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Multiqc nanoplot #145

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Merged
robert-a-forsyth merged 14 commits into from
Mar 13, 2026
Merged

Multiqc nanoplot #145

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37eae5f
Merge branch 'dev' of https://github.com/intgenomicslab/lrsomatic int…
ljwharbers Mar 12, 2026
6c61cb6
Merge branch 'dev' of https://github.com/intgenomicslab/lrsomatic int…
ljwharbers Mar 13, 2026
173c182
add nanoplot to multiqc output
ljwharbers Mar 13, 2026
47f690a
prettier
ljwharbers Mar 13, 2026
cf90856
Potential fix for pull request finding
ljwharbers Mar 13, 2026
22fc6de
snapshot, prettier and add skip_nanoplot
ljwharbers Mar 13, 2026
1694671
update snapshot, fix bugs
ljwharbers Mar 13, 2026
d2928a9
Merge branch 'multiqc_nanoplot' of https://github.com/intgenomicslab/…
ljwharbers Mar 13, 2026
da3abaf
fix snapshots
ljwharbers Mar 13, 2026
a3a2655
fix snapshots again
ljwharbers Mar 13, 2026
9fa3803
surely last snapshot update
ljwharbers Mar 13, 2026
d9a084e
surely last one
ljwharbers Mar 13, 2026
648722f
idk what happened
ljwharbers Mar 13, 2026
943533a
surely last time
ljwharbers Mar 13, 2026
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10 changes: 7 additions & 3 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -42,31 +42,35 @@ process {
}

withName: '.*:CRAMINO_PRE' {
ext.prefix = { "${meta.id}_${meta.type}" }
ext.args = '--ubam'
publishDir = [
path: { "${params.outdir}/${meta.id}/qc/${meta.type}/cramino_ubam_${meta.replicate}/" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.arrow') ? null : filename }
]
}

withName: '.*:CRAMINO_POST' {
ext.prefix = { "${meta.id}_${meta.type}" }
publishDir = [
path: { "${params.outdir}/${meta.id}/qc/${meta.type}/cramino_aln" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
saveAs: { filename -> filename.equals('versions.yml') || filename.endsWith('.arrow') ? null : filename }
]
}

withName: '.*:NANOPLOT_PRE' {
ext.prefix = { "${meta.id}_${meta.type}_ubam" }
publishDir = [
path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam_${meta.replicate}/" },
path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_ubam_${meta.replicate}" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
}

withName: '.*:NANOPLOT_POST' {
ext.prefix = { "${meta.id}_${meta.type}_aln" }
publishDir = [
path: { "${params.outdir}/${meta.id}/qc/${meta.type}/nanoplot_aln" },
mode: params.publish_dir_mode,
Comment on lines 75 to 76
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28 changes: 19 additions & 9 deletions modules/nf-core/nanoplot/main.nf
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1 change: 1 addition & 0 deletions nextflow.config
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Expand Up @@ -32,6 +32,7 @@ params {
// Skip options
skip_qc = false
skip_cramino = false
skip_nanoplot = false
skip_mosdepth = false
skip_bamstats = false
skip_ascat = false
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4 changes: 4 additions & 0 deletions nextflow_schema.json
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Expand Up @@ -210,6 +210,10 @@
"skip_m6a": {
"type": "boolean",
"description": "Skip m6a calling by Fibertools"
},
"skip_nanoplot": {
"type": "boolean",
"description": "Skip Nanoplot"
}
}
},
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15 changes: 8 additions & 7 deletions tests/.nftignore
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Expand Up @@ -17,10 +17,11 @@ pipeline_info/*.{html,json,txt,yml}
*/variants/severus/read_ids.csv
*/variants/severus/severus.log
*/variants/severus/{all_SVs,somatic_SVs}/*.{vcf.gz,vcf.gz.tbi}
*/qc/{tumor,normal}/{cramino_aln}/*_cramino.txt
*/qc/{tumor,normal}/{cramino_ubam}_*/*_cramino.txt
*/qc/{tumor,normal}/{nanoplot_ubam}_*/*.html
*/qc/{tumor,normal}/{nanoplot_aln}/*.html
*/qc/{tumor,normal}/{nanoplot_ubam}_*/*.txt
*/qc/{tumor,normal}/{nanoplot_aln}/*.txt
*/qc/{tumor,normal}/{mosdepth}/*.txt
*/variants/phased/*.{vcf.gz,vcf.gz.tbi}
*/qc/{tumor,normal}/cramino_ubam_*/*_cramino.txt
*/qc/{tumor,normal}/cramino_aln/*_cramino.txt
*/qc/{tumor,normal}/nanoplot_ubam_*/*.html
*/qc/{tumor,normal}/nanoplot_aln/*.html
*/qc/{tumor,normal}/nanoplot_ubam_*/*.txt
*/qc/{tumor,normal}/nanoplot_aln/*.txt
*/qc/{tumor,normal}/mosdepth/*.txt
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