Manta, svtools and manta_filter fix

structuralvariants/nextflow/main.nf

@@ -140,7 +140,7 @@ workflow {
 
   if( params.enable_manta )
     SUB_CNV_MANTA (
-      SUB_BAM_FILTERING.out,
+      SUB_BAM_FILTERING.out.collect(),
       samples,
       reference_fasta,
       indexFiles,
@@ -155,7 +155,7 @@ workflow {
     
   if( params.enable_gridss )
     SUB_CNV_GRIDSS (
-      SUB_BAM_FILTERING.out,
+      SUB_BAM_FILTERING.out.collect(),
       samples,
       indexFiles,
       blacklist,
@@ -169,7 +169,7 @@ workflow {
 
   if( params.enable_exomeDepth )
     SUB_CNV_EXOMEDEPTH (
-        SUB_BAM_FILTERING.out,
+        SUB_BAM_FILTERING.out.collect(),
         samples,
         indexFiles,
         batch_parser_script,
@@ -183,7 +183,7 @@ workflow {
 
   if( params.enable_codex )
     SUB_CNV_CODEX (
-        SUB_BAM_FILTERING.out,
+        SUB_BAM_FILTERING.out.collect(),
         samples,
         bed,
         params.codex_max_len

structuralvariants/nextflow/modules/manta.nf

 process MANTA {
-  tag "manta"
+  tag { "manta" }
   container 'quay.io/biocontainers/manta:1.6.0--py27_0'
 
   input:
@@ -15,8 +15,12 @@ process MANTA {
   script:
   def exomeArgument = params.manta_exome ? "--exome" : ""
   """
-  configManta.py --bam $input --referenceFasta $reference_genome --runDir generated --callRegions $regions $exomeArgument
-  python generated/runWorkflow.py
-  cp generated/results/variants/diploidSV.vcf.gz ./${input.simpleName}.manta.raw.vcf.gz
+  for i in $input
+  do
+    srr=\$(echo \$i | cut -f 1 -d '.')
+    configManta.py --bam \$i --referenceFasta $reference_genome --runDir generated\$(echo \$srr) --callRegions $regions $exomeArgument
+    python generated\$(echo \$srr)/runWorkflow.py
+    cp generated\$(echo \$srr)/results/variants/diploidSV.vcf.gz ./\$(echo \$srr).manta.raw.vcf.gz
+  done
   """
 }
\ No newline at end of file

structuralvariants/nextflow/modules/manta_filter.nf

 process MANTA_FILTER {
-  tag "manta filter"
+  tag { "manta filter" }
 
   input:
     path script

structuralvariants/nextflow/modules/svtools.nf

 process SVTOOLS {
-  tag "svtools"
+  tag { "svtools" }
   container 'quay.io/biocontainers/svtools:0.5.1--py_0'
   
   input: