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Merged
ljwharbers merged 7 commits into from
Mar 12, 2026
Merged

add replicates, perform QC on individual replicates before merge #138

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cda4aa4
add replicates, perform QC on individual replicates before merge
robert-a-forsyth Mar 11, 2026
e3fcfe2
add nanoplot output
robert-a-forsyth Mar 11, 2026
1240d83
update syntax + snapshot
robert-a-forsyth Mar 12, 2026
963eb88
update snapshot + nftignore
robert-a-forsyth Mar 12, 2026
f632496
precommit
robert-a-forsyth Mar 12, 2026
ca2b603
fix snap
robert-a-forsyth Mar 12, 2026
18706bf
make pretty
ljwharbers Mar 12, 2026
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8 changes: 8 additions & 0 deletions assets/schema_input.json
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Original file line number Diff line number Diff line change
Expand Up @@ -50,6 +50,14 @@
},
"clairS_model": {
"type": "string"
},
"tumor_replicate": {
"type": "integer",
"default": 1
},
"normal_replicate": {
"type": "integer",
"default": 1
}
},
"required": ["sample", "bam_tumor", "platform", "sex", "fiber"]
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3 changes: 1 addition & 2 deletions conf/modules.config
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Original file line number Diff line number Diff line change
Expand Up @@ -41,11 +41,10 @@ process {
]
}


withName: '.*:CRAMINO_PRE' {
ext.args = '--ubam'
publishDir = [
path: { "${params.outdir}/${meta.id}/qc/${meta.type}/cramino_ubam" },
path: { "${params.outdir}/${meta.id}/qc/${meta.type}/cramino_ubam_${meta.replicate}/" },
mode: params.publish_dir_mode,
saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
]
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35 changes: 33 additions & 2 deletions subworkflows/local/utils_nfcore_lrsomatic_pipeline/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -86,25 +86,56 @@ workflow PIPELINE_INITIALISATION {

channel
.fromList(samplesheetToList(params.input, "${projectDir}/assets/schema_input.json"))
.map { meta, bam_tumor, bam_normal, method, sex, fiber, clair3_model, clairSTO_model, clairS_model ->
.map { meta, bam_tumor, bam_normal, method, sex, fiber, clair3_model, clairSTO_model, clairS_model, tumor_replicate, normal_replicate ->
def real_clair3_model = (clair3_model == null ) ? null : clair3_model
def real_clairS_model = (clairS_model == null ) ? null : clairS_model
def real_clairSTO_model = (clairSTO_model == null ) ? null : clairSTO_model
def paired_data = bam_normal ? true : false
def meta_info = meta + [ paired_data: paired_data, platform: method, sex: sex, fiber: fiber, clair3_model: real_clair3_model, clairS_model : real_clairS_model, clairSTO_model: real_clairSTO_model]
def meta_info = meta + [ paired_data: paired_data,
platform: method,
sex: sex,
fiber: fiber,
clair3_model: real_clair3_model,
clairS_model : real_clairS_model,
clairSTO_model: real_clairSTO_model,
tumor_replicate : tumor_replicate,
normal_replicate : normal_replicate]
return [ meta_info, [ bam_tumor ], [ bam_normal ?: [] ] ]
}
.map { meta, bam_tumor, bam_normal ->
[ meta, bam_tumor.flatten(), bam_normal.flatten() ]
}
.view()

Copilot AI Mar 11, 2026

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The .view() call in PIPELINE_INITIALISATION appears to be left-over debugging and will print samplesheet entries (including file paths) to stdout for every run. Consider removing it or gating it behind a debug/trace parameter.

Suggested change
.view()

Copilot uses AI. Check for mistakes.
.flatMap { meta, tumor_bam, normal_bam ->
def meta_tumor = meta.clone()
meta_tumor.type = 'tumor'
meta_tumor.replicate = meta_tumor.tumor_replicate
meta_tumor = meta_tumor.subMap('id',
'paired_data',
'type',
'platform',
'sex',
'fiber',
'clair3_model',
'clairS_model',
'clairSTO_model',
'replicate')
def result = [[meta_tumor, tumor_bam]]

if (normal_bam) {
def meta_normal = meta.clone()
meta_normal.type = 'normal'
meta_normal.replicate = meta_normal.normal_replicate
meta_normal = meta_normal.subMap('id',
'paired_data',
'type',
'platform',
'sex',
'fiber',
'clair3_model',
'clairS_model',
'clairSTO_model',
'replicate')
result << [meta_normal, normal_bam]
}

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117 changes: 104 additions & 13 deletions tests/default.nf.test.snap
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Original file line number Diff line number Diff line change
Expand Up @@ -128,8 +128,8 @@
"sample1/qc/normal",
"sample1/qc/normal/cramino_aln",
"sample1/qc/normal/cramino_aln/sample1_cramino.txt",
"sample1/qc/normal/cramino_ubam",
"sample1/qc/normal/cramino_ubam/sample1_cramino.txt",
"sample1/qc/normal/cramino_ubam_1",
"sample1/qc/normal/cramino_ubam_1/sample1_cramino.txt",
"sample1/qc/normal/mosdepth",
"sample1/qc/normal/mosdepth/sample1.mosdepth.global.dist.txt",
"sample1/qc/normal/mosdepth/sample1.mosdepth.summary.txt",
Expand All @@ -140,8 +140,8 @@
"sample1/qc/tumor",
"sample1/qc/tumor/cramino_aln",
"sample1/qc/tumor/cramino_aln/sample1_cramino.txt",
"sample1/qc/tumor/cramino_ubam",
"sample1/qc/tumor/cramino_ubam/sample1_cramino.txt",
"sample1/qc/tumor/cramino_ubam_1",
"sample1/qc/tumor/cramino_ubam_1/sample1_cramino.txt",
"sample1/qc/tumor/mosdepth",
"sample1/qc/tumor/mosdepth/sample1.mosdepth.global.dist.txt",
"sample1/qc/tumor/mosdepth/sample1.mosdepth.summary.txt",
Expand Down Expand Up @@ -190,8 +190,8 @@
"sample2/qc/normal",
"sample2/qc/normal/cramino_aln",
"sample2/qc/normal/cramino_aln/sample2_cramino.txt",
"sample2/qc/normal/cramino_ubam",
"sample2/qc/normal/cramino_ubam/sample2_cramino.txt",
"sample2/qc/normal/cramino_ubam_1",
"sample2/qc/normal/cramino_ubam_1/sample2_cramino.txt",
"sample2/qc/normal/mosdepth",
"sample2/qc/normal/mosdepth/sample2.mosdepth.global.dist.txt",
"sample2/qc/normal/mosdepth/sample2.mosdepth.summary.txt",
Expand All @@ -202,8 +202,8 @@
"sample2/qc/tumor",
"sample2/qc/tumor/cramino_aln",
"sample2/qc/tumor/cramino_aln/sample2_cramino.txt",
"sample2/qc/tumor/cramino_ubam",
"sample2/qc/tumor/cramino_ubam/sample2_cramino.txt",
"sample2/qc/tumor/cramino_ubam_1",
"sample2/qc/tumor/cramino_ubam_1/sample2_cramino.txt",
"sample2/qc/tumor/mosdepth",
"sample2/qc/tumor/mosdepth/sample2.mosdepth.global.dist.txt",
"sample2/qc/tumor/mosdepth/sample2.mosdepth.summary.txt",
Expand Down Expand Up @@ -250,8 +250,8 @@
"sample3/qc/tumor",
"sample3/qc/tumor/cramino_aln",
"sample3/qc/tumor/cramino_aln/sample3_cramino.txt",
"sample3/qc/tumor/cramino_ubam",
"sample3/qc/tumor/cramino_ubam/sample3_cramino.txt",
"sample3/qc/tumor/cramino_ubam_1",
"sample3/qc/tumor/cramino_ubam_1/sample3_cramino.txt",
"sample3/qc/tumor/mosdepth",
"sample3/qc/tumor/mosdepth/sample3.mosdepth.global.dist.txt",
"sample3/qc/tumor/mosdepth/sample3.mosdepth.summary.txt",
Expand Down Expand Up @@ -290,18 +290,86 @@
"sample3/vep/somatic",
"sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz",
"sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz.tbi",
"sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz_summary.html"
"sample3/vep/somatic/sample3_SOMATIC_VEP.vcf.gz_summary.html",
"sample4",
"sample4/bamfiles",
"sample4/bamfiles/sample4_normal.bam",
"sample4/bamfiles/sample4_normal.bam.bai",
"sample4/bamfiles/sample4_tumor.bam",
"sample4/bamfiles/sample4_tumor.bam.bai",
"sample4/qc",
"sample4/qc/normal",
"sample4/qc/normal/cramino_aln",
"sample4/qc/normal/cramino_aln/sample4_cramino.txt",
"sample4/qc/normal/cramino_ubam_1",
"sample4/qc/normal/cramino_ubam_1/sample4_cramino.txt",
"sample4/qc/normal/cramino_ubam_2",
"sample4/qc/normal/cramino_ubam_2/sample4_cramino.txt",
"sample4/qc/normal/mosdepth",
"sample4/qc/normal/mosdepth/sample4.mosdepth.global.dist.txt",
"sample4/qc/normal/mosdepth/sample4.mosdepth.summary.txt",
"sample4/qc/normal/samtools",
"sample4/qc/normal/samtools/sample4.flagstat",
"sample4/qc/normal/samtools/sample4.idxstats",
"sample4/qc/normal/samtools/sample4.stats",
"sample4/qc/tumor",
"sample4/qc/tumor/cramino_aln",
"sample4/qc/tumor/cramino_aln/sample4_cramino.txt",
"sample4/qc/tumor/cramino_ubam_1",
"sample4/qc/tumor/cramino_ubam_1/sample4_cramino.txt",
"sample4/qc/tumor/cramino_ubam_2",
"sample4/qc/tumor/cramino_ubam_2/sample4_cramino.txt",
"sample4/qc/tumor/mosdepth",
"sample4/qc/tumor/mosdepth/sample4.mosdepth.global.dist.txt",
"sample4/qc/tumor/mosdepth/sample4.mosdepth.summary.txt",
"sample4/qc/tumor/samtools",
"sample4/qc/tumor/samtools/sample4.flagstat",
"sample4/qc/tumor/samtools/sample4.idxstats",
"sample4/qc/tumor/samtools/sample4.stats",
"sample4/variants",
"sample4/variants/clair3",
"sample4/variants/clair3/merge_output.vcf.gz",
"sample4/variants/clair3/merge_output.vcf.gz.tbi",
"sample4/variants/clairs",
"sample4/variants/clairs/indel.vcf.gz",
"sample4/variants/clairs/indel.vcf.gz.tbi",
"sample4/variants/clairs/snvs.vcf.gz",
"sample4/variants/clairs/snvs.vcf.gz.tbi",
"sample4/variants/severus",
"sample4/variants/severus/all_SVs",
"sample4/variants/severus/all_SVs/severus_all.vcf.gz",
"sample4/variants/severus/breakpoints_double.csv",
"sample4/variants/severus/read_ids.csv",
"sample4/variants/severus/read_qual.txt",
"sample4/variants/severus/severus.log",
"sample4/variants/severus/somatic_SVs",
"sample4/variants/severus/somatic_SVs/severus_somatic.vcf.gz",
"sample4/vep",
"sample4/vep/SVs",
"sample4/vep/SVs/sample4_SV_VEP.vcf.gz",
"sample4/vep/SVs/sample4_SV_VEP.vcf.gz.tbi",
"sample4/vep/SVs/sample4_SV_VEP.vcf.gz_summary.html",
"sample4/vep/germline",
"sample4/vep/germline/sample4_GERMLINE_VEP.vcf.gz",
"sample4/vep/germline/sample4_GERMLINE_VEP.vcf.gz.tbi",
"sample4/vep/germline/sample4_GERMLINE_VEP.vcf.gz_summary.html",
"sample4/vep/somatic",
"sample4/vep/somatic/sample4_SOMATIC_VEP.vcf.gz",
"sample4/vep/somatic/sample4_SOMATIC_VEP.vcf.gz.tbi",
"sample4/vep/somatic/sample4_SOMATIC_VEP.vcf.gz_summary.html"
],
[
"sample1_normal.bam:md5,60838033f5f24aa90e16a5babcddd45b",
"sample1_normal.bam.bai:md5,d77c4e82c8965132967be86d83a4992d",
"sample1_tumor.bam:md5,bd73e83253c95a5fdc4db39454ee2253",
"sample1_tumor.bam.bai:md5,8b9edeb60b0e3023c97aa4b6e2e61380",
"sample1_cramino.txt:md5,ae3afdf316806ae18e43ca45de39b330",
"sample1.mosdepth.global.dist.txt:md5,4e1c72f8465c18ffd854c42850eb7c5f",
"sample1.mosdepth.summary.txt:md5,cf13d4b24e5ebf31b629a1195a1fff41",
"sample1.flagstat:md5,815a5385bd57ef44847714130b80d630",
"sample1.idxstats:md5,19be02d7e966e4a291b66ab5b14742d3",
"sample1.stats:md5,cf4b23c58e65cb55b31463db14ed6fd3",
"sample1_cramino.txt:md5,ed693bcb35499f67b8e1a30828cca591",
"sample1.mosdepth.global.dist.txt:md5,e04da37ef2b7cd587fa3158b9f36d2cb",
"sample1.mosdepth.summary.txt:md5,ef3aefa72ca2e9bbbe5acc91fc1ecde6",
"sample1.flagstat:md5,34e851b5504d961632f26991160ded5a",
Expand All @@ -313,11 +381,13 @@
"sample2_normal.bam.bai:md5,af193f1922d90b8741212d2bf690c418",
"sample2_tumor.bam:md5,26c4e52c12aa0e874fe52ae3b729beba",
"sample2_tumor.bam.bai:md5,e9e64e13328aa3621e7976f8e3f29a78",
"sample2_cramino.txt:md5,3bf932a1656c5997f48006fefc4418b7",
"sample2.mosdepth.global.dist.txt:md5,6cdc97a81a603db702cb5a113b8bc62a",
"sample2.mosdepth.summary.txt:md5,864370930ec1d695d942f4960bcf8fc6",
"sample2.flagstat:md5,cce0bb7ca79e14d8369ccc714adf4be3",
"sample2.idxstats:md5,e7de97b2362a8e944896dc4eca0b0bd8",
"sample2.stats:md5,2b7f1a2833840d350d2a4d54fed70cf7",
"sample2_cramino.txt:md5,c1842ccc06010e0d282a5f1470547c84",
"sample2.mosdepth.global.dist.txt:md5,eda3bf93b39e342e85e43931ce8b417e",
"sample2.mosdepth.summary.txt:md5,a68ca9504f5c9b73bf697d8ac22a1df0",
"sample2.flagstat:md5,83e7d7d922941691d2b023f0bd9655aa",
Expand All @@ -327,19 +397,40 @@
"read_qual.txt:md5,27edf87814aec6fa18546c8606aae4ed",
"sample3_tumor.bam:md5,2308beb1b4be1f0e1d6c8e52bd4f9266",
"sample3_tumor.bam.bai:md5,840eb3ad5ed3216a97c6a58563d4dcb1",
"sample3_cramino.txt:md5,ed693bcb35499f67b8e1a30828cca591",
"sample3.mosdepth.global.dist.txt:md5,e04da37ef2b7cd587fa3158b9f36d2cb",
"sample3.mosdepth.summary.txt:md5,ef3aefa72ca2e9bbbe5acc91fc1ecde6",
"sample3.flagstat:md5,34e851b5504d961632f26991160ded5a",
"sample3.idxstats:md5,1d43b03114bcc9b70d4333e91498efbe",
"sample3.stats:md5,b0f46b772514f0de08f1b2d88aa5968f",
"breakpoints_double.csv:md5,298a01c868eb493baaaa90ced9a9f17e",
"read_qual.txt:md5,1b4392f3b9071533e9ea77ff9df6c813"
"read_qual.txt:md5,1b4392f3b9071533e9ea77ff9df6c813",
"sample4_normal.bam:md5,b1fca5de53966e0927c557afad3d8df3",
"sample4_normal.bam.bai:md5,d77c4e82c8965132967be86d83a4992d",
"sample4_tumor.bam:md5,493ba7936ae34d0f06d65d416fefb435",
"sample4_tumor.bam.bai:md5,8b9edeb60b0e3023c97aa4b6e2e61380",
"sample4_cramino.txt:md5,ae3afdf316806ae18e43ca45de39b330",
"sample4_cramino.txt:md5,ae3afdf316806ae18e43ca45de39b330",
"sample4.mosdepth.global.dist.txt:md5,4e1c72f8465c18ffd854c42850eb7c5f",
"sample4.mosdepth.summary.txt:md5,cf13d4b24e5ebf31b629a1195a1fff41",
"sample4.flagstat:md5,815a5385bd57ef44847714130b80d630",
"sample4.idxstats:md5,19be02d7e966e4a291b66ab5b14742d3",
"sample4.stats:md5,8830836e19681287abd7eabfc8ac10bd",
"sample4_cramino.txt:md5,ed693bcb35499f67b8e1a30828cca591",
"sample4_cramino.txt:md5,ed693bcb35499f67b8e1a30828cca591",
"sample4.mosdepth.global.dist.txt:md5,e04da37ef2b7cd587fa3158b9f36d2cb",
"sample4.mosdepth.summary.txt:md5,ef3aefa72ca2e9bbbe5acc91fc1ecde6",
"sample4.flagstat:md5,34e851b5504d961632f26991160ded5a",
"sample4.idxstats:md5,1d43b03114bcc9b70d4333e91498efbe",
"sample4.stats:md5,dc8fec65923bf23826689ec1865f6fff",
"breakpoints_double.csv:md5,eafc71d123fb6ea562b5dd1fba243bd7",
"read_qual.txt:md5,1ad9d1900f8dcb291c97adc65c9d341c"
]
],
"meta": {
"nf-test": "0.9.3",
"nextflow": "25.10.2"
},
"timestamp": "2026-01-09T17:08:56.493545818"
"timestamp": "2026-03-11T15:36:10.03288147"
}
}
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