bcftools_tabix generic for any TAB-delimited genome position file

software/bcftools/tabix/main.nf

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

software/bcftools/tabix/meta.yml

@@ -42,8 +42,8 @@ input:
           e.g. [ id:'test', single_end:false ]
     - vcf:
         type: file
-        description: VCF input file
-        pattern: "*.{vcf,bed,sam,gff}"
+        description: TAB-delimited genome position file compressed with bgzip
+        pattern: "*.{vcf.gz,bed.gz,sam.gz,gff.gz}"
 output:
     - meta:
         type: map