Skip to content

Fix logic to accept singplex flex libraries in cellranger_multi #10922

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

Merged
delfiterradas merged 5 commits into from
Mar 17, 2026
Merged

Fix logic to accept singplex flex libraries in cellranger_multi #10922

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
5 commits
Select commit Hold shift + click to select a range
ca4ac56
Bugfix: Revert changes in logic and add a parameter for singleplex flex
delfiterradas Mar 16, 2026
1f850cc
Fix linting
delfiterradas Mar 16, 2026
e12e1a1
Remove parameter and move into config
delfiterradas Mar 17, 2026
744e12e
Merge branch 'master' into cellranger_multi
delfiterradas Mar 17, 2026
96a5237
Make variable name more explicit
delfiterradas Mar 17, 2026
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
7 changes: 4 additions & 3 deletions modules/nf-core/cellranger/multi/main.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -44,8 +44,9 @@ process CELLRANGER_MULTI {
if ([ocm_barcodes, cmo_barcodes, frna_sampleinfo].count { input -> input } >= 2) {
error "The ocm barcodes; cmo barcodes and frna probes are mutually exclusive features. Please use only one per sample, or reach out in slack in case it is really intended."
}
args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
args = task.ext.args ?: ''
prefix = task.ext.prefix ?: "${meta.id}"
force_include_frna = task.ext.force_include_frna ?: ''

// if references + FASTQ are empty, then don't run corresponding analyses
// get names of references, if they exist
Expand Down Expand Up @@ -76,7 +77,7 @@ process CELLRANGER_MULTI {
target_panel = gex_targetpanel_name != '' ? "target-panel,./$gex_targetpanel_name" : ''

// fixed RNA reference (not sample info!) also goes under GEX section
frna_probeset = gex_frna_probeset_name != '' ? "probe-set,./$gex_frna_probeset_name" : ''
frna_probeset = ( include_frna || force_include_frna ) && gex_frna_probeset_name != '' ? "probe-set,./$gex_frna_probeset_name" : ''

// VDJ inner primer set
primer_index = vdj_primer_index ? "inner-enrichment-primers,./references/primers/${vdj_primer_index.getName()}" : ''
Expand Down
2 changes: 2 additions & 0 deletions modules/nf-core/cellranger/multi/tests/main.nf.test
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -879,6 +879,8 @@ nextflow_process {
}
test("cellranger - multi - 10k - kidney - flex - singleplex") {

config "./singleplex_flex.config"

when {
process {
"""
Expand Down
2 changes: 1 addition & 1 deletion modules/nf-core/cellranger/multi/tests/main.nf.test.snap
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -5,7 +5,7 @@
"versions.yml:md5,1e16f7d40ef563f7d0a24f8944374d4d"
]
],
"timestamp": "2026-03-13T15:26:14.828577394",
"timestamp": "2026-03-16T17:20:25.065276862",
"meta": {
"nf-test": "0.9.4",
"nextflow": "25.10.4"
Expand Down
8 changes: 8 additions & 0 deletions modules/nf-core/cellranger/multi/tests/singleplex_flex.config
View file
Open in desktop
Original file line number Diff line number Diff line change
@@ -0,0 +1,8 @@
process {

withName: CELLRANGER_MULTI {
stageInMode = 'copy'
ext.force_include_frna = true
}

}
Loading