🔧 only run cobalt binning for matched

papaemmelab · Dec 20, 2024 · d74dc5c · d74dc5c
1 parent 79e94d9
commit d74dc5c
Show file tree

Hide file tree

Showing 2 changed files with 2 additions and 4 deletions.
diff --git a/main.nf b/main.nf
@@ -275,11 +275,11 @@ workflow {
     sageOutput = runSage(tumorBam, normalBam)
 
     // Bin Cobalt if expected
-    postCobaltOutput = (params.binProbes != 0 || params.binLogR != 0)
+    postCobaltOutput = (params.normalBam) && (params.binProbes != 0 || params.binLogR != 0)
         ? binCobalt(cobaltOutput.cobalt_tumor_ratio_tsv, cobaltOutput.cobalt_tumor_ratio_pcf, cobaltOutput.cobalt_normal_ratio_pcf)
         : cobaltOutput
 
-    cobaltOutdir = (params.binProbes != 0 || params.binLogR != 0)
+    cobaltOutdir = (params.normalBam) && (params.binProbes != 0 || params.binLogR != 0)
         ? "${params.outdir}/cobalt/binned_${params.binProbes}_probes_${params.binLogR}_LogR"
         : "${params.outdir}/cobalt"
 

diff --git a/nextflow.config b/nextflow.config
@@ -1,5 +1,3 @@
-
-
 // Metrics Files
 dag {
     enabled = true