Nextflow

- Fix execution hang when reading empty error file [414240a1a]

- Fix Azure executor fail to cleanup jobs on completion [4d5b71370]
- Fix Missing AWS SSE encryption for begin and exit task files 2452 [841e6101b]
- Fix Azure integration test [a8051bc01]
- Fix false positive detection of publishDir conflict [292b439ad]
- Make Azure executor logging less verbose [7452e386d]
- Change Azure test pool vmType [85682be7d]
- Downgrade Google NIO library to version 0.121.2 [66ae98820]
- Add java 16 and 17 to the launch.sh for debugging 2457 [3ff0a248e] <mmatthews06>

- Fix Azure batch NPE when missing pool spec [84b2983f4]
- Fix Docker bin in image PATH 2445 [d30da377a] <Josh Chorlton>
- Fix failing test with Java 16 [f2d01888d]
- Fix AWS_RETRY_MODE var definition in Batch job [f1a58600d]
- Add docs for AWS endpoints for China region [e96c56d1e]
- Correct description of cross 2446 [e4c7f3d98]
- Dump resolved config when log trace is enabled [2580fb108]
- Bump nf-azure0.11.1 [eb1e6fbd2]
- Bump nf-amazon1.3.2 - bump nxf-s3fs1.1.2 [ae9e885a8]

- Add support for Java 17 [cb207cd64]
- Allow override Bash wrapper template files [e6e25ed7c]
- Fix issue with plugins local root sync [1d974a4eb]
- Fix Nextflow does not recognised Failed pod (2430) [9c80cdea0] <Mike Smoot>
- Fix Error reporting on Bash launcher creation failure [63e01c324]
- Fix Channel.fromSRA error one some project ids 2156 [dbcbac139]
- Fix Task completion percentage 2440
- Display no workflow warn if no main is defined [0f1295694]
- Invalidate task cache on directive change (EXPERIMENTAL) [62ded3421]
- Upgrade XmlParser used by SraExplorer [543b582b5]
- Use AWS Batch resources requirement for CPUs and memory [1cf2c379c]
- Bump Gradle 7.3 stable + GHA cache [4eaa4f25f]

21.09.1-edge - 28 Oct 2021
- Fix issue with config selectors and DSL2 [4d7d3e972]
- Fix issue evaluating dynamic errorStrategy with AWS Batch [8c6a5a6e2] [ce4d491b1]
- Fix verbose logging [92b113134]
- Fix docker image url [ed24a475d]
- Fix Temporary directories not deleted in on_exit 2406 [181bdf528] <Lukas Jelonek>
- Fix implicit authentication for resources served by Tower [e30310b4f]
- Fix No more of 255 channels can be defined into a workflow context 2417 [7f91ecb39]
- Add tip about escaping variables in env scope 2366 <Ben Shealy>
- Add K8s env fieldPath option to pod directive 2363 <Ben Shealy>
- Improve AWS Batch error report fetching CloudWatch logs [b9f9578f1] [e229700ef]
- Improve docs about IAM policies for AWS Batch 2391 <Manuele Simi>
- Accommodate token in password field for Gitlab 2389 [ee32b7726] <Abhinav Sharma>
- Report a warning when main workflow is not defined [83aec6e8b]
- Bump nf-amazon 1.3.0
- Bump nf-tower1.3.0
- Bump nf-google1.1.2

21.09.0-edge - 12 Oct 2021
- Add secrets manager (preview) [da2a5ff1a] [2d66f83ca]
- Add Built-in support for Azure File Shares 2285 [a4c3e0ad5]
- Add Azure pool node SKU selection 2360 [9afcac756]
- Add support for protocol option to fromSRA 2087 [371f858ab]
- Add retry on AWS Job definition not-found error [452cae5d8]
- Add ability to define templates library at module level 2332 [7e7d52573]
- Add missing information for pulling images from private registry in Azure Batch 2355 [040e190bd]
- Add $NXF_CLI_OPTS env variable [7d57acca5]
- Add NXF_CACHE_MODE env variable [1c345c497]
- Fix asset directory consistent hashing via sha256 checksum [4c5c0ef41]
- Fix issue invoking extension method with GString params [570e5299c]
- Fix Prevent pipeline stopping when K8s pod is evicted [f9db9cc77]
- Fix clean command for Google storage [dc9625eb9]
- Fix plugins detection in local repo [6441a3882]
- Fix S3 canned ACL documentation 2334 [69216e292]
- Fix docker image build with recent docker [2aad36897] [1e485b32b]
- Fix amazon plugin is not used when using bucketDir option [6a8c50ad4]
- Fix Plugin dependency requirement overrides core plugin 2303 [4d1762fb3]
- Fix Make K8s ImagePullBackOff and ErrImagePull recoverable 2302 [766ffde40]
- Improve cache resume strategy [0b0eae225]
- Improve GH action build compressing integration tests [ab9d747d4]
- Prevent NPE if session is not set [83bb46d94]
- Remove deprecated attribute [50d63b6fb]
- Find newest matching plugin 2303 [e6cf79ff3]
- Documents noproxy variable 2325 [bc769b1b4]
- Bump Groovy 3.0.9 [dee2d6c99]
- Bump nf-sqldb0.2.0
- Bump nf-amazon1.2.1
- Bump nf-azure0.11.0
- Bump nf-google1.1.1

21.08.0-edge - 30 Aug 2021
- Fix plugin updater version logging [d162eb8b4]
- Fix Nextflow launcher breaks when java path contains blanks 2265 [8097a2a90]
- Fix docker build [efb2f449b]
- Fix NPE in AnsiLogObserver 2283 [cffc683df]
- Fix run script when fixing ownership in aws batch 2262
- Improve plugins auto start [283144474]
- Improve log error reporting [401863085]
- Improve handling of K8s node shutdown [67250c041]
- Update GitHub docs [4532b8e1e]
- Merge nf-sqldb 0.1.0

21.07.0-edge - 6 Aug 2021
- Add support for AWS_MAX_ATTEMPTS variable [3cc543589]
- Add app plugin to gradle build [007bc1cb4]
- Add self pid to tower client [d2e54ea22]
- Add support for head job operationId + log/out files [a7a76cf91]
- Add enable CA Issuers option to NF launcher [8f51dc787]
- Fix Clean cmd fails removing foreign files [8bf8ab720]
- Fix Prevent script var names conflicting with private names 2246 [82bbc180e]
- Fix ENA download URL 2239 [befbabbc8]
- Fix Tower client is not activated launching all packaging 2145 [c507518c2]
- Fix orphaned AWS Batch jobs after pipeline interruption 2169 [65e2a4d05]
- Fix Process error report on target exception 1896 [1bac3f17b]
- Fix Unexpected bool conversion on publishDir enable/overwrite attributes 2220 [651835d2d]
- Fix BatchCleanup toString method [ec9bb5648]
- Improve error reporting [49ac01dbb]
- Improve Unknown host error message [ad41d1e98]
- Improve AWS Batch task handler [eb1aff275]
- Use AWS cli standard retry mode by default [f2f1fdea4]
- Report warn on cache hashing failures [7bf93de06] [3b579c954]

- Fix Tower client is not activated launching all packaging

- Fix Plugin install lock file is not deleted 2103 [29c3e516c]
- Fix Default plugin version lookup [d340a221f]
- Fix BatchCleanup toString method [3c67fa3ae]
- Implicit variable projectDir breaks caching 2186 [7a4d1f1a2]

21.06.0-edge - 3 Jul 2021
- Add Keep alive option to Google LS executor [994222074]
- Add support for FTP proxy and proxy servers authentication [8ec33b04d]
- Add support for plugins grouping [aa5bc7d34]
- Add More details about the reason why a AWS Batch job has failed 2146 [27a4e88b2]
- Add support for extensions priority [ae083f1aa]
- Add stubRun attribute to workflow metadata 2164 [86cfc66fd]
- Add Run tasks under user accounts in Azure Batch 2157 [1c9fc4a40]
- Refactor GLS executor [2c86b79a4] [97fc49c09]
- Refactor AWS batch job def creation [89ce364c9] [986894287]
- Fix Default plugin version lookup [e0c8151d9]
- Fix Negative labels do not work as expected 2155 [491191811]
- Fix PublishDir overwriting task output files [190aa4eaf]
- Fix directory deletion strategy [b96fcedc8]
- Fix Implicit variable projectDir breaks caching 2186 [76417d273]
- Fix Prevent empty download array [9492cde5d]
- Fix output unstage with glob pattern [2d4c3dfcf]
- Fix Connection-reset crashes the workflow [3ee4fd0eb] [1400ded6d] [61bbc240a] [175c66584]
- Fix Slurm does not send soft kill message 2163 [f0ccfc7e8]
- Fix storeDir directive does not work with S3 2141 [2e95a6a76]
- Fix maven local publish [05cfb7cf7]
- Fix GLS transfer attempts opts [f7c705db5]
- Fix build exportClasspath task [88d27f0c8]
- Fix PbsPro clusterOptions directive priority 2036 [75e3f225e]
- Disallow include nested within a workflow block [7dbf64bea]
- Upgrade AWS SDK minor version 2167 [296afaa8f]
- Improve gsutil transfer throughput [2da120b91]
- Improve config error reporting [6aa102430]

21.05.0-edge - 28 May 2021
- Add support for using mamba with conda (2030) [10c8385b]
- Add AWS cli native error fail-over [fd7670ef]
- Add support for Container Registry to Az Batch executor (2078) [12bf2da6]
- Add support for Tower workspace (2097) [8a4dd3ab]
- Add support custom service account email in Google Cloud LifeSciences executor (2044) [a642c9ea]
- Add support for Java 16 + Gradle 7 [caace1c5] [e2dd4510] [74e466e0] [1245ab1c] [bfc69fb6]
- Improve tower client error reporting [4efb6bf6]
- Fix Plugin install lock file is not deleted 2103 [b7fdffac]
- Fix Use caller runs policy of default thread pool 2021 [48b4e8ee]
- Fix Error reporting for malformed config [68e5ca18]
- Decrease max par transfers to 4 [c7ea816a]
- Prevent fetching aws instance type when missing container id [f5f96049]
- Use default opts for trace file creation [d8ae94bf]
- Improve Azure Batch executor error code and messages for failed Tasks (2099) [1d5fa5d5]
- Bump groovy 3.0.8 [aa695e12]
- Bump snakeyaml1.28 [8d361954]