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Merged
rannick merged 10 commits into from
Sep 9, 2025
Merged

Update modules2 #759

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11303bf
udpate modules
rannick Sep 3, 2025
920313a
update subwfs, solve linting issues
rannick Sep 3, 2025
5276450
prettier
rannick Sep 3, 2025
0fdf38a
update snap
rannick Sep 4, 2025
261d8d8
update qc workflow test
rannick Sep 5, 2025
a8262a8
update build snap
rannick Sep 5, 2025
38f5832
prettier
rannick Sep 5, 2025
901b87f
Merge branch 'dev' into update_modules2
rannick Sep 9, 2025
3656a72
update changelog
rannick Sep 9, 2025
f3e822c
Merge branch 'update_modules2' of https://github.com/nf-core/rnafusio…
rannick Sep 9, 2025
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -96,7 +96,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Changed local `ARRIBA_VISUALIZATION`, `CTATSPLICING_STARTOCANCERINTRONS`, `CTATSPLICING_PREPGENOMELIB`, `FUSIONINSPECTOR`, `STARFUSION_DETECT` for its nf-core module versions [#740](https://github.com/nf-core/rnafusion/pull/740)
- Replaced local subworkflow `TRIM_WORKFLOW` for its nf-core subworkflow equivalent `FASTQ_FASTQC_UMITOOLS_FASTP` [#752](https://github.com/nf-core/rnafusion/pull/752)
- Changed local `FASTQ_ALIGN_STAR` for subworkflow from nf-core [#756](https://github.com/nf-core/rnafusion/pull/756)
- Replaced local subworkflow `STRINGTIE_WORKFLOW` for its nf-core version `BAM_STRINGTIE_MERGE` and the local module module `GTF_TO_REFFLAT` for nf-core's `UCSC_GTFTOGENEPRED` [#758](https://github.com/nf-core/rnafusion/pull/758)
- Replaced local subworkflow `STRINGTIE_WORKFLOW` for its nf-core version `BAM_STRINGTIE_MERGE` and the local module module `GTF_TO_REFFLAT` for nf-core's `UCSC_GTFTOGENEPRED` [#758](https://github.com/nf-core/rnafusion/pull/758
- Update modules and close todos as preparation for release [#759](https://github.com/nf-core/rnafusion/pull/759)

### Fixed

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2 changes: 1 addition & 1 deletion README.md
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Expand Up @@ -6,7 +6,7 @@
</h1>

[![GitHub Actions CI Status](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/nf-test.yml)
[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)
[![GitHub Actions Linting Status](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/rnafusion/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/rnafusion/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.2565517-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.2565517)
[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)

[![Nextflow](https://img.shields.io/badge/version-%E2%89%A524.10.5-green?style=flat&logo=nextflow&logoColor=white&color=%230DC09D&link=https%3A%2F%2Fnextflow.io)](https://www.nextflow.io/)
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54 changes: 27 additions & 27 deletions modules.json
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Expand Up @@ -12,12 +12,12 @@
},
"agat/convertspgff2tsv": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"arriba/arriba": {
"branch": "master",
"git_sha": "077818897bfe993e1ed91a0339bcbe53fe13edc7",
"git_sha": "025a6f75e1f72e4ab60abb4bd65b3f289d4ad910",
"installed_by": ["modules"]
},
"arriba/visualisation": {
Expand All @@ -32,12 +32,12 @@
},
"cat/cat": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"cat/fastq": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"ctatsplicing/prepgenomelib": {
Expand All @@ -54,7 +54,7 @@
},
"fastp": {
"branch": "master",
"git_sha": "d082103d7976a2804f21225446cc110cbd822f4c",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["fastq_fastqc_umitools_fastp", "modules"]
},
"fastqc": {
Expand Down Expand Up @@ -84,62 +84,62 @@
},
"gatk4/bedtointervallist": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
"installed_by": ["modules"]
},
"gatk4/createsequencedictionary": {
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"git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
"installed_by": ["modules"]
},
"gatk4/markduplicates": {
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"git_sha": "1ec937ab3edc307bc0d79a2200d784e9f0868359",
"git_sha": "a57253204b8f4022edfeaa3ae2f5e2abecd8858b",
"installed_by": ["modules"]
},
"gffread": {
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"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"multiqc": {
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"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "a4488d3d09244f29fb4606ba4eef85d59dcc6ad8",
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},
"picard/collectinsertsizemetrics": {
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"installed_by": ["modules"]
},
"picard/collectrnaseqmetrics": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
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},
"picard/collectwgsmetrics": {
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"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"salmon/index": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"salmon/quant": {
"branch": "master",
"git_sha": "db5a84497b80c4932b4498ec231f19403d19bcff",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"samtools/convert": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"samtools/flagstat": {
Expand All @@ -154,7 +154,7 @@
},
"samtools/index": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["bam_sort_stats_samtools", "modules"]
},
"samtools/sort": {
Expand All @@ -169,17 +169,17 @@
},
"star/align": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["fastq_align_star", "modules"]
},
"star/genomegenerate": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"starfusion/build": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "310a7a59c7f2362d25070e5928f3139f92377eaf",
"installed_by": ["modules"]
},
"starfusion/detect": {
Expand All @@ -189,17 +189,17 @@
},
"stringtie/merge": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["bam_stringtie_merge", "modules"]
},
"stringtie/stringtie": {
"branch": "master",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["bam_stringtie_merge", "modules"]
},
"ucsc/gtftogenepred": {
"branch": "master",
"git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"]
},
"umitools/extract": {
Expand Down Expand Up @@ -238,17 +238,17 @@
},
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "51ae5406a030d4da1e49e4dab49756844fdd6c7a",
"git_sha": "05954dab2ff481bcb999f24455da29a5828af08d",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
"git_sha": "dcd088f483cede0c3df4034d405126f05a764cc7",
"installed_by": ["subworkflows"]
}
}
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6 changes: 3 additions & 3 deletions modules/nf-core/agat/convertspgff2tsv/main.nf
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26 changes: 16 additions & 10 deletions modules/nf-core/agat/convertspgff2tsv/meta.yml
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64 changes: 39 additions & 25 deletions modules/nf-core/arriba/arriba/meta.yml
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