Merge branch 'dev/feature-SVCNV' into docker

workflow/modules/variant_calling.nf

@@ -619,6 +619,75 @@ process combineVariants_octopus {
 }
 
 
+
+process bcftools_index_octopus {
+    label 'process_low'
+
+    input:
+        tuple val(sample),
+        path(vcf)
+
+    output:
+        tuple val(sample), 
+        path(vcf), 
+        path("${vcf}.tbi")
+
+    script:    
+    """
+    bcftools index -t ${vcf}
+    """
+
+    stub:
+    """
+    touch ${vcf}
+    touch ${vcf}.tbi
+    """
+
+}
+
+process combineVariants_octopus {
+    label 'process_highmem'
+    publishDir(path: "${outdir}/vcfs/", mode: 'copy')
+
+    input:
+        tuple val(sample), path(vcfs), path(vcfsindex), val(vc)
+
+    output:
+        tuple val(sample), 
+        path("${vc}/${sample}.${vc}.marked.vcf.gz"), path("${vc}/${sample}.${vc}.norm.vcf.gz")
+
+    script:
+    vcfin = vcfs.join(" ")
+
+    """
+    mkdir ${vc}
+    bcftools concat $vcfin -a -Oz -o ${sample}.${vc}.temp.vcf.gz
+    bcftools sort ${sample}.${vc}.temp.vcf.gz -Oz -o ${sample}.${vc}.marked.vcf.gz
+    bcftools norm ${sample}.${vc}.marked.vcf.gz --threads $task.cpus --check-ref s -f $GENOMEREF -O v |\
+        awk '{{gsub(/\\y[W|K|Y|R|S|M]\\y/,"N",\$4); OFS = "\\t"; print}}' |\
+        sed '/^\$/d' > ${sample}.${vc}.temp.vcf
+
+    bcftools view ${sample}.${vc}.temp.vcf -f PASS -Oz -o ${vc}/${sample}.${vc}.norm.vcf.gz
+
+    mv ${sample}.${vc}.marked.vcf.gz ${vc}
+    """
+
+    stub:
+
+    """
+    mkdir ${vc}
+    touch ${vc}/${sample}.${vc}.marked.vcf.gz
+    touch ${vc}/${sample}.${vc}.norm.vcf.gz
+    
+    """
+
+}
+
+
+
+
+
+
 process combineVariants_strelka {
     //Concat all somatic snvs/indels across all files, strelka separates snv/indels
     label 'process_mid'

workflow/modules/variant_calling_tonly.nf

@@ -322,13 +322,13 @@ process octopus_tonly {
     $SOMATIC_FOREST \
     -o ${tumorname}_${bed.simpleName}.tonly.octopus.vcf.gz --threads $task.cpus
 
+
     """
 
     stub:
 
     """
     touch ${tumorname}_${bed.simpleName}.tonly.octopus.vcf.gz
-
     """
 }
 

workflow/modules/workflows_tonly.nf

@@ -173,6 +173,7 @@ workflow VC_TONLY {
     | map{tumor,markedvcf,markedindex,finalvcf,finalindex,stats -> tuple(tumor,"mutect2",finalvcf,finalindex)} 
     annotvep_tonly_mut2(mutect2_tonly_in)
 
+
     //VarDict
     vardict_in_tonly=vardict_tonly(bambyinterval) | groupTuple()| map{tumor,vcf -> tuple(tumor,vcf,"vardict_tonly")} 
     | combineVariants_vardict_tonly
@@ -205,6 +206,11 @@ workflow VC_TONLY {
         | annotvep_tonly_combined
 
 
+
+    emit:
+        somaticcall_input=combineVariants_octopus.out
+
+
     emit:
         somaticcall_input=combineVariants_octopus.out