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Check if flowcell id matches for paired samples #1664

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merged 6 commits into from
Oct 30, 2024
Merged

Check if flowcell id matches for paired samples #1664

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02036f1
Check if flowcell id matches for paired samples
pmoris Sep 26, 2024
fc75a53
Merge branch 'dev' into flowcell-check
maxulysse Oct 4, 2024
349ba42
Update workflows/sarek/main.nf
pmoris Oct 8, 2024
3bdefd8
Fix flowcell ID check
pmoris Oct 8, 2024
200cfae
Update changelog
pmoris Oct 8, 2024
82615ad
Merge branch 'dev' into flowcell-check
maxulysse Oct 30, 2024
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [1653](https://github.com/nf-core/sarek/pull/1653) - Updates `sarek_subway` files with `lofreq`
- [1660](https://github.com/nf-core/sarek/pull/1642) - Add `--length_required` for minimal reads length with `FASTP`
- [1663](https://github.com/nf-core/sarek/pull/1663) - Massive conda modules update
- [1664](https://github.com/nf-core/sarek/pull/1664) - Check if flowcell ID matches for read pair

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10 changes: 7 additions & 3 deletions workflows/sarek/main.nf
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Expand Up @@ -944,11 +944,15 @@ workflow SAREK {
// Add readgroup to meta and remove lane
def addReadgroupToMeta(meta, files) {
def CN = params.seq_center ? "CN:${params.seq_center}\\t" : ''
def flowcell = flowcellLaneFromFastq(files[0])

// Check if flowcell ID matches
if ( flowcell && flowcell != flowcellLaneFromFastq(files[1]) ){
error("Flowcell ID does not match for paired reads of sample ${meta.id} - ${files}")
}

// Here we're assuming that fastq_1 and fastq_2 are from the same flowcell:
// If we cannot read the flowcell ID from the fastq file, then we don't use it
def sample_lane_id = flowcellLaneFromFastq(files[0]) ? "${meta.flowcell}.${meta.sample}.${meta.lane}" : "${meta.sample}.${meta.lane}"
// TO-DO: Would it perhaps be better to also call flowcellLaneFromFastq(files[1]) and check that we get the same flowcell-id?
def sample_lane_id = flowcell ? "${meta.flowcell}.${meta.sample}.${meta.lane}" : "${meta.sample}.${meta.lane}"

// Don't use a random element for ID, it breaks resuming
def read_group = "\"@RG\\tID:${sample_lane_id}\\t${CN}PU:${meta.lane}\\tSM:${meta.patient}_${meta.sample}\\tLB:${meta.sample}\\tDS:${params.fasta}\\tPL:${params.seq_platform}\""
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