callcnv module

modules/cnvpytor/callcnvs/main.nf

@@ -9,10 +9,11 @@ process CNVPYTOR_CALLCNVS {
 
     input:
     tuple val(meta), path(pytor)
+    val bin_sizes
 
     output:
-    tuple val(meta), path("*.tsv"), emit: cnvs
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("${pytor.baseName}.pytor")	, emit: pytor
+    path "versions.yml"                                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -23,22 +24,21 @@ process CNVPYTOR_CALLCNVS {
     """
     cnvpytor \\
         -root $pytor \\
-        -call $args > ${prefix}.tsv
+        -call $bin_sizes
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 
     stub:
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.tsv
+    touch ${pytor.baseName}.pytor
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/^.*pyCNVnator //; s/Using.*\$//' ))
+        cnvpytor: \$(echo \$(cnvpytor --version 2>&1) | sed 's/CNVpytor //' ))
     END_VERSIONS
     """
 }

modules/cnvpytor/callcnvs/meta.yml

@@ -17,8 +17,11 @@ input:
         e.g. [ id:'test']
   - pytor:
       type: file
-      description: cnvpytor root file
+      description: pytor file containing partitions of read depth histograms using mean-shift method
       pattern: "*.{pytor}"
+  - bin_sizes:
+      type: string
+      description: list of binsizes separated by space e.g. "1000 10000" and "1000"
 
 output:
   - meta:
@@ -26,10 +29,10 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - cnvs:
+  - pytor:
       type: file
-      description: file containing identified copy numer variations
-      pattern: "*.{tsv}"
+      description: pytor files containing cnv calls
+      pattern: "*.{pytor}"
   - versions:
       type: file
       description: File containing software versions