Fix cellranger multi handling of crispr data

modules/nf-core/cellranger/multi/main.nf

@@ -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}" : ''

modules/nf-core/cellranger/multi/templates/cellranger_multi.py

@@ -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}"