fix: issue nf-core#5863

Whitelist is set as optional because it is only used by `CB_UMI_Simple` and `CB_UMI_Complex`
matq007 · Jul 31, 2024 · 53d68d6 · 53d68d6
1 parent e8770b8
commit 53d68d6
Showing 1 changed file with 3 additions and 2 deletions.
diff --git a/modules/nf-core/star/starsolo/main.nf b/modules/nf-core/star/starsolo/main.nf
@@ -9,6 +9,7 @@ process STARSOLO {
 
     input:
     tuple val(meta), val(solotype), path(reads)
+    path(opt_whitelist)
     tuple val(meta2), path(index)
 
     output:
@@ -31,7 +32,7 @@ process STARSOLO {
     switch(solotype) {
         case "CB_UMI_Simple":
             solotype_args = meta.umi_len ? "--soloUMIlen ${meta.umi_len} " : "";
-            solotype_args = solotype_args + (meta.whitelist ? "--soloCBwhitelist ${meta.whitelist} " : "--soloCBwhitelist None ");
+            solotype_args = solotype_args + (opt_whitelist.name != 'NO_FILE' ? "--soloCBwhitelist ${opt_whitelist} " : "--soloCBwhitelist None ");
             solotype_args = solotype_args + (meta.umi_start ? "--soloUMIstart ${meta.umi_start} " : "");
             solotype_args = solotype_args + (meta.cb_len ? "--soloCBlen ${meta.cb_len} " : "");
             solotype_args = solotype_args + (meta.cb_start ? "--soloCBstart ${meta.cb_start} " : "");
@@ -40,7 +41,7 @@ process STARSOLO {
             break
         case "CB_UMI_Complex":
             solotype_args = meta.cb_position ? "--soloCBposition ${meta.cb_position}" : "";
-            solotype_args = solotype_args + (meta.whitelist ? "--soloCBwhitelist ${meta.whitelist} " : "--soloCBwhitelist None ");
+            solotype_args = solotype_args + (opt_whitelist.name != 'NO_FILE' ? "--soloCBwhitelist ${opt_whitelist} " : "--soloCBwhitelist None ");
             solotype_args = solotype_args + (meta.umi_position ? "--soloUMIposition ${meta.umi_position} " : "");
             solotype_args = solotype_args + (meta.adapter_seq ? "--soloAdapterSequence ${meta.adapter_seq} " : "");
             solotype_args = solotype_args + (meta.max_mismatch_adapter ? "--soloAdapterMismatchesNmax ${meta.max_mismatch_adapter} " : "");