Adressing general comments on PR #134

software/bcftools/isec/main.nf

@@ -18,7 +18,7 @@ process BCFTOOLS_ISEC {
     }
 
     input:
-    tuple val(meta), path('vcfs/*')
+    tuple val(meta), path(vcfs), path(tbis)
 
     output:
     tuple val(meta), path("${prefix}"), emit: results
@@ -31,7 +31,7 @@ process BCFTOOLS_ISEC {
     bcftools isec  \\
         $options.args \\
         -p $prefix \\
-        */*.vcf.gz
+        *.vcf.gz
     echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
     """
 }

software/bcftools/isec/meta.yml

@@ -40,21 +40,26 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - vcf:
+    - vcfs:
         type: files
         description: |
-          List containing 2 or more vcf files and their respective index (tbi files)
+          List containing 2 or more vcf files
-          e.g. [ 'file1.vcf', 'file1.vcf.tbi', 'file2.vcf', 'file2.vcf.tbi' ]
+          e.g. [ 'file1.vcf', 'file2.vcf' ]
+    - tbis:
+        type: files
+        description: |
+          List containing the tbi index files corresponding to the vcfs input files
+          e.g. [ 'file1.vcf.tbi', 'file2.vcf.tbi' ]
 output:
     - meta:
         type: map
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - vcf:
+    - results:
-        type: file
+        type: directory
-        description: VCF filtered output file
+        description: Folder containing the set operations results perform on the vcf files
-        pattern: "*.{vcf}"
+        pattern: "${prefix}"
     - version:
         type: file
         description: File containing software version

software/bcftools/stats/meta.yml

@@ -49,7 +49,7 @@ output:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - txt:
+    - stats:
         type: file
         description: Text output file containing stats
         pattern: "*.{txt}"

software/bcftools/tabix/main.nf

@@ -18,7 +18,7 @@ process BCFTOOLS_TABIX {
     }
 
     input:
-    tuple val(meta), path(gz_genome_position_file)
+    tuple val(meta), path(vcf)
 
     output:
     tuple val(meta), path("*.tbi"), emit: tbi
@@ -27,7 +27,7 @@ process BCFTOOLS_TABIX {
     script:
     def software = getSoftwareName(task.process)
     """
-    tabix $options.args $gz_genome_position_file
+    tabix $options.args $vcf
     echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
     """
 }