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Merged
maxulysse merged 7 commits into from
Feb 20, 2026
Merged

Update all modules and subworkflows + migrate to topics versions #175

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714672a
update all modules and subworkflows
maxulysse Feb 19, 2026
88038dc
snapshot for subworkflows
maxulysse Feb 19, 2026
e5c40d0
fix conda setup
maxulysse Feb 19, 2026
713a7c9
update more modules
maxulysse Feb 19, 2026
117cb2e
no channel versions in qc_bam
maxulysse Feb 19, 2026
41862e3
no channel versions in qc_bam
maxulysse Feb 19, 2026
98dff34
update seqfu and picard
maxulysse Feb 20, 2026
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2 changes: 1 addition & 1 deletion .github/actions/nf-test/action.yml
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Expand Up @@ -52,7 +52,7 @@ runs:
with:
auto-update-conda: true
conda-solver: libmamba
channels: conda-forge
channels: conda-forge,bioconda
channel-priority: strict
conda-remove-defaults: true

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2 changes: 2 additions & 0 deletions CHANGELOG.md
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Expand Up @@ -58,6 +58,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
- [#172](https://github.com/nf-core/seqinspector/pull/172) More complete conda environment for rundir parser
- [#173](https://github.com/nf-core/seqinspector/pull/173) Fix warning message for tag name collision
- [#174](https://github.com/nf-core/seqinspector/pull/174) Fix null message when no rundir information is available
- [#175](https://github.com/nf-core/seqinspector/pull/175) Fix conda setup in CI

### `Changed`

Expand All @@ -79,6 +80,7 @@ Initial release of nf-core/seqinspector, created with the [nf-core](https://nf-c
- [#174](https://github.com/nf-core/seqinspector/pull/174) Refactor tests
- [#174](https://github.com/nf-core/seqinspector/pull/174) More strict syntax
- [#174](https://github.com/nf-core/seqinspector/pull/174) No params included in workflows
- [#175](https://github.com/nf-core/seqinspector/pull/175) Update all modules and migrate the whole pipeline to using topic versions

### `Dependencies`

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14 changes: 14 additions & 0 deletions README.md
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Expand Up @@ -50,6 +50,20 @@ If provided, nf-core/seqinspector can also parse statistics from an Illumina run
<img alt="Fallback image description" src="docs/images/seqinspector_tubemap_V1.0.png">
</picture>

### Summary of tools and version used in the pipeline

| Tool | Version |
| ----------- | ------- |
| bowtie2 | 2.5.4 |
| bwamem2 | 2.3 |
| fastqc | 0.12.1 |
| fastqscreen | 0.16.0 |
| multiqc | 1.33 |
| picard | 3.4.0 |
| samtools | 1.22.1 |
| seqfu | 1.22.3 |
| seqtk | 1.4 |

## Usage

> [!NOTE]
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31 changes: 11 additions & 20 deletions conf/modules.config
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Expand Up @@ -14,8 +14,7 @@ process {

publishDir = [
path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]

withName: 'SEQTK_SAMPLE' {
Expand All @@ -31,64 +30,57 @@ process {
publishDir = [
path: { "${params.outdir}/seqfu_stats" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : "${meta.sample_id}_$filename" }
saveAs: { filename -> "${meta.sample_id}_${filename}" }
]
}

withName: 'BWAMEM2_INDEX' {
publishDir = [
path: { "${params.outdir}/bwamem2_index" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

withName: 'PICARD_CREATESEQUENCEDICTIONARY' {
publishDir = [
path: { "${params.outdir}/picard_createsequencedictionary" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

withName: 'BWAMEM2_MEM' {
publishDir = [
path: { "${params.outdir}/bwamem2_mem" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

withName: 'PICARD_COLLECTMULTIPLEMETRICS' {
publishDir = [
path: { "${params.outdir}/picard_collectmultiplemetrics" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

withName: 'PICARD_COLLECTHSMETRICS' {
publishDir = [
path: { "${params.outdir}/picard_collecthsmetrics" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
ext.args = {"--TMP_DIR ."}
}

withName: 'SAMTOOLS_FAIDX' {
publishDir = [
path: { "${params.outdir}/samtools_faidx" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

withName: 'SAMTOOLS_INDEX' {
publishDir = [
path: { "${params.outdir}/bwamem2_mem" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

Expand All @@ -99,16 +91,15 @@ process {
// The process _mqc.txt outputs should have identical names for the same sequencing platforms
// in order to be grouped together in the MultiQC report, but here we need to enforce uniqueness
// to avoid overwriting results in the publishDir.
saveAs: { filename -> "${meta.dirname}_$filename" }
saveAs: { filename -> "${meta.dirname}_${filename}" }
]
}

withName: 'MULTIQC_GLOBAL' {
ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' }
publishDir = [
path: { "${params.outdir}/multiqc/global_report" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
mode: params.publish_dir_mode
]
}

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1 change: 0 additions & 1 deletion main.nf
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Expand Up @@ -41,7 +41,6 @@ workflow NFCORE_SEQINSPECTOR {
samplesheet // channel: samplesheet read in from --input

main:

//
// WORKFLOW: Run pipeline
//
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35 changes: 17 additions & 18 deletions modules.json
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Expand Up @@ -7,75 +7,74 @@
"nf-core": {
"bowtie2/build": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
"installed_by": ["modules"]
},
"bwamem2/index": {
"branch": "master",
"git_sha": "b2902040b9cb9b7b32b62400f1c024a709bd4812",
"git_sha": "5dd46a36fca68d6ad1a6b22ec47adc8c6863717d",
"installed_by": ["modules"]
},
"bwamem2/mem": {
"branch": "master",
"git_sha": "d86336f3e7ae0d5f76c67b0859409769cfeb2af2",
"git_sha": "8325a8155a77a336a613a504b8e4d6cea7a2344a",
"installed_by": ["modules"],
"patch": "modules/nf-core/bwamem2/mem/bwamem2-mem.diff"
},
"fastqc": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "3009f27c4e4b6e99da4eeebe82799e13924a4a1f",
"installed_by": ["modules"]
},
"fastqscreen/buildfromindex": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"installed_by": ["modules"],
"patch": "modules/nf-core/fastqscreen/buildfromindex/fastqscreen-buildfromindex.diff"
"git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49",
"installed_by": ["modules"]
},
"fastqscreen/fastqscreen": {
"branch": "master",
"git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
"git_sha": "ab2e7b785ee4fa6d108472862edbf983cea7db49",
"installed_by": ["modules"],
"patch": "modules/nf-core/fastqscreen/fastqscreen/fastqscreen-fastqscreen.diff"
},
"multiqc": {
"branch": "master",
"git_sha": "82a79183037a403ad1b6714e5dbcff25500efaf6",
"git_sha": "575e1a4b51a9bad7a8cd1316a88fb85684ef7c7b",
"installed_by": ["modules"]
},
"picard/collecthsmetrics": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
"installed_by": ["modules"]
},
"picard/collectmultiplemetrics": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
"installed_by": ["modules"]
},
"picard/createsequencedictionary": {
"branch": "master",
"git_sha": "df124e87c74d8b40285199f8cc20151f5aa57255",
"git_sha": "a631e12055f6c23ba2c942d3902b3ed1b9eed859",
"installed_by": ["modules"]
},
"samtools/faidx": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"git_sha": "b2e78932ef01165fd85829513eaca29eff8e640a",
"installed_by": ["modules"]
},
"samtools/index": {
"branch": "master",
"git_sha": "c8be52dba1166c678e74cda9c3a3c221635c8bb1",
"git_sha": "1d2fbdcbca677bbe8da0f9d0d2bb7c02f2cab1c9",
"installed_by": ["modules"]
},
"seqfu/stats": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"git_sha": "6b81c03dc4465ac9351b293dc6caada2a5e7556c",
"installed_by": ["modules"]
},
"seqtk/sample": {
"branch": "master",
"git_sha": "e753770db613ce014b3c4bc94f6cba443427b726",
"git_sha": "a46713779030a5f508117080cbf4b693dd4c6e33",
"installed_by": ["modules"]
}
}
Expand All @@ -89,12 +88,12 @@
},
"utils_nfcore_pipeline": {
"branch": "master",
"git_sha": "271e7fc14eb1320364416d996fb077421f3faed2",
"git_sha": "65f5e638d901a51534c68fd5c1c19e8112fb4df1",
"installed_by": ["subworkflows"]
},
"utils_nfschema_plugin": {
"branch": "master",
"git_sha": "4b406a74dc0449c0401ed87d5bfff4252fd277fd",
"git_sha": "fdc08b8b1ae74f56686ce21f7ea11ad11990ce57",
"installed_by": ["subworkflows"]
}
}
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11 changes: 1 addition & 10 deletions modules/nf-core/bowtie2/build/main.nf
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30 changes: 23 additions & 7 deletions modules/nf-core/bowtie2/build/meta.yml
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6 changes: 3 additions & 3 deletions modules/nf-core/bwamem2/index/environment.yml
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18 changes: 4 additions & 14 deletions modules/nf-core/bwamem2/index/main.nf
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