Nextflow

- Allow unqualified stdin/stdout definitions with DSL2 [bcdcaab6]

- 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

- 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]

- 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]

- 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]

- 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 scripts 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