]
- Fixed properties access for TaskConfig and LazyMap [09b74a52]
- Fixed Invalid decimal separator in mem unit string #999
- Fixed tail error on launcher script [38afea6c]
- Improved Execution and Timeline memory reporting #980 #986 #1012 #1014 #1016 #1018 [01426097] [7d6c29f0]
- Improved Google pipelines file copy strategy [678405b2]
- Improved output file stage out behaviour docs #961 #1013
- Upgraded Groovy runtime to version 2.5.6
19.01.0 - 22 Jan 2019
- Added Google Cloud Platform integration
- Added support for K8s nodeSelector #955
- Added new AWS regions #935
- Added json/yaml output to info command #657
- Added More duration and memory unit syntax sugar #921
- Added NO_PROXY env variable should be honoured #864
- Added keepHeader option to splitText operator #912
- Added countLines, countFasta and countFastq methods #972
- Added an env variable to define default cloud driver #973
- Fixed Unable to find JVM 1.8 err message #1000
- Fixed Memory unit should contain thousand separator [e6ec4c84] #989
- Fixed LSF long user names breaks jobs status parsing [b4306151] #988
- Fixed Move output files to storeDir instead of copying them #745
- Fixed Interpolated strings in a from statement are misinterpreted #978
- Fixed ConcurrentModificationException when publishing output files #971
- Fixed Launcher fails with Java 10 or later #953
- Fixed remote bin directory when using bucketDir option [6d796783]
- Fixed foreign file system detection [1489cc72]
- Fixed Ansi logger division by zero [ae2b1380]
- Fixed Unparseable Data format on http file #962
- Fixed Log command history #405
- Fixed Too long process tag name can cause SLURM failure #941
- Fixed LSF can return an inconsistent jobs status #927
- Fixed dump last queue status on failure [36e80242]
- Fixed Allow the usage of a custom docker image for K8s driver pod #877
- Fixed K8s executor when the cluster has no available cpus #824
- Fixed Prevent duplicate process definitions #920
- Fixed Update queue statuses used by PBS Pro #908
- Fixed K8s launcher fails to set pod work directory [dc8bfead]
- Fixed cmd cloud error message [14d603b9]
- Fixed RejectedExecutionException on successive Console executions #906
- Fixed Invalid config rendering #801
- Fixed Invalid warning message for config selector #905
- Fixed Queue status command fail on LSF version 8 #910
- Fixed Use `bash` instead of `sh` to fetch queue status
- Improved script runner api [da4a6c17]
- Improved file hashing logging [0d35b2b4]
- Refactored ScriptRunner class [15ee2f1c]
- Refactored DSL code visitor [67904c1f]
- Revert "Apache Ignite to version 2.6" #909
- Better report warning when grid status command fails [3ac8b972]
19.01.0-edge - 10 Jan 2019
- Enhanced timeline and execution reports #985 #986 [fb00c3a6] [092f0b9e]
- Enhanced BashWrapperBuilder using template file [7d7e116a] [c62b9dff]
- Fixed CPU usage accounting #982 [7d7e116a] [c62b9dff]
- Fixed Move output files to storeDir instead of copying them #745
- Fixed Interpolated strings in a from statement are misinterpreted #978
- Fixed Launcher fails with Java 10 or later #953
- Fixed LSF long user names breaks jobs status parsing [b4306151] #988
- Fixed Memory unit should contain thousand separator [e6ec4c84] #989
- Fixed Allows fromFilePairs to handle non globs #946
- Added an env variable to define default cloud driver #973
- Added countLines, countFasta and countFastq methods #972
- Added NXF_DIST launcher variable #954
- Added NXF_SMOKE var to disable long running tests
- Deprecated groupBy and route operators [b7ca53d2]
- Updated S3 storage classes #977
- Updated groovy to version 2.5.5
- Updated copyright disclaimer
- Refactored project structure [516294e7]
- Speed-up CI tests [3320dcec]
18.12.0-edge - 18 Dic 2018
- Add Google Cloud Platform integration
- Added support for K8s nodeSelector #955
- Added new AWS regions #935
- Added json/yaml output to info command #657
- Fixed remote bin directory when using buckerDir option [6d796783]
- Fixed foreign file system detection [1489cc72]
- Fixed Ansi logger division by zero [ae2b1380]
- Fixed Unparseable Data format on http file #962
- Fixed Log command history #405
- Fixed Too long process tag name can cause SLURM failure #941
- Fixed LSF can return an inconsistent jobs status #927
- Fixed dump last queue status on failure [36e80242]
- Fixed Allow the usage of a custom docker image for K8s driver pod #877
- Fixed K8s executor when the cluster has no available cpus #824
- Fixed Prevent duplicate process definitions #920
- Fixed Update queue statuses used by PBS Pro #908
- Fixed K8s launcher fails to set pod work directory [dc8bfead]
- Fixed cmd cloud error message [14d603b9]
- Improved script runner api [da4a6c17]
- Revert "Apache Ignite to version 2.6" #909
- Fixed Invalid config rendering #801
- Improved file hashing logging [0d35b2b4]
- Refactored ScriptRunner class [15ee2f1c]
- Refactored DSL code visitor [67904c1f]
18.11.0-edge - 12 Nov 2018
- Added More duration and memory unit syntax sugar #921
- Added NO_PROXY env variable should be honoured #864
- Added keepHeader option to splitText operator #912
- Fixed Invalid warning message for config selector #905
- Fixed Queue status command fail on LSF version 8 #910
- Fixed Use `bash` instead of `sh` to fetch queue status
- Better report warning when grid status command fails [3ac8b972]
- Fixed RejectedExecutionException on successive Console executions #906
18.10.1 - 24 Oct 2018
- Fixed test [011e8e23]
- Fixed version number check [fb780347]
18.10.0 - 24 Oct 2018
- Added lenient cache mode #828 [ba907a2f]
- Added support for java 11 [60da50b5]
- Added support for Singularity 3.0 library #898
- Added support for AWS Batch hybrid executions #744
- Added weblog JSON format docs #882
- Added weblog example documentation #891
- Added PbsPro executor [33ae1104]
- Added support for ANSI console logging [9c14a947]
- Fixed License prevents scientific use #788
- Fixed process submitter slow-down [495e900a]
- Fixed Comparing duration and memory units with null throws an exception #872
- Fixed Html format dag fails when 'each' qualifier is used #887
- Fixed Collate/Buffer hangs with one emission after Collect operator #868
- Fixed Option checkIfExists should be applied when a glob pattern does not match any file #874
- Fixed Add name to manifest and reject other attributes #871
- Fixed warning message grammar when resuming on new project #885
- Fixed Missing DSL Xform transformation in console execution [9621f8c6]
- Fixed Enum declared in nextflow script causes error #878
- Fixed Report a warning message when queue status fetch fails [39aae6a2]
- Fixed Pbs executor may return nonzero exit code when checking queue status #904
- Renamed weblog `runStatus` to `event` #892
- Renamed K8s config attribute userDir to launchDir #895
- Merged tests as subtree [a03eb59a]
- Refactored service discovery
- Removed FastXxxYyyyStream
- Demoted igfs subsystem
- Upgraded Groovy to version 2.5.3 [119300b3]
- Upgrade Gradle to version 4.10
- Updated AWS batch docs
0.32.0 - 8 Aug 2018
- Fixed CPU usage metrics can be wrongly reported #858
- Fixed Allow a process to access input file metadata #731
- Fixed Completed jobs are detected with a big delay #799
- Fixed Misleading message is shown when pulling a project with a invalid config #863
- Fixed Allow groupTuple operator to handle multi-size tuples #796
- Fixed Ignite executor fills up logs when node is disconnected #810
- Fixed Log filter option is misinterpreted when enclosed in double quotes #846
- Fixed Metrics collector process may cause the main process to report a false non-zero exit status #836
- Fixed K8s imagePullPolicy is not included in the pod spec #815
- Fixed Splitter caching is too eager when caching path is specified #835
- Fixed Improve error message for missing git provider configuration #847
- Fixed Byte hashing is never reached in CacheHelper class 9ac81153
- Fixed K8s launcher should not delete pod when `login` command fails (5175942a)
- Fixed Dump operator should nicely print ArrayBag content (91e371ba)
- Added manifest data in workflow metadata object #841
- Added support for K8s imagePullSecrets pod attribute #800
- Added option "checkIfExists" to Channel.fromPath method #666
- Upgraded Apache Groovy to version 2.5.1
- Upgraded Apache Ignite to version 2.6
- Upgraded Slf4j to version 1.7.25
- Upgraded Logback to version 1.1.11
- Upgraded Grengine to version 1.3.0
- Upgraded LevelDB to version 0.10
- Upgraded Guava to version 21.0
- Upgraded Spock to version 1.2
- Using javax.activation:activation:1.1.1 (from com.sun.activation:javax.activation:1.2.0)
0.31.1 - 7 Aug 2018
- Fixed AWS Batch execution hangs when running on 1 cpu machine #825
- Fixed AWS Batch fails if process tag length is too long #822
- Fixed AWS Batch executor creates timeline report with missing time data #816
- Added Ignite failure detection timeout configuration parameters #820
- Added VersionNumber class to CacheHelper handler [90fb69fa]
- Added CONTRIBUTING file #564
0.31.0 - 25 Jul 2018
- Fixed CLI parameter value starting with a `-` is misinterpreted #808
- Added keep-logs option to clean command #775
0.31.0-RC1 - 19 Jul 2018
- Fixed K8s pod request should include resources spec when 1 cpu is specified #806
- Fixed PBS executor should fail when submit response contains invalid data #753
- Fixed SLURM executor fail to submit jobs when cluster option is specified #805
- Fixed Allow the use relative paths for symlinks process input files #296
- Fixed AWS batch jobs are not properly stopped when execution is interrupted #782
- Fixed splitCsv is not properly handling blank lines #795
- Fixed K8s pod runAsUser definition #707
- Fixed Prevent NPE when K8s reports an empty pod state [dcc7ec5f]
- Fixed Allow list of patterns for fromPath and fromFilePairs channel factories #732
- Fixed K8s execution hangs if an invalid pod secret file is specified #754
- Fixed Correctly shutdown executor service #732
- Fixed bug in dot rendering due to unquoted graph name when DOT language keyword used #783
- Fixed Execution hangs if one or more inputs evaluate to null #764
- Fixed Method `file` should thrown an error null is given as input #765
- Fixed invalid relative link resolution with `readlink`
- Added AWS batch requests throttling handling #710 #709
- Added AWS Batch parallel downloads/uploads [codefest] [8ba1716b,ba5ad7a8]
- Added K8s pod config and security context definition #707
- Added Container env variables whitelist #803
- Added support for K8s pod labels #762
- Added support for K8s volume mount subPath #758
- Added Nextflow required version in the config manifest #752
- Added disk resource requirement in LSF executor #747
- Added GA4GH TES executor [experimental] #794
- Added System info to workflow metadata object #759
- Added weblog feature #681
- Deprecated process.$name syntax to define process specific settings #713
- Upgrade to Gradle 4.9
0.30.2 - 16 Jun 2018
- Fixed Output declarations with a glob pattern fail when AWS Batch executor is used #748
- Fixed Scratch directive not working for AWS Batch executor #740
- Fixed K8s launcher does not parse remote config files #738
- Minor refactoring to enable Groovy 2.5 compilation 20b6d933 a8b994f1
0.30.1 - 11 Jun 2018
- Use a daemon thread for watchPath method #735
- Fixed Gitlab API v3 has been deprecated and does not work any more #734
- Fixed Unable to access params defined in the top scope from a nested profile #733
- Fixed Process config selectors do not work when the config is included #729
- Fixed Improve the error message when a missing property is used in the config file #730
- Added Travis build support for jdk10
- Added documentation for `until` operator #736
- Added mailer recipients check
- Increased Singularity pull timeout to 20 minutes
- Updated build to Gradle 4.8
0.30.0 - 5 Jun 2018
- Added the support for Bioconda #493
- Added support for AWS Batch job timeout #648
- Added jobs submit rate limit #198
- Added offline option #665
- Enabling Java 9/10 support for build and launcher scripts #674
- Fixed Expose Kubernetes Secrets to worker pods #651
- Fixed K8s execution hangs when a non-existing docker image is specified #697
- Fixed K8s execution terminates abruptly if a pod requires more resources than available ones #676
- Fixed K8s executor does not report command log when a task fail #699
- Fixed Configuration profile is not handled properly by the kuberun command #696
- Fixed Enhance process metrics to avoid usage of ps tool #499
- Fixed PublishDir should use copy mode by default when the target is a S3 path #718
- Fixed Unbounded variable breaks task launcher script #722
- Fixed Escape filenames when copying from S3 #717
- Fixed AWS executor should use putObject API to upload job scripts to S3 #712
- Fixed Exception is thrown when an output folder contains a circular symlink path #701
0.29.1 - 10 May 2018
- Fixed Default ext property are not included in process context #673
- Fixed Operator concat throws a ConcurrentModificationException #675
- Fixed Output file is not recognised when it's created into a subdir and the name matches an input #688
- Fixed Empty container definition being ignored when default one is specified #691
- Fixed K8s client fails to connect the cluster when client key nor certificate is specified #692
- Fixed K8s executor hang on pod creation failure
- Added select in -R for memory for LSF executor #683
0.29.0 - 24 Apr 2018
- Fixed Buffer operator fails to recognise optional parameter when a closing condition is specified #652
- Fixed PublishDir mode "copyNoFollow" does not work for directories #658
- Update NameGenerator adjectives #656
0.29.0-RC1 - 8 Apr 2018
- Added `containerOptions` directive #415
- Added support for multiple `publishDir` directives for process #256
- Added cleanup feature to delete workflow work dir on completion #649
- Added label directive and process configuration selectors `withLabel` and `withName` #623
- Fixed Invalid process cache when using a different environment module #627
- Upgrading groovy runtime to version 2.4.15
0.28.2 - 6 Apr 2018
- Fixed Class FtpURLConnection is not accessible when using Java 9 #646
- Fixed Lengthen mktemp TEMPLATE so works on BusyBox #647
- Fixed Report HTML/CSS tweaks to make progress bar text overflow work properly #645
- Fixed typo in the nextflow launcher #643
0.28.1 - 27 Mar 2018
- Fixed A HTTP access error is raised when the URL contains a ? character #634
- Fixed Creation of temp files in the /dev/shm directory can result in a permission
error in some Linux installations #638
- Make process echo safer
0.28.0 - 10 Mar 2018
- Fixed Singularity pull is executed even when container execution is disabled #628
- Fixed issue when setting container attribute to `false` [9de636c5]
- Added MemoryUnit getters [f99d2dc9]
- Added default NXF_TEMP variable [d36ac4dd]
- Added progress stacked bars to workflow report #534 [455fcb4f]
- Added namespace option to `kuberun` command [50154ec5]
- Improved workflow stats and warn report [e795b134]
- Improved K8s error reporting [86f172eb]
0.28.0-RC1 - 27 Feb 2018
- Added support for directory wildcards in input file declarations #568
- Added ability to access task existStatus value as an output value #577
- Added ability to use property syntax in the declaration of output values #578
- Added NXF_JAVA_HOME variable to specify nextflow nextflow JVM #607
- Added support for docker mount flags #572
- Added ability to select multiple configuration profiles #370
- Added ability to copy symlinks to publishDir directive #592
- Added missing native_id TraceRecord field to K8s and AWS Batch task handlers
- Enhanced support for Kubernetes #468
- Fixed Launcher breaks when JAVA_HOME path contains a blank char #616
- Fixed Operator toList hangs when applied to a value channel #612
- Workflow report should warn if some task executions were ignored #534
- Enable support for large execution reports #547
- Replaced the use of named pipes with anonymous pipes #606
- Enhance the config command show dynamic attributes #604
- Fixed bin path is not recognised when contains a blank char #603
- Fixed A NPE exception is thrown when a env variable is assigned to an null value #593
- Fixed summary stats when for empty series #547
- Removed support for Extrae #588
- Removed support for DRMAA #587
0.27.6 - 19 Feb 2018
- Fixed Operator toList hangs when applied to a value channel #612
- Allow launcher to track installation verb
0.27.5 - 15 Feb 2018
- Fixed dir/* input file pattern invalidate cached processes #610
- Fixed Mail attachment are not correctly recognised by the email client #609
- Fixed Workflow metadata container attribute is not resolved when it's defined dynamically #602
0.27.4 - 5 Feb 2018
- Fixed Resume does not work for tasks successfully executed in a re-submit attempt #591
- Fixed An error is reported when a NF script contains a class definition #594
- Fixed Launcher error when download target path contains a blank character
0.27.3 - 29 Jan 2018
- Fixed publishDir directive fails on S3 when attempting to copy objects larger than 5 GB #585
- Process name does not reflect dynamic tag declaration when a task execution is retried #586
- Fixed examples in the documentation
- Update to Gradle 4.5
0.27.2 - 23 Jan 2018
- Fixed Config property keys may contain invalid characters
- Fixed Local process kill signal is not propagated to children processes #581
- Fixed Operator join throws a stack overflow exception when an invalid argument type is specified #582
0.27.1 - 18 Jan 2018
- Fixed Invalid cast exception when cpus value is missing #575
- Fixed Kill the tee commands when the launcher script exit #574
- Fixed Splitter `limit` option is not honored when splitting more than one file #573
- Fixed AWS CLI operations with S3 should use the --only-show-errors options #567
- Fixed Splitter by option is not honored when splitting more than one file #570
- Documentation editing/improvement
0.27.0 - 9 Jan 2018
- Fixed Log command prints true instead of actual message #561
- Fixed NXF_TEMP definition when instanceStorageMount is set
- Improved S3 exitfile logging
- Improved cloud config canonical formatting
0.27.0-RC2 - 29 Dic 2017
- Fixed Ignore Windows instances from AWS cloud price listing
- Fixed AWS price reader catching unexpected errors
- Fixed sendMail access to owner variables
- Fixed NPE when creating task with ignite executor
- Fixed null exit status in notification template #554
- Added XPath serialiser
- Added mail smtp proxy configuration #375
- Added built-in notification documentation #554
- Added built-in mail documentation #375
- Added support for Syslog logging #330 #557
- Improved support for AWS EC2 instance storage #558
- Improved documentation #558
- Improved config command adding `-flat` and `-properties` formats and using canonical curly brackets format as default
- Update copyright info
0.27.0-RC1 - 20 Dic 2017
- AWS Batch increased queue to 1000 tasks and poll interval to 10 secs
- AWS Batch improved executor scalability caching recurrent API call and batching similar requests together
- Added notification message on workflow completion #554
- Added Built `sendMail` function #375
- Added Warning message when a local version on a GH repo is different from remote #376
- Added keepHeader option to collectFile #479
- Added Dump operator to enable easier debugging #517
- Fixed Report an error message when a config file contains an unresolved attribute #525
- Fixed Session working file system not defined when staging input files with Ignite executor #555
- Fixed storeDir writes output files even when process fails #227
- Fixed storeDir does not work with S3 targets #247
- Fixed Config file available in introspection #264
- Fixed Enhance container interoperability between Docker and Singularity #503
- Fixed Process environment is not exported in the container context when a process uses an interpreter other than BASH #495
- Deprecated support for executable containers #529
- Deprecated DRMAA executor #488
- Deprecated Extrae profiling #543
- Renamed .command.run.1 to .command.stub #523
0.26.4 - 11 Dec 2017
- Fixed GitLab auth token is not applied when user credentials are not provided #542
0.26.3 - 30 Nov 2017
- Fixed AWS Batch S3 upload function does not work if output is a directory #539
- Fixed AWS Batch S3 uploaded function does not resolve glob patterns containing curly brackets #535
- Added author field in the config manifest scope #537
- Upgrading s3fs library to 1.0.2 version supporting `signerOverride` S3 config property.
0.26.2 - 27 Nov 2017
- Fixed readlink illegal option when installing in macOS #527
- Fixed Getting not descriptive error when using a when condition and script statement is not explicit #528
- Fixed Function nxf_module_load matches partial names #530
0.26.1 - 17 Nov 2017
- Execution report enhancements #521
- Fixed Add AWS_DEFAULT_REGION environment variable to bash wrapper scripts #512 #513
- Fixed New launcher script does not allow the execution of legacy version with Java 7 #519
- Fixed Error message reporting file name collision is misleading #516
0.26.0 - 8 Nov 2017
- Fixed file method does not interpret correctly S3 path with globs #509
- Fixed Execution hangs when the amount of requested resources exceed the available ones #502
- Minor change in the execution report #507 #508
- Make AWS clustering compliant with billing by seconds
- Refactored `nf-token` AWS job definition parameter #475
- Run Batch task in a scratch directory to avoid undefined execution folder #475
- Renamed `iamProfile` to `instanceRole` #422
- Renamed ProcessNotRecoverableException to ProcessUnrecoverableException
0.26.0-RC2 - 30 Oct 2107
- Fixed TMP and TMPDIR variables are not passed in Singularity environment #496
- Fixed Dynamic resources directive when defined both in a process and the config file cause an error #497
- Added Experimental support for Shifter containers #500 #501
- Improved AWS Batch task logging and task attempts
- Improved Execution report showing task realtime instead of task duration on time box plot
0.26.0-RC1 - 24 Oct 2017
- Added support for AWS Batch #475
- Added support for AWS IAM role #422
- Added Experimental support for Java 9 #462
- Added transpose operator #440
- Added join operator #460
- Added html report (-with-report option)
- Added Gzip compression support to splitXxx operators #484
- Added Support PE Fastq files splitting #436
- Added Operator splitFasta should allow the creation of chunk having the same size #472
- Added HTML execution report #490 #491
- Added New scientist names #485
- Improved merge operator #458
- Improved value channel handling for reduce, filter, first, take and randomSample operators
- Prints a warning message when the config file defines setting not matching any process definition
- Fixed HEAD is detached error #389
- Fixed Include container name when calculating cache key #443
- Fixed Invalidate process cache when a referenced external script is modified #413
- Fixed Execution failure is not reported in the trace file when retry error strategy is used #404
- Fixed "when" directive should not allow staging of input files for a process, if the criteria are not met #424
- Fixed Failure during foreign files download cause execution to stop abruptly #295
- Fixed The parameter groupName cannot be used with the parameter subnet #465
- Fixed unable to download from gitlab.com public repository #457
- Fixed Print work directory when a task fails #445
- Fixed Misleading command line parameter type conversion #434
- Fixed Nextflow should not stage files that have the same name #470
- Fixed SplitCsv returns array objects instead of Lists #487
- Fixed Cannot cast object FtpURLConnection error #482
- Fixed Nested Environment Module names are not loaded properly #489
- Removed support support for Java 7 #385
- Removed deprecated Cirrus/ClusterK executor
- Removed deprecated support for DNAnexus #386
0.25.7 - 6 Sep 2017
- Fixed Unable to parse the AWS price list API #444
- Added seed parameter to `randomSample` operator #410
0.25.6 - 13 Aug 2017
- Fixed Empty channel waiting forever when viewed and mixed #428
- Fixed Error Channels cannot be used as input in more than one process or operator #429
- Fixed Script body is resolved even if the `when` guard evaluate to false
- Added queue process directive as option for trace file
0.25.5 - 4 Aug 2017
- Fixed NF fails to pull images hosted in the Singularity Hub #414
- Added `-y` to cloud create command to skip confirmation request
0.25.4 - 31 Jul 2017
- Removed invalid debug information
0.25.3 - 31 Jul 2017
- Fixed NPE when parsing AWS price file #408
- Fixed Grid queue status return wrong data when a process change the submission queue dynamically #412
- Fixed MPI-like execution for SLURM batch scheduler
- Fixed NPE when log params key is not defined
- Fixed Optional parameter for set #399
- Added automatic pull for Singularity remote images #356
- Added London and Canada AWS regions
- Merged Pass NXF_OPTS to JVM during the java version check to allow memory definition on memory-restricted environments #411
- Improved error message in launcher file
0.25.2 - 3 Jul 2017
- Fixed Execution hangs if a job submission fail #396
- Fixed stdout can not be sent into multiple channels #388
- Fixed Pipeline execution hangs when a process exceed the time limit and retry error strategy is used #387
- Added scientists and adjectives to run name generator
- Deprecated `route` operator
0.25.1 - 27 Jun 2017