nextflow
-
Version 20.01.0
Published by pditommaso over 4 years ago
- 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]
(included with 20.01.0-rc1)
- 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]
(included with 20.01.0-edge )
- 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]
(included with 19.12.0-edge)
- 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]
(included with 19.11.0-edge)
- 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]