nextflow

• 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)
• Improve NF version checking [d33ea642]
• Bump plugins minor upgrade [f91bc21e]

• 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]

• Add support for charliecloud container engine #1809
• Fix glitch on K8s task progress update [668434f6]
• Upgrade to groovy 3.0.7 [27056035]

• 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]

• Add warning for AWS Batch mem request lower than 4 MB [e9240fc9]
• Add support for Bitbucket tags and branches retrieval [5083066e]
• Add support for Tower client bearer authentication [532282ae]
• Add support for Java 15 [b1f48884]
• Fix issue with docker images tagged by SHA #1777
• Fix Skip FS lock when Conda dir exist #1771
• Fix build with Gradle 6.7 [8d7227f0]

(from 20.09.1-edge)

• 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]

(from 20.09.0-edge)

• 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]
• Patch use of GString for fromSra apiKey option [a8b81ada]

(from 20.08.1-edge)

• Add variable NXF_CONFIG_FILE [d15edcb8]

(from 20.08.0-edge)

• 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

• 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]

• 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]

Add variable NXF_CONFIG_FILE [d15edcb8]

• 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

• 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]
• Allow unqualified stdin/stdout defintions with DLS2 [bcdcaab6]

• 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 #1632 (#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]

• 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]

• Add executor display name rendering [41e12a86]
• Add Aws Batch container image validation[e73951fa]
• Add SGE hr status handling (#1558) [f4db0049]
• Add Recognition for more UGE states (#1536) [4dacebbf]
• Fix Prevent invalid process tag values [f2da1357]
• Fix issue applying branch/multiMap to value channel [691963db]
• Fix AWS auth with temporary security token [e445b5eb]
• Fix Report Tower backend error cause on failure [da8ac8f5]
• Fix Config cmd should resolve remote projects #889 [62d54ac6]
• Fix for accelerator docs (#1578) e13f632d
• Update cloud docs [509d9966]
• Revert "Bump jline 2.14.9" [4078b860]
• Add docs tip [a215947d]
• Plus changes from 20.03.0-edge and 20.02.0-edge

• Fix AWS auth with temporary security token [6a7b11b8]

• 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

• 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]

• 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

• 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]

• 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]

• Add Google Life sciences (GLS) executor #1406 [ead29c11] [8228e9b4]
• Add GLS assigned zone discovery #1406
• 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]