Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Check if flowcell id matches for paired samples #1664

Merged
merged 6 commits into from
Oct 30, 2024
Merged

Check if flowcell id matches for paired samples #1664

Changes from 2 commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
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
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
9 changes: 7 additions & 2 deletions workflows/sarek/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -944,11 +944,16 @@ 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 for paired samples
pmoris marked this conversation as resolved.
Show resolved Hide resolved
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]) ? "${flowcell}.${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?

// 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}\""
Expand Down
Loading