update meta files

modules/cnvpytor/histogram/main.nf

@@ -38,7 +38,7 @@ process CNVPYTOR_HISTOGRAM {
 
     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/histogram/meta.yml

@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@sima-r"
+  - "@ramprasadn"

modules/cnvpytor/importreaddepth/main.nf

@@ -32,7 +32,7 @@ process CNVPYTOR_IMPORTREADDEPTH {
 
     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/importreaddepth/meta.yml

@@ -52,3 +52,4 @@ output:
 
 authors:
   - "@sima-r"
+  - "@ramprasadn"

modules/cnvpytor/partition/main.nf

@@ -37,7 +37,7 @@ process CNVPYTOR_PARTITION {
 
     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/partition/meta.yml

@@ -43,3 +43,4 @@ output:
 
 authors:
   - "@sima-r"
+  - "@ramprasadn"

modules/cnvpytor/view/main.nf

@@ -23,13 +23,14 @@ process CNVPYTOR_VIEW {
 
     script:
     def output_suffix = output_format ?: 'vcf'
+    def bins = bin_sizes ?: '1000'
     """
 
     python3 <<CODE
     import cnvpytor,os
     from pathlib import Path
     pytor_files = Path.cwd().glob("*.pytor")
-    binsizes = "${bin_sizes}".split(" ")
+    binsizes = "${bins}".split(" ")
     for pytor_file in pytor_files:
         for binsize in binsizes:
             file_list = [str(pytor_file)]

modules/cnvpytor/view/meta.yml

@@ -31,10 +31,18 @@ output:
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test' ]
-  - partitions:
+  - tsv:
       type: file
-      description: pytor file containing partitions of read depth histograms using mean-shift method
+      description: tsv file containing cnv calls
-      pattern: "*.{pytor}"
+      pattern: "*.{tsv}"
+  - vcf:
+      type: file
+      description: vcf file containing cnv calls
+      pattern: "*.{vcf}"
+  - xls:
+      type: file
+      description: xls file containing cnv calls
+      pattern: "*.{xls}"
   - versions:
       type: file
       description: File containing software versions
@@ -42,3 +50,4 @@ output:
 
 authors:
   - "@sima-r"
+  - "@ramprasadn"

tests/modules/cnvpytor/view/main.nf

@@ -23,10 +23,9 @@ workflow test_cnvpytor_view_tsvout {
         file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
     ]
 
-    bin_sizes = "10000"
     output_suffix = "tsv"
 
-    CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
+    CNVPYTOR_VIEW ( input, [], output_suffix )
 }
 
 workflow test_cnvpytor_view_stub {
@@ -36,8 +35,8 @@ workflow test_cnvpytor_view_stub {
         file(params.test_data['homo_sapiens']['illumina']['test_pytor'], checkIfExists: true)
     ]
 
-    bin_sizes = "10000"
+    bin_sizes = []
-    output_suffix = "tsv"
+    output_suffix = []
 
     CNVPYTOR_VIEW ( input, bin_sizes, output_suffix )
 }

tests/modules/cnvpytor/view/test.yml

@@ -13,7 +13,7 @@
     - cnvpytor
     - cnvpytor/view
   files:
-    - path: output/cnvpytor/test.tsv
+    - path: output/cnvpytor/test_1000.tsv
     - path: output/cnvpytor/versions.yml
 
 - name: cnvpytor view test_cnvpytor_view stub