Merge branch 'master' of https://gitlab.bsc.es/amunoz/structuralvariants_poc

structuralvariants/nextflow/nextflow.config

@@ -22,7 +22,8 @@ params {
     samples = "data/samples_test.txt"
     bed = "data/gencode.v19.genes.v7_model.patched_contigs.gtf.bed.*"
     blacklist = "data/hg19-blacklist.v2.num.bed.gz"
-
+    tbi = "data/gencode.v19.genes.v7_model.patched_contigs.gtf.bed.gz.tbi"
+    
     //scripts
     manta_filter_script = "templates/manta_filter.sh"
     gridss_filter_script = "templates/gridss_filter.sh"

structuralvariants/nextflow/subworkflows/cnv_gridss.nf

@@ -27,6 +27,10 @@ workflow SUB_CNV_GRIDSS {
         samples
         reference_genome
         indexs
+        blacklist
+        structural_variants_script
+        gridss_filter_script
+        collapse_script
         max_len
         min_len
         min_q