Merge counts per pool

nf-cmgg · Apr 23, 2024 · 5bd91eb · 5bd91eb
1 parent df7e622
commit 5bd91eb
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Showing 2 changed files with 6 additions and 6 deletions.
diff --git a/modules/local/exomedepth/merge_count/main.nf b/modules/local/exomedepth/merge_count/main.nf
@@ -12,10 +12,10 @@ process EXOMEDEPTH_COUNT_MERGE {
     """
     for file in $files; do
         if [ -f ${meta.id}_${meta.chr}.txt ]; then
-			paste ${meta.id}_${meta.chr}.txt <(awk '{print \$5}' \$file) > temp_auto.txt
-			mv temp_auto.txt ${meta.id}_${meta.chr}.txt
-			else
-			cp \$file ${meta.id}_${meta.chr}.txt
+		paste ${meta.id}_${meta.chr}.txt <(awk '{print \$5}' \$file) > temp_auto.txt
+		mv temp_auto.txt ${meta.id}_${meta.chr}.txt
+		else
+		cp \$file ${meta.id}_${meta.chr}.txt
         fi
     done
     """

diff --git a/workflows/exomecnv.nf b/workflows/exomecnv.nf
@@ -47,8 +47,8 @@ workflow EXOMECNV {
             .set{ ch_input_prepare }
 
 
-   //ch_input_prepare.BAM.view { "BAM: $it" }
-   //ch_input_prepare.CRAM.view { "CRAM: $it" }
+    //ch_input_prepare.BAM.view { "BAM: $it" }
+    //ch_input_prepare.CRAM.view { "CRAM: $it" }
 
 
     ch_fasta        = Channel.fromPath(params.fasta).map{ [[id:"reference"], it]}.collect()