Nextflow

- Fix nested params file parse 2091
- Fix Malformed config error reporting 2105
- Fix Use default opts for trace file creation [09e6c6ac]

- Fix NPE when AWS Batch job container is not returned [412b6fde]
- Fix execution hang when native task fail to submit 2060 [1253485d]
- Update preview message [e1eebdcd]
- Fix nf-ignite all packaging [72b6a428]
- Fix GS failing tests [be4f91e9]
- Fix AWS batch executor fails when using self-contained distribution 2058 [2e344c18]
- Fix groupTuple sort criteria with closure 2020 [28a579a9]
- Patch invalid double number cli parsing 2039 [4de4670c] [dcadaaeb]
- Update sphinx_rtd_theme 0.5.2 [4a165f43]
- Disable cpus option when running docker with legacy opt [1a7854a5]

21.04.0-edge - 8 Apr 2021
- Add readOnly flag to k8s volume mounts (2013) [33bd24ac]
- Add Start default plugins on-demand 1964 [cf2a9d73]
- Add support for tower workspaceId [e2977688]
- Improve support for BitBucket server repos [eb946e27]
- Fix toInt/Long/Float/Double operator hangs with value channel [7c35d985]
- Fix regression caused by nested params handling 1923 [b25af49b]
- Fix Cache invalidation when repo is cloned between runs 1989 [ac526f38]
- Fix Invalid setting of TMP var with singularity 1997 [23f80121] [472cfbdd]
- Fix issue overriding nested params from cli 1923 [cfe6b1d1]
- Fix az path handling curly brackets globs 1969 [c78a1bbf]
- Fix Missing git credentials when checking last commit id [f101308e]
- Fix plugins version check against local installation [535c2bb5]
- Fix local dependent formatting 1962 [2a5cbac1]
- Fix Encode path parameter at GitLab getContentUrl [6f80f651]
- Fix Only use sudo rm with docker 1956 [f9490423]
- Prevent AZ NPE when missing vmtype + better logging 1992 [711362ca]
- Refactor params file var binding 1860 1972 [330f044a]
- Prevent jobs names longer than 100 chars OAR exec [6daa21b9]
- Bump nf-azure0.9.6 + nf-amazon1.0.3 [aff1d355]
- Bump nf-amazon1.0.3 - s3fs1.0.9 - solve 1830 [b3b221c1]
- Bump nf-tower1.1.0 [29fdd9f7]
- Bump nf-amazon1.0.4 + nxf-s3fs1.1.0 [c638af80]
- Bump nf-azure0.9.7 [07c59946]

21.03.0-edge - 5 Mar 2021
- Add support for serializable ValueObject [8dfaadf3]
- Add abilitity to fetch revisioned git assets
- Add support for FixOwnership to AWS batch [24f83741]
- Add support for custom network to GLS 1810 [171f4aa8]
- Add ability to handle list of az vm types [00ced0b3]
- Add tower config scope to docs 1890 f2bd96fa
- Add charliecloud container environment from file (1909) 4553648b
- Add azcopy tool install mode opts [9e9337d3]
- Update Az default vm type to Standard_D4_v3 [4c6e76b6]
- Update NF console dependency [a2d06e15]
- Remove CDN from timeline reports and make them offline readable 1927 [c0e5a941]
- Fix plugins install failing in some file systems 1882 [8cc43391]
- Fix catch failing commands in nxf_parallel 1884 [dd56f6c1]
- Fix missing error on empty process script [3607f84e]
- Fix GSL path de-serialization issue [c6cf784f]
- Fix Memory unit cannot be a negative number 1902 [abd1c9d9]
- Fix pod spec labels to start with numbers in addition to alphas [79740edf]
- Fix OAR executor log files 1761 [6f2ff4e4]
- Fix issue cause by sleep with subsecond argument [c4be8d00] [63974ac6]
- Fix az blob storage SAS permissions [18a33213]
- Fix sort human-readable tasks in report [6d68f28d]

21.02.0-edge - 1 Feb 2021
- Fix Issue when merging nested cli params 1856 [275e54c4] [fe37da6d]
- Fix job status detection on PBS pro 1840 [c1598908]
- Fix Issue when merging nested cli params 1856 (19 hours ago) <Paolo Di Tommaso>
- Revert the CPU/memory options being passed to singularity VM instead of singularity container [0d04e0f9]
- Add ability to specify plugins with cli [de91218f]
- Decrease upload/download process polling to 0.2secs [6ca2d6ca]
- Remove nf-amazon as default [e6810e90]
- Make plugin services singleton [cacd9328] [5787be6d]
- Make repository provider accessible to subclasses [988bccc6]
- Fix error on plugin downloading 1859 [77cabb3c]

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 contains 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]

- 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 subscribe{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

- see 20.07.0 and 20.07.0-RC1

- 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