diff --git a/CHANGELOG.md b/CHANGELOG.md index a4ec1c8..d2a120f 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,22 +3,27 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## [[0.5.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.5.0)] - 2024-10-24 +## [[0.5.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.5.0)] - 2024-11-12 ### Credits Special thanks to the following for their contributions to the release: - [Adam Talbot](https://github.com/adamrtalbot) +- [Esha Joshi](https://github.com/ejseqera) +- [Jonathan Manning](https://github.com/pinin4fjords) +- [Maxime Garcia](https://github.com/maxulysse) - [Rob Syme](https://github.com/robsyme) Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. ### Enhancements & fixes -[PR #61](https://github.com/seqeralabs/nf-aggregate/pull/61) - Remove dependency on external library/grape -[PR #63](https://github.com/seqeralabs/nf-aggregate/pull/63) - Add `maxForks` setting for Seqera CLI to overcome API issues -[PR #65](https://github.com/seqeralabs/nf-aggregate/pull/65) - Replace eclint GHA by pre-commit +- [PR #61](https://github.com/seqeralabs/nf-aggregate/pull/61) - Remove dependency on external library/grape +- [PR #63](https://github.com/seqeralabs/nf-aggregate/pull/63) - Add `maxForks` setting for Seqera CLI to overcome API issues +- [PR #65](https://github.com/seqeralabs/nf-aggregate/pull/65) - Replace eclint GHA by pre-commit +- [PR #67](https://github.com/seqeralabs/nf-aggregate/pull/67) - Update tests to use a non-fusion run from Seqera Cloud community/showcase +- [PR #69](https://github.com/seqeralabs/nf-aggregate/pull/69) - Fix parsing of extra args to tw CLI ## [[0.4.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.4.0)] - 2024-07-26 @@ -32,9 +37,9 @@ Thank you to everyone else that has contributed by reporting bugs, enhancements ### Enhancements & fixes -[PR #52](https://github.com/seqeralabs/nf-aggregate/pull/52) - Organise results folder structure by pipeline -[PR #53](https://github.com/seqeralabs/nf-aggregate/pull/53) - Throw exception and terminate workflow in case config can't be read -[PR #57](https://github.com/seqeralabs/nf-aggregate/pull/57) - Check if fusion is enabled via the Platform API +- [PR #52](https://github.com/seqeralabs/nf-aggregate/pull/52) - Organise results folder structure by pipeline +- [PR #53](https://github.com/seqeralabs/nf-aggregate/pull/53) - Throw exception and terminate workflow in case config can't be read +- [PR #57](https://github.com/seqeralabs/nf-aggregate/pull/57) - Check if fusion is enabled via the Platform API ## [[0.3.0](https://github.com/seqeralabs/nf-aggregate/releases/tag/0.3.0)] - 2024-07-01 diff --git a/modules/local/seqera_runs_dump/nextflow.config b/modules/local/seqera_runs_dump/nextflow.config index 6e516ae..97cf636 100644 --- a/modules/local/seqera_runs_dump/nextflow.config +++ b/modules/local/seqera_runs_dump/nextflow.config @@ -1,7 +1,7 @@ process { withName: 'SEQERA_RUNS_DUMP' { maxForks = 5 - ext.args = { params.seqera_cli_extra_args ? params.seqera_cli_extra_args.split("\\s(?=--)") : '' } + ext.args = { params.seqera_cli_extra_args ? params.seqera_cli_extra_args.split(/[\s,]+(?=--)/).join(' ') : '' } ext.args2 = { params.skip_run_gantt ? '' : '--add-task-logs' } containerOptions = { params.java_truststore_path ? "--volume ${params.java_truststore_path}:${params.java_truststore_path}" : '' } publishDir = [ diff --git a/modules/local/seqera_runs_dump/tests/main.nf.test.snap b/modules/local/seqera_runs_dump/tests/main.nf.test.snap index 8a2279a..af0fe79 100644 --- a/modules/local/seqera_runs_dump/tests/main.nf.test.snap +++ b/modules/local/seqera_runs_dump/tests/main.nf.test.snap @@ -2,7 +2,7 @@ "Should run without failures": { "content": [ [ - "service-info.json:md5,6988ae3ef3c822007075726ecc73ba9c", + "service-info.json:md5,75a5b8cded8f0ce9aab2125c0ee89f63", "workflow-load.json:md5,4f02d5a24ab89aa648cd4346785c8f2c", "workflow-metadata.json:md5,b37b4faeddf283a2c44cbe4000e4ab6e", "workflow-metrics.json:md5,13a5b5d7447fad4a8baa053d1abf85e5", @@ -12,9 +12,9 @@ null ], "meta": { - "nf-test": "0.8.4", - "nextflow": "24.04.2" + "nf-test": "0.9.2", + "nextflow": "23.10.1" }, - "timestamp": "2024-07-25T10:21:06.447483" + "timestamp": "2024-11-11T11:53:03.835699" } -} \ No newline at end of file +} diff --git a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap index 07757e6..41e25e3 100644 --- a/subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap +++ b/subworkflows/local/utils_nf_aggregate/tests/main.nf.test.snap @@ -2,10 +2,6 @@ "Should run without failures": { "content": [ [ - { - "id": "1oXDHFHywk3wR2", - "workspace": "scidev/testing" - }, { "id": "2lXd1j7OwZVfxh", "workspace": "community/showcase" @@ -14,6 +10,10 @@ "id": "38QXz4OfQDpwOV", "workspace": "community/showcase" }, + { + "id": "3iFMo0NtH1Byvy", + "workspace": "community/showcase" + }, { "id": "4Bi5xBK6E2Nbhj", "workspace": "community/showcase" @@ -25,9 +25,9 @@ ] ], "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" + "nf-test": "0.9.2", + "nextflow": "24.04.2" }, - "timestamp": "2024-05-07T10:41:28.603749237" + "timestamp": "2024-11-11T11:32:52.476285" } } \ No newline at end of file