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Fix cellranger multi handling of crispr data #7175

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Fix cellranger multi handling of crispr data #7175

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b6b0434
Fix cellranger multi handling of crispr data
svigneau Dec 6, 2024
77f2b16
Merge branch 'master' into bugfix/cellrangermulti-crispr
famosab Dec 10, 2024
ff170fa
Merge branch 'master' into bugfix/cellrangermulti-crispr
fmalmeida Dec 11, 2024
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2 changes: 1 addition & 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 @@ -59,7 +59,7 @@ process CELLRANGER_MULTI {
include_vdj = vdj_fastqs.first().getName() != 'fastqs' && vdj_reference ? '[vdj]' : ''
include_beam = beam_fastqs.first().getName() != 'fastqs' && beam_control_panel ? '[antigen-specificity]' : ''
include_cmo = cmo_fastqs.first().getName() != 'fastqs' && cmo_barcodes ? '[samples]' : ''
include_fb = ab_fastqs.first().getName() != 'fastqs' && fb_reference ? '[feature]' : ''
include_fb = (ab_fastqs.first().getName() != 'fastqs' || crispr_fastqs.first().getName() != 'fastqs') && fb_reference ? '[feature]' : ''
include_frna = gex_frna_probeset_name && frna_sampleinfo ? '[samples]' : ''

gex_reference_path = include_gex ? "reference,./${gex_reference_name}" : ''
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2 changes: 1 addition & 1 deletion modules/nf-core/cellranger/multi/templates/cellranger_multi.py
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Expand Up @@ -29,7 +29,7 @@ def chunk_iter(seq, size):
# do not match "SRR12345", "file_INFIXR12", etc
filename_pattern = r"([^a-zA-Z0-9])R1([^a-zA-Z0-9])"

for modality in ["gex", "vdj", "ab", "beam", "cmo", "cirspr"]:
for modality in ["gex", "vdj", "ab", "beam", "cmo", "crispr"]:
# get fastqs, ordered by path. Files are staged into
# - "fastq_001/{original_name.fastq.gz}"
# - "fastq_002/{original_name.fastq.gz}"
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