Revert "remove gex_barcode_sample_assignment parameter"

This reverts commit 03a38cd.
nf-core · May 17, 2024 · 882812c · 882812c
1 parent 0d0275e
commit 882812c
Show file tree

Hide file tree

Showing 2 changed files with 6 additions and 0 deletions.
diff --git a/nextflow.config b/nextflow.config
@@ -62,6 +62,7 @@ params {
     gex_cmo_set = null
     fb_reference = null
     vdj_inner_enrichment_primers = null
+    gex_barcode_sample_assignment = null
     cellranger_multi_barcodes = null
 
 

diff --git a/subworkflows/local/align_cellrangermulti.nf b/subworkflows/local/align_cellrangermulti.nf
@@ -57,6 +57,7 @@ workflow CELLRANGER_MULTI_ALIGN {
         ch_gex_frna_probeset      = params.gex_frna_probe_set            ? file(params.gex_frna_probe_set)            : []
         ch_gex_target_panel       = params.gex_target_panel              ? file(params.gex_target_panel)              : []
         ch_gex_cmo_set            = params.gex_cmo_set                   ? file(params.gex_cmo_set)                   : []
+        ch_gex_barcodes           = params.gex_barcode_sample_assignment ? file(params.gex_barcode_sample_assignment) : []
         ch_fb_reference           = params.fb_reference                  ? file(params.fb_reference)                  : []
         ch_vdj_primer_index       = params.vdj_inner_enrichment_primers  ? file(params.vdj_inner_enrichment_primers)  : []
         ch_beam_antigen_panel_csv = [] // currently not implemented
@@ -177,7 +178,11 @@ workflow CELLRANGER_MULTI_ALIGN {
             ch_beam_control_panel_csv,
             ch_gex_cmo_set,
             ch_cmo_barcode_csv,
+<<<<<<< HEAD
             [], // currently not supported
+=======
+            ch_gex_barcodes,
+>>>>>>> parent of 03a38cd (remove gex_barcode_sample_assignment parameter)
             ch_frna_sample_csv,
             params.skip_cellranger_renaming
         )