gridss updated

structuralvariants/nextflow/modules/gridss.nf

 process GRIDSS {
-  tag "gridss"
+  tag { "gridss" }
   container 'quay.io/biocontainers/gridss:2.9.3--0'
 
   input:
     tuple path(input), path(bai)
-    tuple path(reference_genome), path(index_files), path(fai)
+    path reference_genome
+    path indexs
     path blacklist    
 
   output:
@@ -13,12 +14,17 @@ process GRIDSS {
   script:
   def threadsArgument = params.threads_gridss ? "--threads $params.threads_gridss" : ""
   """
-  gridss --reference $reference_genome \\
-         --output ${input.simpleName}.gridss.raw.vcf.gz \\
-         --assembly "$params.assemblyFilename" \\
-         $threadsArgument \\
-         --jar "/usr/local/share/gridss-2.9.3-0/gridss.jar" \\
-         --blacklist $blacklist \\
-         $input
+  for i in $input
+  do
+    srr=\$(echo \$i | cut -f 1 -d '.')
+
+    gridss --reference $reference_genome \\
+           --output \$(echo \${i%%.*}).gridss.raw.vcf.gz \\
+           --assembly "\$(echo \$srr).$params.assemblyFilename" \\
+           $threadsArgument \\
+           --jar "/usr/local/share/gridss-2.9.3-0/gridss.jar" \\
+           --blacklist $blacklist \\
+           \$i
+  done
   """
 }

structuralvariants/nextflow/modules/gridss_filter.nf

 process GRIDSS_FILTER {
-  tag "gridss filter"
+  tag { "gridss filter" }
 
   input:
     path script
@@ -14,6 +14,9 @@ process GRIDSS_FILTER {
 
   script:
   """
-  sh $script $input $sample $min_len $max_len $min_q
+  for i in $input
+  do
+    sh $script \$i $sample $min_len $max_len $min_q
+  done
   """
 }

structuralvariants/nextflow/modules/structural_variants.nf

 process STRUCTURAL_VARIANTS {
-  tag "structural variants"
+  tag { "structural variants" }
   container 'quay.io/biocontainers/bioconductor-structuralvariantannotation:1.6.0--r40_0'
 
   input:
@@ -11,6 +11,9 @@ process STRUCTURAL_VARIANTS {
 
   script:
   """
-  Rscript $script $input 
+  for i in $input
+  do
+    Rscript $script \$i 
+  done
   """
 }
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