From 4c81a35b9f817661af684a50dec2a5a3eb297df2 Mon Sep 17 00:00:00 2001 From: MazzaLab Date: Wed, 22 Jan 2025 08:31:40 +0100 Subject: [PATCH] Update print format of BBMAP/repair.sh version (#7332) MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit * Refactor fastq and report variable names for consistency across wipertools modules * Refactor variable names for consistency in fastq and report processing modules * Update test assertions to reflect changes in output variable names in fastqwiper module * Update test assertions to match changes in report output structure in fastqwiper tests * pypgx/runngspipeline (#6823) * pypgx/runngspipeline * update PR comments --------- Co-authored-by: Jorisvansteenbrugge <7196110+Jorisvansteenbrugge@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Update actions/upload-artifact digest to 65c4c4a (#7293) Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> * fixed typo that produces "unknown recognition error type: groovyjarja… (#7295) fixed typo that produces "unknown recognition error type: groovyjarjarantlr4.v4.runtime.LexerNoViableAltException" in pipelines * Update Galah & add nf-tests (#7291) * Update Galah & add nf-tests * Fix linting * Update main.nf * Update inputs in meta.yml * Fix missing snapshot output from broken test * Added nftests to gseagsea (#7266) * Added nftests to gseagsea * Update input files * fix nftests * Address PR comments * Add seed setting parameter for stabilizing results * Fix linting * Add default random seed * Update datasets paths --------- Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> * Bumped lima to 2.12.0 (#7294) * Update container version to 1.1.4 and modify test names for clarity * Remove obsolete test cases from fastqscatter and clean up pytest module configuration * Update wipertools version to 1.1.4 in environment.yml files for fastqgather, fastqscatter, fastqwiper, and reportgather * Update timestamps in fastqscatter test snapshots for consistency * Update BBMAP_REPAIR process to use bbversion.sh for version retrieval * Update test snapshots with new version hashes and timestamps --------- Co-authored-by: Joris van Steenbrugge Co-authored-by: Jorisvansteenbrugge <7196110+Jorisvansteenbrugge@users.noreply.github.com> Co-authored-by: Simon Pearce <24893913+SPPearce@users.noreply.github.com> Co-authored-by: renovate[bot] <29139614+renovate[bot]@users.noreply.github.com> Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com> Co-authored-by: Jim Downie <19718667+prototaxites@users.noreply.github.com> Co-authored-by: Nicolás Schcolnicov <90359308+nschcolnicov@users.noreply.github.com> Co-authored-by: Usman Rashid --- modules/nf-core/bbmap/repair/main.nf | 4 +-- .../bbmap/repair/tests/main.nf.test.snap | 28 +++++++++---------- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/modules/nf-core/bbmap/repair/main.nf b/modules/nf-core/bbmap/repair/main.nf index 9c12be2cf53..ec868fa7270 100644 --- a/modules/nf-core/bbmap/repair/main.nf +++ b/modules/nf-core/bbmap/repair/main.nf @@ -37,7 +37,7 @@ process BBMAP_REPAIR { cat <<-END_VERSIONS > versions.yml "${task.process}": - repair.sh: \$(repair.sh --version |& sed '2!d ; s/BBMap version //') + bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset") END_VERSIONS """ @@ -51,7 +51,7 @@ process BBMAP_REPAIR { cat <<-END_VERSIONS > versions.yml "${task.process}": - repair.sh: \$(repair.sh --version |& sed '2!d ; s/BBMap version //') + bbmap: \$(bbversion.sh | grep -v "Duplicate cpuset") END_VERSIONS """ } diff --git a/modules/nf-core/bbmap/repair/tests/main.nf.test.snap b/modules/nf-core/bbmap/repair/tests/main.nf.test.snap index 54e929b0611..d10edaf13aa 100644 --- a/modules/nf-core/bbmap/repair/tests/main.nf.test.snap +++ b/modules/nf-core/bbmap/repair/tests/main.nf.test.snap @@ -2,14 +2,14 @@ "sarscov2_illumina_paired - fastq_gz": { "content": [ [ - "versions.yml:md5,006e8f2167df95a778b428413ed9d859" + "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-19T11:01:18.284624712" + "timestamp": "2025-01-18T18:32:09.249624" }, "sarscov2_illumina_interleaved - fastq_gz - stub": { "content": [ @@ -36,7 +36,7 @@ ] ], "2": [ - "versions.yml:md5,006e8f2167df95a778b428413ed9d859" + "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" ], "3": [ "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -66,27 +66,27 @@ ] ], "versions": [ - "versions.yml:md5,006e8f2167df95a778b428413ed9d859" + "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-19T11:02:01.385727451" + "timestamp": "2025-01-18T18:32:38.864295" }, "sarscov2_illumina_interleaved - fastq_gz": { "content": [ [ - "versions.yml:md5,006e8f2167df95a778b428413ed9d859" + "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" ] ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-19T11:01:32.752620818" + "timestamp": "2025-01-18T18:32:18.562698" }, "sarscov2_illumina_paired - fastq_gz - stub": { "content": [ @@ -113,7 +113,7 @@ ] ], "2": [ - "versions.yml:md5,006e8f2167df95a778b428413ed9d859" + "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" ], "3": [ "test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e" @@ -143,14 +143,14 @@ ] ], "versions": [ - "versions.yml:md5,006e8f2167df95a778b428413ed9d859" + "versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892" ] } ], "meta": { "nf-test": "0.9.2", - "nextflow": "24.10.2" + "nextflow": "24.10.3" }, - "timestamp": "2024-12-19T11:01:47.341193946" + "timestamp": "2025-01-18T18:32:28.275703" } } \ No newline at end of file