fix: make HTSLIB_TABIX more modular

software/htslib/tabix/main.nf

@@ -5,7 +5,7 @@ params.options = [:]
 def options    = initOptions(params.options)
 
 process HTSLIB_TABIX {
-    tag "$vcf"
+    tag "$tab"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -19,7 +19,7 @@ process HTSLIB_TABIX {
     }
 
     input:
-    path vcf
+    path tab
 
     output:
     path("*.tbi")        , emit: tbi
@@ -28,7 +28,7 @@ process HTSLIB_TABIX {
     script:
     def software = getSoftwareName(task.process)
     """
-    tabix -p vcf $vcf
+    tabix $options.args $tab
 
     echo \$(tabix -h 2>&1) | sed 's/^.*Version: //; s/(.*\$//' > ${software}.version.txt
     """

software/htslib/tabix/meta.yml

@@ -32,10 +32,10 @@ params:
             Instead of directly downloading Singularity images for use with Singularity,
             force the workflow to pull and convert Docker containers instead.
 input:
-    - vcf:
+    - tab:
         type: file
-        description: vcf.gz file
+        description: TAB-delimited genome file
-        pattern: "*.{vcf.gz}"
+        pattern: "*"
 output:
     - tbi:
         type: file

tests/software/htslib/tabix/main.nf

@@ -2,8 +2,18 @@
 
 nextflow.enable.dsl = 2
 
-include { HTSLIB_TABIX } from '../../../../software/htslib/tabix/main.nf' addParams( options: [:] )
+include { HTSLIB_TABIX as TABIX_BED } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p bed'] )
+include { HTSLIB_TABIX as TABIX_GFF } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p gff'] )
+include { HTSLIB_TABIX as TABIX_VCF } from '../../../../software/htslib/tabix/main.nf' addParams( options: ['args': '-p vcf'] )
 
-workflow test_htslib_tabix {
+workflow test_htslib_tabix_bed {
-    HTSLIB_TABIX ( file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) )
+    TABIX_BED ( file("${launchDir}/tests/data/bed/B.bed.gz", checkIfExists: true) )
+}
+
+workflow test_htslib_tabix_gff {
+    TABIX_GFF ( file("${launchDir}/tests/data/gff/a.gff3.gz", checkIfExists: true) )
+}
+
+workflow test_htslib_tabix_vcf {
+    TABIX_VCF ( file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) )
 }

tests/software/htslib/tabix/test.yml

@@ -1,8 +1,27 @@
-- name: htslib tabix
+- name: htslib tabix bed
-  command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix -c tests/config/nextflow.config
+  command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_bed -c tests/config/nextflow.config
   tags:
     - htslib
     - htslib_tabix
+    - bed
   files:
-    - path: output/htslib/test.vcf.gz.tbi
+    - path: output/tabix/B.bed.gz.tbi
+      md5sum: 6d657159c283200109f2ed082296f853
+- name: htslib tabix gff
+  command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_gff -c tests/config/nextflow.config
+  tags:
+    - htslib
+    - htslib_tabix
+    - gff
+  files:
+    - path: output/tabix/a.gff3.gz.tbi
+      md5sum: 77f666b63da45c6af8a394ab5642602e
+- name: htslib tabix vcf
+  command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_vcf -c tests/config/nextflow.config
+  tags:
+    - htslib
+    - htslib_tabix
+    - vcf
+  files:
+    - path: output/tabix/test.vcf.gz.tbi
       md5sum: a03f56d3e968f32256ffb9f6b7d01812