minor changes in main.nf

6f16906b · lrodrig1 · 1343d467 · 6f16906b
Commit 6f16906b authored 2 years ago by lrodrig1
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with 4 additions and 10 deletions
+4 -10
--- a/structuralvariants/nextflow/main.nf
+++ b/structuralvariants/nextflow/main.nf
@@ -96,24 +96,18 @@ workflow {
    SUB_SAMTOOLS_SORT.out.unpairedR2
  )

-  SAMTOOLS_INDEX(
-    SAMTOOLS_MERGE.out.output
-  )
+  SAMTOOLS_INDEX(SAMTOOLS_MERGE.out.output)

-  SUB_PICARD_MARKDUPLICATES(
-    SUB_SAMTOOLS_INDEX.out.output
-  )
+  SUB_PICARD_MARKDUPLICATES(SAMTOOLS_INDEX.out.output)

-  SUB_BAM_FILTERING(
-    SUB_PICARD_MARKDUPLICATES.out.alignments
-  )
+  SUB_BAM_FILTERING(SUB_PICARD_MARKDUPLICATES.out.alignments)

  bamsChr = SUB_BAM_FILTERING.out
  refChr = reference_fasta.combine(indexFiles)
  bedChr = bed.combine(bed_tbi)
  bamsbedChr = bamsChr.combine(bedChr)
  cnvChr = bamsbedChr.combine(refChr)
-  
+
  cnv_manta_results = Channel.empty()
  cnv_gridss_results = Channel.empty()
  cnv_exomedepth_results = Channel.empty()