fix: rename file to input and gz, plus fix tests

software/tabix/bgzip/main.nf

@@ -18,17 +18,17 @@ process TABIX_BGZIP {
     }
 
     input:
-    tuple val(meta), path(file)
+    tuple val(meta), path(input)
 
     output:
-    tuple val(meta), path("*.gz"), emit: file
+    tuple val(meta), path("*.gz"), emit: gz
     path  "*.version.txt"        , emit: version
 
     script:
     def software = getSoftwareName(task.process)
     def prefix   = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
-    bgzip -c $options.args $file > ${prefix}.${file.getExtension()}.gz
+    bgzip -c $options.args $input > ${prefix}.${input.getExtension()}.gz
     echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
     """
 }

tests/software/tabix/bgzip/main.nf

@@ -4,7 +4,7 @@ nextflow.enable.dsl = 2
 
 include { TABIX_BGZIP } from '../../../../software/tabix/bgzip/main.nf' addParams( options: [:] )
 
-workflow test_tabix_bgzip_vcf {
+workflow test_tabix_bgzip {
 
     def input = []
     input = [ [ id:'test' ], // meta map

tests/software/tabix/bgzip/test.yml

@@ -1,8 +1,8 @@
 - name: tabix bgzip
-  command: nextflow run ./tests/software/tabix/bgzip -entry test_tabix_bgzip_vcf -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/tabix/bgzip -entry test_tabix_bgzip -c tests/config/nextflow.config
   tags:
     - tabix
     - tabix_bgzip
   files:
-    - path: output/bgzip/test.vcf.gz
+    - path: output/tabix/test.vcf.gz
       md5sum: 40419fb7562475d1c8ec4ab725796de2