Merge pull request #1617 from ramprasadn/feat/update_cnvpytor

Cnvpytor - merging calls from multiple samples

modules/cnvpytor/callcnvs/main.nf

@@ -20,7 +20,6 @@ process CNVPYTOR_CALLCNVS {
 
     script:
     def bins = bin_sizes ?: '1000'
-    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     cnvpytor \\
         -root $pytor \\

modules/cnvpytor/view/main.nf

@@ -8,7 +8,7 @@ process CNVPYTOR_VIEW {
         'quay.io/biocontainers/cnvpytor:1.2.1--pyhdfd78af_0' }"
 
     input:
-    tuple val(meta), path(pytor)
+    tuple val(meta), path(pytor_files)
     val bin_sizes
     val output_format
 
@@ -23,17 +23,18 @@ process CNVPYTOR_VIEW {
 
     script:
     def output_suffix = output_format ?: 'vcf'
-    def bins = bin_sizes ?: '1000'
+    def bins   = bin_sizes ?: '1000'
+    def input  = pytor_files.join(" ")
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
 
     python3 <<CODE
     import cnvpytor,os
-    from pathlib import Path
-    pytor_file = Path("$pytor")
     binsizes = "${bins}".split(" ")
     for binsize in binsizes:
-        app = cnvpytor.Viewer(["$pytor"], params={} )
+        file_list = "${input}".split(" ")
-        outputfile = "{}_{}.{}".format(pytor_file.stem,binsize.strip(),"${output_suffix}")
+        app = cnvpytor.Viewer(file_list, params={} )
+        outputfile = "{}_{}.{}".format("${prefix}",binsize.strip(),"${output_suffix}")
         app.print_filename = outputfile
         app.bin_size = int(binsize)
         app.print_calls_file()
@@ -47,8 +48,9 @@ process CNVPYTOR_VIEW {
 
     stub:
     def output_suffix = output_format ?: 'vcf'
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${pytor.baseName}.${output_suffix}
+    touch ${prefix}.${output_suffix}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/cnvpytor/view/meta.yml

@@ -17,9 +17,9 @@ input:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - pytor:
+  - pytor_files:
       type: file
-      description: pytor file containing read depth data
+      description: pytor file containing cnv calls. To merge calls from multiple samples use a list of files.
       pattern: "*.{pytor}"
   - bin_sizes:
       type: string

tests/modules/cnvpytor/view/main.nf

@@ -8,7 +8,7 @@ workflow test_cnvpytor_view {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
     ]
 
     bin_sizes = "10000 100000"
@@ -20,7 +20,7 @@ workflow test_cnvpytor_view_tsvout {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
     ]
 
     output_suffix = "tsv"
@@ -32,7 +32,7 @@ workflow test_cnvpytor_view_stub {
 
     input = [
         [ id:'test'], // meta map
-        file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
+        [file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)]
     ]
 
     bin_sizes = []