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@pditommaso pditommaso released this May 31, 2020

  • Add support for NXF_LOG_NAME env var [cf49661]
  • Add exception specialiation for ambiguous repo [a34b1d2]
  • Add support for tower_workflow_id env var [5318812]
  • Add config profile names accessor [2784cdb]
  • Add support for Google Cloud buckets with Requester Pays set #1466 [bc9db8d]
  • Add Git tag and branch retrieval [7c97f23]
  • Fix PublishDir error caused by duplicates output files [5f3b69c]
  • Fix weird issue on config resolution [0d0fef4]
  • Fix resolution of malformed configs [fe213e4]
  • Fix K8s labels and annotation normalization [6434b9d] #1577 #1584
  • Fix minor git path provider ending slash [9888be2]
  • Fix bugs in GA4GH TES support (#1589) [2670833]
Assets 4

@pditommaso pditommaso released this May 3, 2020 · 68 commits to master since this release

Assets 4
Pre-release
Pre-release

@pditommaso pditommaso released this Apr 19, 2020 · 38 commits to master since this release

  • Fix AWS auth with temporary security token [6a7b11b]
Assets 4
Pre-release
Pre-release

@pditommaso pditommaso released this Apr 13, 2020 · 41 commits to master since this release

  • Add SGE hr status handling (#1558) [f4db004]
  • Add moduleDir, projectDir and launchDir vars [7832a69] [576a569]
  • Add executor display name rendering [74c90ca]
  • Add ability to pipe custom fun [DSL2] [80bb648]
  • Add Aws Batch container image validation [e73951f]
  • Recognizes more UGE states (#1536) [4dacebb]
  • Prevent invalid process tag values [f2da135]
  • Report Tower backend error cause on failure [da8ac8f]
  • Fix Config cmd should resolve remote projects #889 [c2e0ac0]
  • Fix issue applying branch/multiMap to value channel [e69f39f]
  • Fix Kill signal is not propagated for Singularity container #1561
  • Fix docs typos [d7261d2]
  • Fix Minor docs update #1545
  • Revert "Bump jline 2.14.9" [ef7040c]
  • Deprecate validExitStatus directive #1564
  • Improve error message [DSL2] [f8a0ee1]
  • Add sluper parse method for Path [a54fd03]
  • Report error message when accessing invalid out #1553 [83bd009]
  • Remove deprecated $ config syntax [0a31f9d]
  • Remove deprecated workflow publish [DSL2] [1bd7b4a]
  • Remove support for workflow 'get' [d9b9114]
  • Remove deprecated process output getter [013a323]
  • Remove deprecated out cardinal getters [414fae9]
  • Remove deprecated gpu directive [f48b2c2]
  • Minor executor logging [7f94299]
  • Minor improvement createDirIfNotExists API [3421167]
  • Bump groovy 2.5.11
Assets 4
Pre-release
Pre-release

@pditommaso pditommaso released this Mar 28, 2020 · 77 commits to master since this release

  • Add support for GLS private addr #1545 [a481b42]
  • Add AWS batch job def normalise function [79239f0]
  • Fix Escape Singularity env variables #1535 [b651a37]
  • Add Local executor file system check [ffc9292]
  • Add Launch Id to Tower client [d768d2d]
  • Add workflow progress on completion [aea41f3]
  • Remove deprecated onFlowStart method [14f12b5]
  • Minor method visibility change [43bc969]
  • Minor log change [130a963]
  • Fix docs broken link [0a1ec9a]
  • Fix typo CVS -> CSV #1500 [d89281c]
Assets 4
Pre-release
Pre-release

@pditommaso pditommaso released this Feb 29, 2020 · 92 commits to master since this release

  • 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 7f315a6
Assets 4

@pditommaso pditommaso released this Feb 12, 2020 · 105 commits to master since this release

  • Fix ansi logging and line count [4f5c718]
  • 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 [7892854]
  • Bump jline 2.14.9 [5df2b27]

(included with 20.01.0-rc1)

  • Add ability to extend module params #1484 [17c6acc]
  • Add dsl2 command line opt [1cf544d]
  • Add GLS executor docs [574f209] [7ce2597]
  • Add HTCondor detail on data sharing #1473 [f0af66d]
  • Allow aliased process to inherit config settings [DSL2] [1c447e8]
  • Allow module inclusion to inherit context params #1484
  • Allow multiple inclusion from the same module [DSL2] [a9ae36f]
  • Fix Script template fails to render list of files #1478 [2e97bbb]
  • Fix process name validation when using legacy script [1543365]
  • Fix Early detection Dsl2 declaration #1468 [93a642a]
  • Fix Missing script validation checks #1468 [5d0cf14]
  • Revert "Disable ansi log on non-tty env #1417" [98e6758]
  • Minor changes gradle build [619385f]
  • Minor AWS Batch api refactor [c20abc1]
  • Improve foreign file detection [5050868]
  • Improve GLS location validation [5b89ab5]
  • Removed unused module flag [cf19cc9]
  • Update dsl2 docs [5c57c3a]

(included with 20.01.0-edge )

  • Add Prevent negative progress stats [87cdddc]
  • Add More cloud tests [7a5dd82]
  • Add support for UGE throttled jobs (Tr) #1461 [20408e4]
  • Add progress stats to tower client [781116a] [138cf0b]
  • Add experimental Podman containers support (#1451) 026866c
  • Add support for Gexf format for DAG rendering [28bfe0e]
  • Improve ansi logging for multilines output [1ce978c] [004e23e]
  • Improve progress stats and ansi log [0212ba1]
  • Improve api to enable wr executor #1148 [21088ad]
  • Update tower trace client requests [138cf0b]
  • Enhance progress execution stats & tracking [a30e2b9]
  • Unexpected output when using Google Storage as work dir #1452
  • Fix typos and minor changes [fb2f954]
  • Fix Operator splitFastq fails with PE option and DSL2 enabled #1390
  • Fix Container entrypoint when using GLS executor #1291
  • Fix GLS file unstaging #1406 [e67ef3b]
  • Fix GLS unstage for file patterns #1406
  • Fix Scratch directive does not work #1280 [644e9ac] [6c7291f]
  • Fix Resume fails due to LevelDB exception #1358 [28fa3a6]
  • Fix Conda env activation #1195 [e391927]
  • Fix java command in launch script #1436 [f28b015]
  • Rename variable java to JAVA_BIN [086377d]
  • Removed unused compile deps [686bcd9]
  • Bump capsule-maven 1.0.3.2 and fix broken env [004684e]
  • Bump capsule-maven 1.0.3.1 and seqera repo [62964ee]

(included with 19.12.0-edge)

  • Add GLS assigned zone discovery #1406
  • Add Google Life sciences (GLS) executor improvements #1406 [ead29c1] [8228e9b]
  • Add GLS bootDiskSize support #1331 [f118798] [af8fe16]
  • Add GLS job debugging #1351
  • Fix NPE when file pattern is missing [1cbb6e4]
  • 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 [85cd0cd]
  • Fix fromFilePairs can't take list of paths #1405 [c00f566]
  • Refactor onFlowInit to onFlowCreate event [c477eea]
  • Improve err msg when input files are remove from output [5d5744a]
  • Upgrade to Gradle 6.0.1 [e0c1a3a]

(included with 19.11.0-edge)

  • Increase tasks.module to 255 [7332c60]
  • Fix Allow the output of process env variables #69 [1c1befc]
  • Fix docs rounding issue #1350 [af824fc]
  • Fix Join operation incorrectly represented in DAG #1346 [9d83ed5]
  • Fix Tiny typo in docs #1361
  • Fix lost trace/report/timeline file name
  • Fix invalid class exception [4308d6a]
  • Fix Invalid dynamic resolution of stageIn/OutMode directive #1374
  • Fix No such property stackTraceDepth error #1387 [49450f6] [f5342e7]
  • Fix Singularity env variables are not accessible #1386 [036af4a]
  • 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 [a1addc8]
  • 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) [cc58436] [3523f17]
  • Introduce workflow take in place of get [DSL2] [e8cbbf0]
  • Disable ansi log when using dockerized run [86bc2ad]
  • Minor logging change [238b0e6] [f5342e7] [b707882] [ce97f07]
  • Add multiMap in place of fork operator [afd671c]
  • Add Show Tower init response message as warning
  • Add output path includeInputs docs [2ce7e86]
  • Add metrics fields check #1360 [5b7f42e] [caf9f13]
  • Add console command to cli help #1347
  • Add OAR executor #1343
  • Add graphiviz to Docker image #1370
  • Removed unused property [9c65426]
Assets 4
Pre-release
Pre-release

@pditommaso pditommaso released this Feb 6, 2020 · 118 commits to master since this release

  • Add ability to extend module params #1484 [17c6acc]
  • Add dsl2 command line opt [1cf544d]
  • Add GLS executor docs [574f209] [7ce2597]
  • Add HTCondor detail on data sharing #1473 [f0af66d]
  • Allow aliased process to inherit config settings [DSL2] [1c447e8]
  • Allow module inclusion to inherit context params #1484
  • Allow multiple inclusion from the same module [DSL2] [a9ae36f]
  • Fix Script template fails to render list of files #1478 [2e97bbb]
  • Fix process name validation when using legacy script [1543365]
  • Fix Early detection Dsl2 declaration #1468 [93a642a]
  • Fix Missing script validation checks #1468 [5d0cf14]
  • Revert "Disable ansi log on non-tty env #1417 [98e6758]
  • Minor changes gradle build [619385f]
  • Minor AWS Batch api refactor [c20abc1]
  • Improve foreign file detection [5050868]
  • Improve GLS location validation [5b89ab5]
  • Removed unused module flag [cf19cc9]
  • Update dsl2 docs [5c57c3a]
Assets 4
Pre-release
Pre-release

@pditommaso pditommaso released this Jan 20, 2020 · 144 commits to master since this release

  • Add Prevent negative progress stats [87cdddc]
  • Add More cloud tests [7a5dd82]
  • Add support for UGE throttled jobs (Tr) #1461 [20408e4]
  • Add progress stats to tower client [781116a] [138cf0b]
  • Add experimental Podman containers support (#1451) 026866c
  • Add support for Gexf format for DAG rendering [28bfe0e]
  • Improve ansi logging for multilines output [1ce978c] [004e23e]
  • Improve progress stats and ansi log [0212ba1]
  • Improve api to enable wr executor #1148 [21088ad]
  • Update tower trace client requests [138cf0b]
  • Enhance progress execution stats & tracking [a30e2b9]
  • Unexpected output when using Google Storage as work dir #1452
  • Fix typos and minor changes [fb2f954]
  • Fix Operator splitFastq fails with PE option and DSL2 enabled #1390
  • Fix Container entrypoint when using GLS executor #1291
  • Fix GLS file unstaging #1406 [e67ef3b]
  • Fix GLS unstage for file patterns #1406
  • Fix Scratch directive does not work #1280 [644e9ac] [6c7291f]
  • Fix Resume fails due to LevelDB exception #1358 [28fa3a6]
  • Fix Conda env activation #1195 [e391927]
  • Fix java command in launch script #1436 [f28b015]
  • Rename variable java to JAVA_BIN [086377d]
  • Removed unused compile deps [686bcd9]
  • Bump capsule-maven 1.0.3.2 and fix broken env [004684e]
  • Bump capsule-maven 1.0.3.1 and seqera repo [62964ee]
Assets 4
Pre-release
Pre-release

@pditommaso pditommaso released this Dec 20, 2019 · 180 commits to master since this release

  • Add Google Life sciences (GLS) executor #1406 [ead29c1] [8228e9b]
  • Add GLS assigned zone discovery #1406
  • Add GLS bootDiskSize support #1331 [f118798] [af8fe16]
  • Add GLS job debugging #1351
  • Fix NPE when file pattern is missing [1cbb6e4]
  • 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 [85cd0cd]
  • Fix fromFilePairs can't take list of paths #1405 [c00f566]
  • Refactor onFlowInit to onFlowCreate event [c477eea]
  • Improve err msg when input files are remove from output [5d5744a]
  • Upgrade to Gradle 6.0.1 [e0c1a3a]
Assets 4
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