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Update print format of BBMAP/repair.sh version (#7332)
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* 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 <Jorisvansteenbrugge@users.noreply.github.com>
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 <usman@smme.edu.pk>
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@mazzalab @Jorisvansteenbrugge
@SPPearce @renovate @vagkaratzas @prototaxites @nschcolnicov @GallVp
9 people authored Jan 22, 2025
1 parent b651d72 commit 4c81a35
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Showing 2 changed files with 16 additions and 16 deletions.
4 changes: 2 additions & 2 deletions modules/nf-core/bbmap/repair/main.nf
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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
"""

Expand All @@ -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
"""
}
28 changes: 14 additions & 14 deletions modules/nf-core/bbmap/repair/tests/main.nf.test.snap
View file
Original file line number Diff line number Diff line change
Expand Up @@ -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": [
Expand All @@ -36,7 +36,7 @@
]
],
"2": [
"versions.yml:md5,006e8f2167df95a778b428413ed9d859"
"versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892"
],
"3": [
"test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
Expand Down Expand Up @@ -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": [
Expand All @@ -113,7 +113,7 @@
]
],
"2": [
"versions.yml:md5,006e8f2167df95a778b428413ed9d859"
"versions.yml:md5,71de954cc3b49c64d7bd86ed82d3e892"
],
"3": [
"test.repair.sh.log:md5,d41d8cd98f00b204e9800998ecf8427e"
Expand Down Expand Up @@ -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"
}
}

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