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NEXTFLOW CHANGE-LOG
===================
22.02.1-edge - 3 Mar 2022
- Prevent multiple parsing of params file [38bb1f71]
22.02.0-edge - 25 Feb 2022
- Fix Prevent S3 tagging with empty list [ae7db466]
- Fix Azure repos tests [856aacf0]
- Fix isse on includeConfig resolution #2675 [6591a9e1]
- Fix NPE when accessing not existing Git file [6c79f8fd]
- Fix Batch Job name exceed max allowed size [e8b70ca3]
- Fix detect and skip bom mark in files (#2645) [02b06ba3] <Jorge Aguilera>
- Feature: Abort session if publish fails (#2643) [79b3836b] <Jorge Aguilera>
- Fix report overwrite cannot be disabled [202b5c9c] #2647
- Fix match bash interpreter irrespective the path [c2d2b9b2]
- Fix build warning + plugins assemble (#2634) [00dd143a] <Jorge Aguilera>
- Fix CITATION.cff and add automatic validation of your citation metadata [15698a45] <Faruk D>
- Bump [email protected] [a4496bb2]
- Bump [email protected] [e51139bb]
22.01.0-edge - 7 Feb 2022
- Add support for Tower reports (#2523) [de3d76349] <Jordi Deu-Pons>
- Add RateLimitExceededException when GitHub api limit is reached [ff123c605]
- Add fetch tags and branches to local git provider [e1de8e0ac]
- Add K8s priorityClassName pod option, updated tests (#2585) [51650f8c4] <Ben Sherman>
- Add securityContext pod option to docs (#2584) [19f16f0da] <Ben Sherman>
- Add automountServiceAccountToken option for k8s executor (#2562) [1b5908e4c] <xhejtman>
- Add warn about AWS CLI grandparent path in container (#2565) [67073b0c5] <Simon Li>
- Add affinity option to pod directive (#2522) [640cbed48](3 weeks ago) <Ben Sherman>
- Add ability to specify memory/cpu resources for the control pod (#2559) [13f3e036d] <xhejtman>
- Add `-entry` parameter to pass in k8s executor (#2525) [a96233af6] <xhejtman>
- Add AWS Athena JDBC driver for nf-sqldb plugin (#2500) [462575f05] <Abhinav Sharma>
- Fix process output 'env' as array (#2624) [0a246dc2c] <Jorge Aguilera>
- Fix make date format to change independent from system locale [d1e5f6e76] <Jorge Aguilera>
- Fix double access of params file [459ebab7b] <Paolo Di Tommaso>
- Fix Use account SAS token instead of service SAS token (#2576) [d5125975d] <Florian De Temmerman>
- Fix upload of nested directory outputs on azure (#2578) [85ad55225] [744447155] <Florian De Temmerman>
- Fix Docs Typo (#2556) [942be46f6] <Kibubu>
- Fix NXF_PARAMS_FILE is not recognised #2549 [62f5fe1d9]
- Fix failing tests (4 weeks ago) <Paolo Di Tommaso>
- Fix Unable to use output path with nested properties [ceceb0784]
- Fix Nextflow couldn't parse generated nextflow.config under some circumstances (#2496) [2dfbbc63c] <Fabian Lehmann>
- Fix invalid use of `var` keyword [8418cc8d6]
- Improve k8s executor throwing NodeTerminationException on node shutdown (#2590) [084c8d6ca] <Patrick Hüther>
- Improve docs on `include` statements (#2520) [9c140cee3] <Alexander Toenges>
- Improve core plugins info & logging [dfa544ac9]
- Improve Secrets handling [1c0ad4679] [329502d19] [[26b4be906]]
- Improve DSL2 documentation [048b026f2] [e2e8b5557] <Manuele Simi>
- Improve documentation (#2600) [787a1fd84] <Ben Sherman>
- Allow disabling history file unique check [c3677c311]
- Make S3 parallel download as default [b490f146d] [03dae9d6e]
- Run Azure integration tests only with Java 11 [0890ceeb3]
- Prepare for Java >= 11 build [8c0566fc3] [5ba16dd18] [405b67365]
- Use Standard_A3 instance type for Azure tests [67e7d3ab3] [b97b0010c]
- Refactor cache store using plugins [54bf7a61d]
- Update google cloud docs (#2594) [dfa867953] <Ben Sherman>
- Update the azure docs for registry [96baf288e] <Abhinav Sharma>
- Update copyright info [807a816a5]
- Remove gradle logs about tasks dependencies (#2618) [cae44e00b] <Jorge Aguilera>
- Remove Tika deps for nf-amazon module [95620d42b]
- Remove deprecated validExitStatuas directive [b3117e789] [2188d51a0]
- Remove support for Apache Ignite [d4dc1cfe1] [64d2773fd]
- Bump [email protected] as default plugin
- Bump Gradle 7.3.3 [f00bfb0d3]
- Bump [email protected] [40f90aa92] [[2bc16732e]]
21.12.1-edge - 22 Dec 2021
- Add tags attribute to publishDir directive [e78a997b5]
- Add ability to disable running jobs cancellation [a13af9a3c]
- Add ability to define containerProperties with using AWS Batch #2471 [ac7f1e71e] <Manuele Simi>
- Add NXF_JVM_ARGS env variable [7afb2deed]
- Improve paths validation [0849d583f]
- Include S3FS provider into nf-amazon plugin [3a7bf8c7a]
- Fix error reporting on missing script file #1951 [e1a0b240a]
- Fix singularity docs #2493 [c66cb3ba7] <Jose Espinosa-Carrasco>
- Fix cross compilation error cause by ByteBuffer [74916100f]
- Fix File staging race condition + beta AWS parallel downloader [b7c262de3]
- Fix enableAIAcaIssuers launcher flag [cd780aabd]
- Fix task index sequence generation [3447e735b]
- Fix Changes process directives invalidates tasks cache [967c1adff]
- Fix Interrupted download of staged files cause execution to fail #1552 [847789fad]
- Fix plugins start/stop for fs command [88d8be1f4]
- Fix for nested params with the same name #2485 [02de4147c] <Jay Carey>
- Fix race condition on plugin autoload status [ab00a50f5]
- Fix failing test with Java 17 [1c6183c92] [4daf8d0a1]
- Note on Azure Batch inactive pools #2483 [7fc116067] <Manuele Simi>
- Remove drip launcher [909f95279]
- Update azure test image [de9d5ee8c]
- Update logging library [a957db646]
- Bump [email protected] [93193a3f3]
- Bump version 21.12.0-edge [9cb7ee81f]
- Bump AWS sdk 1.12.129 [bd7ba1706]
- Bump logback 1.2.9 [29f260717]
- Bump Jsoup 1.14.3 [5776c0391]
- Bump corretto:17.0.1 [f7e047ea4]
21.12.0-edge - 22 Dec 2021 [SKIPPED]
21.10.6 - 21 Dec 2021
- Bump Slf4j 1.7.32
- Bump Logback 1.2.9
21.10.5 - 8 Dec 2021
- Fix race condition on plugin autoload status [73a0893ce]
21.11.0-edge - 5 Dec 2021
- Add process and workflow recursion (PREVIEW) [9f51155e9]
- Fix include no longer works for custom methods [6adfce099]
- Fix Azure executor fail to cleanup jobs on completion [533448be4]
- Fix Missing AWS SSE encryption for begin and exit task files #2452 [2c6665ef9]
- Fix false positive detection of publishDir conflict [6ea54eaea]
- Fix execution hang when reading empty error file [414240a1a]
- Test with java-17 LTS [c2141e826] <Abhinav Sharma>
- Improve plugins dev root detection [b095bee15]
- Change Azure test pool vmType [ad5ad97ab]
- Downgrade Google NIO library to version 0.121.2 [896ec3abd]
- Bump [email protected] - bump [email protected] (6 days ago)
- Bump gradle 7.3.1 [2c34a3a27]
21.10.4 - 30 Nov 2021
- Fix include no longer works for custom functions #2469 [e17f6155d]
- Bump [email protected] - bump [email protected] [be893dcb1]
21.10.3 - 23 Nov 2021
- Fix execution hang when reading empty error file [414240a1a]
21.10.2 - 22 Nov 2021
- 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>
21.10.1 - 18 Nov 2021
- 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 [email protected] [eb1e6fbd2]
- Bump [email protected] - bump [email protected] [ae9e885a8]
21.10.0 - 11 Nov 2021
- 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] (3 days ago) <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 implict 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 [email protected]
- Bump [email protected]
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 [email protected]
- Bump [email protected]
- Bump [email protected]
- Bump [email protected]
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]
21.04.3 [stable] - 21 Jl 2021
- Fix Tower client is not activated launching all packaging
21.04.2 [stable] - 12 Jul 2021
- 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 groupping [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 [email protected] [8d361954]
21.04.1 [stable] - 14 May 2021
- Fix nested params file parse #2091
- Fix Malformed config error reporting #2105
- Fix Use default opts for trace file creation [09e6c6ac]
21.04.0 [stable] - 2 May 2021
- 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 suppor 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 dependant 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 [email protected] + [email protected] [aff1d355]
- Bump [email protected] - [email protected] - solve #1830 [b3b221c1]
- Bump [email protected] [29fdd9f7]
- Bump [email protected] + [email protected] [c638af80]
- Bump [email protected] [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 containes 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]
20.10.0 - 1 Nov 2020
- 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 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
20.07.1 - 24 Jul 2020
- see 20.07.0 and 20.07.0-RC1
20.07.0 - (skipped)
- Allow unqualified stdin/stdout defintions with DSL2 [bcdcaab6]
20.07.0-RC1 - 21 Jul 2020
- 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
20.01.0 - 12 Feb 2020
- 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]
20.01.0-rc1 - 6 Feb 2020
- 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]
19.10.0 - 21 Oct 2019
- 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]
19.07.0 - 27 Jul 2019
- 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 scrips 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
19.04.0 - 15 Apr 2019
- Added support for NCBI_API_KEY variable [e4d9b62c]
- Added warning message when using untested Java version [35acd1cb]
- Added parameter and workflow metadata to weblog payload #1077
- Added warning on publish with a null var [7d58bfb7] [95c219fb]
- Fixed Echo directive when Ansi log is enabled #1112 #996
- Fixed Do not mount inputs when `stageInMode == copy` #1105
- Fixed `splitCsv` operator fails to parse values containing commas #1102
- Fixed missing return type for Date.format method
- Fixed Channel operations `toList` followed by `merge` hang execution #1083
- Avoid printing execution summary when no processes are computed #996
- Improved error reporting for null publishDir [0b9b52f0]
19.03.0-edge - 14 Mar 2019
- Fix Nextflow hangs submitting jobs to AWS Batch #1024
- Fix process builder incomplete output [2fe1052c]
- Fix Grid executor reports invalid queue status #1045
- Fix Script execute permission is lost in container #1060
- Fix K8s serviceAccount is not honoured #1049
- Fix K8s kuberun login path #1072
- Fix K8s imagePullSecret and imagePullPolicy #1062
- Fix Google Storage docs #1023
- Fix Env variable NXF_CONDA_CACHEDIR is ignored #1051
- Fix failing task due to legacy sleep command [3e150b56]
- Fix SplitText operator should accept a closure parameter #1021
- Add Channel.fromSRA factory method #1070
- Add voluntary/involuntary context switches to metrics #1047
- Add noHttps option to singularity config #1041)
- Add docker-daemon Singularity support #1043 [dfef1391]
- Use peak_vmem and peak_rss as default output in the trace file instead of rss and vmem #1020
- Improve ansi log rendering #996 [33038a18]
19.02.0-edge - 6 Feb 2019
- Added foreign files caching ability #686
- Added Ansi logging as default console output
- Added Gitea source code provider [ae04fc37]
- Fixed Join operator returns invalid remainder values #1015
- Fixed Invalid trigger of integration tests [7aa5908a]
- Fixed memory allocation for SGE executor [29353c90]
- Fixed properties access for TaskConfig and LazyMap [09b74a52]
- Fixed Invalid decimal separator in mem unit string #999
- Fixed tail error on launcher script [38afea6c]
- Improved Execution and Timeline memory reporting #980 #986 #1012 #1014 #1016 #1018 [01426097] [7d6c29f0]
- Improved Google pipelines file copy strategy [678405b2]
- Improved output file stage out behaviour docs #961 #1013
- Upgraded Groovy runtime to version 2.5.6
19.01.0 - 22 Jan 2019
- Added Google Cloud Platform integration
- Added support for K8s nodeSelector #955
- Added new AWS regions #935
- Added json/yaml output to info command #657
- Added More duration and memory unit syntax sugar #921
- Added NO_PROXY env variable should be honoured #864
- Added keepHeader option to splitText operator #912
- Added countLines, countFasta and countFastq methods #972
- Added an env variable to define default cloud driver #973
- Fixed Unable to find JVM 1.8 err message #1000
- Fixed Memory unit should contain thousand separator [e6ec4c84] #989
- Fixed LSF long user names breaks jobs status parsing [b4306151] #988
- Fixed Move output files to storeDir instead of copying them #745
- Fixed Interpolated strings in a from statement are misinterpreted #978
- Fixed ConcurrentModificationException when publishing output files #971
- Fixed Launcher fails with Java 10 or later #953
- Fixed remote bin directory when using bucketDir option [6d796783]
- Fixed foreign file system detection [1489cc72]
- Fixed Ansi logger division by zero [ae2b1380]
- Fixed Unparseable Data format on http file #962
- Fixed Log command history #405
- Fixed Too long process tag name can cause SLURM failure #941
- Fixed LSF can return an inconsistent jobs status #927
- Fixed dump last queue status on failure [36e80242]
- Fixed Allow the usage of a custom docker image for K8s driver pod #877
- Fixed K8s executor when the cluster has no available cpus #824
- Fixed Prevent duplicate process definitions #920
- Fixed Update queue statuses used by PBS Pro #908
- Fixed K8s launcher fails to set pod work directory [dc8bfead]
- Fixed cmd cloud error message [14d603b9]
- Fixed RejectedExecutionException on successive Console executions #906
- Fixed Invalid config rendering #801
- Fixed Invalid warning message for config selector #905
- Fixed Queue status command fail on LSF version 8 #910
- Fixed Use `bash` instead of `sh` to fetch queue status
- Improved script runner api [da4a6c17]
- Improved file hashing logging [0d35b2b4]
- Refactored ScriptRunner class [15ee2f1c]
- Refactored DSL code visitor [67904c1f]
- Revert "Apache Ignite to version 2.6" #909
- Better report warning when grid status command fails [3ac8b972]
19.01.0-edge - 10 Jan 2019
- Enhanced timeline and execution reports #985 #986 [fb00c3a6] [092f0b9e]
- Enhanced BashWrapperBuilder using template file [7d7e116a] [c62b9dff]
- Fixed CPU usage accounting #982 [7d7e116a] [c62b9dff]
- Fixed Move output files to storeDir instead of copying them #745
- Fixed Interpolated strings in a from statement are misinterpreted #978
- Fixed Launcher fails with Java 10 or later #953
- Fixed LSF long user names breaks jobs status parsing [b4306151] #988
- Fixed Memory unit should contain thousand separator [e6ec4c84] #989
- Fixed Allows fromFilePairs to handle non globs #946
- Added an env variable to define default cloud driver #973
- Added countLines, countFasta and countFastq methods #972
- Added NXF_DIST launcher variable #954
- Added NXF_SMOKE var to disable long running tests
- Deprecated groupBy and route operators [b7ca53d2]
- Updated S3 storage classes #977
- Updated groovy to version 2.5.5
- Updated copyright disclaimer
- Refactored project structure [516294e7]
- Speed-up CI tests [3320dcec]
18.12.0-edge - 18 Dic 2018
- Add Google Cloud Platform integration
- Added support for K8s nodeSelector #955
- Added new AWS regions #935
- Added json/yaml output to info command #657
- Fixed remote bin directory when using buckerDir option [6d796783]
- Fixed foreign file system detection [1489cc72]
- Fixed Ansi logger division by zero [ae2b1380]
- Fixed Unparseable Data format on http file #962
- Fixed Log command history #405
- Fixed Too long process tag name can cause SLURM failure #941
- Fixed LSF can return an inconsistent jobs status #927
- Fixed dump last queue status on failure [36e80242]
- Fixed Allow the usage of a custom docker image for K8s driver pod #877
- Fixed K8s executor when the cluster has no available cpus #824
- Fixed Prevent duplicate process definitions #920
- Fixed Update queue statuses used by PBS Pro #908
- Fixed K8s launcher fails to set pod work directory [dc8bfead]
- Fixed cmd cloud error message [14d603b9]
- Improved script runner api [da4a6c17]
- Revert "Apache Ignite to version 2.6" #909
- Fixed Invalid config rendering #801
- Improved file hashing logging [0d35b2b4]
- Refactored ScriptRunner class [15ee2f1c]
- Refactored DSL code visitor [67904c1f]
18.11.0-edge - 12 Nov 2018
- Added More duration and memory unit syntax sugar #921
- Added NO_PROXY env variable should be honoured #864
- Added keepHeader option to splitText operator #912
- Fixed Invalid warning message for config selector #905
- Fixed Queue status command fail on LSF version 8 #910
- Fixed Use `bash` instead of `sh` to fetch queue status
- Better report warning when grid status command fails [3ac8b972]
- Fixed RejectedExecutionException on successive Console executions #906
18.10.1 - 24 Oct 2018
- Fixed test [011e8e23]
- Fixed version number check [fb780347]
18.10.0 - 24 Oct 2018
- Added lenient cache mode #828 [ba907a2f]
- Added support for java 11 [60da50b5]
- Added support for Singularity 3.0 library #898
- Added support for AWS Batch hybrid executions #744
- Added weblog JSON format docs #882
- Added weblog example documentation #891
- Added PbsPro executor [33ae1104]
- Added support for ANSI console logging [9c14a947]