Merge branch 'master' of https://gitlab.bsc.es/lrodrig1/structuralvariants_poc

structuralvariants/nextflow/modules/bedops_union.nf

 process BEDOPS_UNION {
-  tag "bedops union"
+  tag { "bedops union" }
   container 'quay.io/biocontainers/bedops:2.4.39--h7d875b9_1'
 
   input:
     path input
 
   output:
-    path "${input[0].simpleName}.all.filtered.bed"
+    path "${input[0].baseName.tokenize('.')[1]}.all.filtered.bed"
 
   script:
   """
-  bedops -u $input > ${input[0].simpleName}.all.filtered.bed
+  bedops -u $input > ${input[0].baseName.tokenize('.')[1]}.all.filtered.bed
   """
 }

structuralvariants/nextflow/modules/collapse.nf

 process COLLAPSE {
-  tag "collapse"
+  tag { "collapse "}
   container 'quay.io/biocontainers/bedtools:2.26.0gx--he513fc3_4'
 
+  publishDir "${params.outputDir}", mode: 'copy'
+
   input:
     path script
     path input
 
   output:
     path "*.bed", emit: output
-  
+
   script:
   """
   sh $script $input
   """
-}
\ No newline at end of file
+}

structuralvariants/nextflow/modules/manta.nf

@@ -3,22 +3,23 @@ process MANTA {
   container 'quay.io/biocontainers/manta:1.6.0--py27_0'
 
   input:
-    tuple path(input), path(bai)
+    tuple path(bams), path(bais)
     path reference_genome
     path indexs
-    path regions
-    path tbi
+    path bed
+    path bed_tbi
+    val exome
 
   output:
     tuple path("*.manta.raw.vcf.gz"), emit: output
 
   script:
-  def exomeArgument = params.manta_exome ? "--exome" : ""
+  def exomeArgument = exome ? "--exome" : ""
   """
-  for i in $input
+  for i in $bams
   do
     srr=\$(echo \$i | cut -f 1 -d '.')
-    configManta.py --bam \$i --referenceFasta $reference_genome --runDir generated\$(echo \$srr) --callRegions $regions $exomeArgument
+    configManta.py --bam \$i --referenceFasta $reference_genome --runDir generated\$(echo \$srr) --callRegions $bed $exomeArgument
     python generated\$(echo \$srr)/runWorkflow.py
     cp generated\$(echo \$srr)/results/variants/diploidSV.vcf.gz ./\$(echo \$srr).manta.raw.vcf.gz
   done

structuralvariants/nextflow/modules/manta_filter.nf

@@ -4,11 +4,11 @@ process MANTA_FILTER {
   input:
     path script
     path input
-    path sample
+    path samples
     val max_len
     val min_len
     val min_q
-  
+
   output:
     path "*", emit: output
 
@@ -16,7 +16,7 @@ process MANTA_FILTER {
   """
   for i in $input
   do
-    sh $script \$i $sample $min_len $max_len $min_q
+    sh $script \$i $samples $min_len $max_len $min_q
   done
   """
-}
\ No newline at end of file
+}

structuralvariants/nextflow/modules/svtools.nf

 process SVTOOLS {
   tag { "svtools" }
   container 'quay.io/biocontainers/svtools:0.5.1--py_0'
-  
+
   input:
     path input
 
@@ -15,4 +15,4 @@ process SVTOOLS {
     svtools vcftobedpe -i \$i -o \$(echo \${i%.*} | sed 's/vcf/bed/g')
   done
   """
-}
\ No newline at end of file
+}

structuralvariants/nextflow/subworkflows/cnv_manta.nf

-    /*
+/*
  * Include for cnv_manta
 */
 include {
@@ -23,25 +23,27 @@ include {
 workflow SUB_CNV_MANTA {
     take:
        bams
+       bais
        samples
        reference_genome
        indexs
        bed
+       bed_tbi
+       exome
        manta_filter_script
        collapse_script
-       tbi
+       max_len
+       min_len
+       min_q
+
 
     main:
-        MANTA(bams,
-              reference_genome,
-              indexs,
-              bed,
-              tbi)
-        SVTOOLS( MANTA.out )
-        MANTA_FILTER( manta_filter_script, SVTOOLS.out, samples )
-        MANTA_UNION( MANTA_FILTER.out )
-        MANTA_MERGE( collapse_script, MANTA_UNION.out )
+        MANTA(bams, bais, reference_genome, indexs, bed, bed_tbi, exome)
+        SVTOOLS(MANTA.out)
+        MANTA_FILTER(manta_filter_script, SVTOOLS.out, samples, max_len, min_len, min_q)
+        MANTA_UNION(MANTA_FILTER.out)
+        MANTA_MERGE(collapse_script, MANTA_UNION.out)
 
     emit:
-        output = MANTA_MERGE.out
-}
\ No newline at end of file
+      output = MANTA_MERGE.out
+}