Param added to cnv_gridss

e6f71ceb · Adrián Muñoz · lrodrin · 9f6f3a6f · e6f71ceb · e6f71ceb
Commit e6f71ceb authored Jun 23, 2022 by Adrián Muñoz Committed by lrodrin Jun 23, 2022
--- a/structuralvariants/nextflow/main.nf
+++ b/structuralvariants/nextflow/main.nf
@@ -157,6 +157,7 @@ workflow {
    SUB_CNV_GRIDSS (
      SUB_BAM_FILTERING.out.collect(),
      samples,
+      reference_fasta,
      indexFiles,
      blacklist,
      structural_variants_script,

--- a/structuralvariants/nextflow/subworkflows/cnv_gridss.nf
+++ b/structuralvariants/nextflow/subworkflows/cnv_gridss.nf
@@ -26,6 +26,7 @@ workflow SUB_CNV_GRIDSS {
        bams
        samples
        reference_genome
+        indexs
        max_len
        min_len
        min_q
@@ -33,6 +34,7 @@ workflow SUB_CNV_GRIDSS {
    main:
        GRIDSS(bams,
               reference_genome,
+               indexs,
               blacklist)
        STRUCTURAL_VARIANTS( GRIDSS.out, structural_variants_script )
        GRIDSS_FILTER( gridss_filter_script, STRUCTURAL_VARIANTS.out, samples, max_len, min_len, min_q )