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fix probe-set inclusion assertion #12601

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fix probe-set inclusion assertion #12601

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c58e945
fix probe-set inclusion assertion
fmalmeida Aug 6, 2026
0843e28
add probe-set when mutually exclusive features are not available.
fmalmeida Aug 6, 2026
ad88241
remove trailling whitespace
fmalmeida Aug 6, 2026
f11c654
add test for "pipeline scenario"
fmalmeida Aug 6, 2026
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4 changes: 3 additions & 1 deletion modules/nf-core/cellranger/multi/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,9 @@ process CELLRANGER_MULTI {
if (has_gex) {
gex_section << '[gene-expression]'
gex_section << "reference,\$PWD/${gex_reference.name}"
if (gex_frna_probeset) gex_section << "probe-set,\$PWD/${gex_frna_probeset.name}"

// still allow frna probe-set for flex, but avoid adding when CMO or OCM barcodes are present, since those are mutually exclusive with frna
if (gex_frna_probeset && !has_cmo && !has_ocm) gex_section << "probe-set,\$PWD/${gex_frna_probeset.name}"

// GEX options forwarded from the gex_options input map
['filter-probes', 'r1-length', 'r2-length', 'chemistry', 'expect-cells', 'force-cells',
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