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maxulysse merged 3 commits into from
Jun 10, 2025
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back to dev + nft-utils 0.0.4 #1568

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5a7079c
back to dev + nft-utils 0.0.4
maxulysse Jun 10, 2025
e555276
update CHANGELOG
maxulysse Jun 10, 2025
c396509
update CHANGELOG
maxulysse Jun 10, 2025
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4 changes: 2 additions & 2 deletions .nf-core.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,12 +13,12 @@ lint:
nf_core_version: 3.3.1
repository_type: pipeline
template:
author: "Harshil Patel, Phil Ewels, Rickard Hammar\xE9n"
author: "Harshil Patel, Phil Ewels, Rickard Hammarén"
description: RNA sequencing analysis pipeline for gene/isoform quantification and
extensive quality control.
force: false
is_nfcore: true
name: rnaseq
org: nf-core
outdir: .
version: 3.19.0
version: 3.20.0dev
18 changes: 16 additions & 2 deletions CHANGELOG.md
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Expand Up @@ -3,7 +3,20 @@
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).

# 3.19.0 - 2025-06-06
## 3.20.0dev

### Credits

Special thanks to the following for their contributions to the release:

- [Jonathan Manning](https://github.com/pinin4fjords)
- [Maxime Garcia](https://github.com/maxulysse)

### Enhancements & fixes

- [PR #1568](https://github.com/nf-core/rnaseq/pull/1568) - Bump version after release 3.19.0

## [[3.19.0](https://github.com/nf-core/rnaseq/releases/tag/3.19.0)] - 2025-06-10

### Credits

Expand All @@ -15,6 +28,7 @@ Special thanks to the following for their contributions to the release:
- [Ben Sherman](https://github.com/bentsherman)
- [Dave Carlson](https://github.com/davidecarlson)
- [Gabriel Lichtenstein](https://github.com/glichtenstein)
- [Jonathan Manning](https://github.com/pinin4fjords)
- [Lorenzo Fontana](https://github.com/fntlnz)
- [Matthias Hörtenhuber](https://github.com/mashehu)
- [Milos Micik](https://github.com/milos7250)
Expand All @@ -41,7 +55,7 @@ Special thanks to the following for their contributions to the release:
- [PR #1565](https://github.com/nf-core/rnaseq/pull/1565) - Improve reproducibility with Conda
- [PR #1567](https://github.com/nf-core/rnaseq/pull/1567) - Prerelease 3.19.0 fixes

# 3.18.0 - 2024-12-19
## [[3.18.0](https://github.com/nf-core/rnaseq/releases/tag/3.18.0)] - 2024-12-19

### Credits

Expand Down
2 changes: 1 addition & 1 deletion nextflow.config
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Expand Up @@ -416,7 +416,7 @@ manifest {
mainScript = 'main.nf'
defaultBranch = 'master'
nextflowVersion = '!>=24.04.2'
version = '3.19.0'
version = '3.20.0dev'
doi = 'https://doi.org/10.5281/zenodo.1400710'
}

Expand Down
2 changes: 1 addition & 1 deletion nf-test.config
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Expand Up @@ -20,6 +20,6 @@ config {
// load the necessary plugins
plugins {
load "[email protected]"
load "[email protected].3"
load "[email protected].4"
}
}
198 changes: 99 additions & 99 deletions ro-crate-metadata.json
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Large diffs are not rendered by default.

8 changes: 4 additions & 4 deletions tests/default.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -22,8 +22,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down Expand Up @@ -53,8 +53,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
34 changes: 14 additions & 20 deletions tests/default.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -34,20 +34,17 @@
"gunzip": 1.13
},
"STAR_GENOMEGENERATE": {
"star": "2.7.11b",
"gawk": "5.1.0",
"samtools": 1.21,
"gawk": "5.1.0"
"star": "2.7.11b"
},
"TRIMGALORE": {
"trimgalore": "0.6.10",
"cutadapt": 4.9,
"pigz": 2.8
"pigz": 2.8,
"trimgalore": "0.6.10"
},
"UNTAR_SALMON_INDEX": {
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -126,12 +123,12 @@
"python": "3.10.4"
},
"DESEQ2_QC_PSEUDO": {
"r-base": "4.0.3",
"bioconductor-deseq2": "1.28.0"
"bioconductor-deseq2": "1.28.0",
"r-base": "4.0.3"
},
"DESEQ2_QC_STAR_SALMON": {
"r-base": "4.0.3",
"bioconductor-deseq2": "1.28.0"
"bioconductor-deseq2": "1.28.0",
"r-base": "4.0.3"
},
"DUPRADAR": {
"bioconductor-dupradar": "1.32.0"
Expand Down Expand Up @@ -212,14 +209,14 @@
"bioconductor-summarizedexperiment": "1.32.0"
},
"STAR_ALIGN": {
"star": "2.7.11b",
"gawk": "5.1.0",
"samtools": 1.21,
"gawk": "5.1.0"
"star": "2.7.11b"
},
"STAR_GENOMEGENERATE": {
"star": "2.7.11b",
"gawk": "5.1.0",
"samtools": 1.21,
"gawk": "5.1.0"
"star": "2.7.11b"
},
"STRINGTIE_STRINGTIE": {
"stringtie": "2.2.3"
Expand All @@ -228,9 +225,9 @@
"subread": "2.0.6"
},
"TRIMGALORE": {
"trimgalore": "0.6.10",
"cutadapt": 4.9,
"pigz": 2.8
"pigz": 2.8,
"trimgalore": "0.6.10"
},
"TXIMETA_TXIMPORT": {
"bioconductor-tximeta": "1.20.1"
Expand All @@ -243,9 +240,6 @@
},
"UNTAR_SALMON_INDEX": {
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down
8 changes: 4 additions & 4 deletions tests/featurecounts_group_type.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down Expand Up @@ -55,8 +55,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
34 changes: 14 additions & 20 deletions tests/featurecounts_group_type.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -34,20 +34,17 @@
"gunzip": 1.13
},
"STAR_GENOMEGENERATE": {
"star": "2.7.11b",
"gawk": "5.1.0",
"samtools": 1.21,
"gawk": "5.1.0"
"star": "2.7.11b"
},
"TRIMGALORE": {
"trimgalore": "0.6.10",
"cutadapt": 4.9,
"pigz": 2.8
"pigz": 2.8,
"trimgalore": "0.6.10"
},
"UNTAR_SALMON_INDEX": {
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -126,12 +123,12 @@
"python": "3.10.4"
},
"DESEQ2_QC_PSEUDO": {
"r-base": "4.0.3",
"bioconductor-deseq2": "1.28.0"
"bioconductor-deseq2": "1.28.0",
"r-base": "4.0.3"
},
"DESEQ2_QC_STAR_SALMON": {
"r-base": "4.0.3",
"bioconductor-deseq2": "1.28.0"
"bioconductor-deseq2": "1.28.0",
"r-base": "4.0.3"
},
"DUPRADAR": {
"bioconductor-dupradar": "1.32.0"
Expand Down Expand Up @@ -209,22 +206,22 @@
"bioconductor-summarizedexperiment": "1.32.0"
},
"STAR_ALIGN": {
"star": "2.7.11b",
"gawk": "5.1.0",
"samtools": 1.21,
"gawk": "5.1.0"
"star": "2.7.11b"
},
"STAR_GENOMEGENERATE": {
"star": "2.7.11b",
"gawk": "5.1.0",
"samtools": 1.21,
"gawk": "5.1.0"
"star": "2.7.11b"
},
"STRINGTIE_STRINGTIE": {
"stringtie": "2.2.3"
},
"TRIMGALORE": {
"trimgalore": "0.6.10",
"cutadapt": 4.9,
"pigz": 2.8
"pigz": 2.8,
"trimgalore": "0.6.10"
},
"TXIMETA_TXIMPORT": {
"bioconductor-tximeta": "1.20.1"
Expand All @@ -237,9 +234,6 @@
},
"UNTAR_SALMON_INDEX": {
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down
8 changes: 4 additions & 4 deletions tests/hisat2.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -23,8 +23,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down Expand Up @@ -55,8 +55,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
18 changes: 6 additions & 12 deletions tests/hisat2.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -37,18 +37,15 @@
"hisat2": "2.2.1"
},
"TRIMGALORE": {
"trimgalore": "0.6.10",
"cutadapt": 4.9,
"pigz": 2.8
"pigz": 2.8,
"trimgalore": "0.6.10"
},
"UNTAR_HISAT2_INDEX": {
"untar": 1.34
},
"UNTAR_SALMON_INDEX": {
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down Expand Up @@ -127,8 +124,8 @@
"python": "3.10.4"
},
"DESEQ2_QC_PSEUDO": {
"r-base": "4.0.3",
"bioconductor-deseq2": "1.28.0"
"bioconductor-deseq2": "1.28.0",
"r-base": "4.0.3"
},
"DUPRADAR": {
"bioconductor-dupradar": "1.32.0"
Expand Down Expand Up @@ -222,9 +219,9 @@
"subread": "2.0.6"
},
"TRIMGALORE": {
"trimgalore": "0.6.10",
"cutadapt": 4.9,
"pigz": 2.8
"pigz": 2.8,
"trimgalore": "0.6.10"
},
"TXIMETA_TXIMPORT": {
"bioconductor-tximeta": "1.20.1"
Expand All @@ -240,9 +237,6 @@
},
"UNTAR_SALMON_INDEX": {
"untar": 1.34
},
"Workflow": {
"nf-core/rnaseq": "v3.19.0"
}
},
[
Expand Down
8 changes: 4 additions & 4 deletions tests/kallisto.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -25,8 +25,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down Expand Up @@ -59,8 +59,8 @@ nextflow_pipeline {
{ assert snapshot(
// Number of successful tasks
workflow.trace.succeeded().size(),
// pipeline versions.yml file for multiqc from which Nextflow version is removed because we tests pipelines on multiple Nextflow versions
removeNextflowVersion("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml"),
// pipeline versions.yml file for multiqc from which Nextflow and pipeline versions are removed (all from the workflow key)
removeFromYamlMap("$outputDir/pipeline_info/nf_core_rnaseq_software_mqc_versions.yml", "Workflow"),
// All stable path name, with a relative path
stable_name,
// All files with stable contents
Expand Down
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