fix: merge bcftools/tabix and htslib/tabix tests into tabix/tabix

tests/software/bcftools/tabix/main.nf

@@ -1,14 +0,0 @@
-#!/usr/bin/env nextflow
-
-nextflow.enable.dsl = 2
-
-include { BCFTOOLS_TABIX } from '../../../../software/bcftools/tabix/main.nf' addParams( options: [:] )
-
-workflow test_bcftools_tabix {
-
-    def input = []
-    input = [ [ id:'test' ], // meta map
-              [ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ] ]
-
-    BCFTOOLS_TABIX ( input )
-}

tests/software/bcftools/tabix/test.yml

@@ -1,8 +0,0 @@
-- name: bcftools tabix
-  command: nextflow run ./tests/software/bcftools/tabix -entry test_bcftools_tabix -c tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools_tabix
-  files:
-    - path: output/bcftools/test.vcf.gz.tbi
-      md5sum: 06d52177f819730dd409157914534e8d

tests/software/tabix/tabix/main.nf

@@ -2,18 +2,30 @@
 
 nextflow.enable.dsl = 2
 
-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'] )
+include { TABIX_TABIX as TABIX_BED } from '../../../../software/tabix/tabix/main.nf' addParams( options: ['args': '-p bed'] )
+include { TABIX_TABIX as TABIX_GFF } from '../../../../software/tabix/tabix/main.nf' addParams( options: ['args': '-p gff'] )
+include { TABIX_TABIX as TABIX_VCF } from '../../../../software/tabix/tabix/main.nf' addParams( options: ['args': '-p vcf'] )
 
-workflow test_htslib_tabix_bed {
-    TABIX_BED ( file("${launchDir}/tests/data/bed/B.bed.gz", checkIfExists: true) )
+workflow test_tabix_tabix_bed {
+    def input = []
+    input = [ [ id:'B.bed' ], // meta map
+              [ file("${launchDir}/tests/data/bed/B.bed.gz", checkIfExists: true) ] ]
+
+    TABIX_BED ( input )
 }
 
-workflow test_htslib_tabix_gff {
-    TABIX_GFF ( file("${launchDir}/tests/data/gff/a.gff3.gz", checkIfExists: true) )
+workflow test_tabix_tabix_gff {
+    def input = []
+    input = [ [ id:'a.gff3' ], // meta map
+              [ file("${launchDir}/tests/data/gff/a.gff3.gz", checkIfExists: true) ] ]
+
+    TABIX_GFF ( input )
 }
 
-workflow test_htslib_tabix_vcf {
-    TABIX_VCF ( file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) )
+workflow test_tabix_tabix_vcf {
+    def input = []
+    input = [ [ id:'test.vcf' ], // meta map
+              [ file("${launchDir}/tests/data/vcf/test.vcf.gz", checkIfExists: true) ] ]
+
+    TABIX_VCF ( input )
 }

tests/software/tabix/tabix/test.yml

@@ -1,27 +1,27 @@
-- name: htslib tabix bed
-  command: nextflow run ./tests/software/htslib/tabix -entry test_htslib_tabix_bed -c tests/config/nextflow.config
+- name: tabix tabix bed
+  command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_bed -c tests/config/nextflow.config
   tags:
-    - htslib
-    - htslib_tabix
+    - tabix
+    - tabix_tabix
     - bed
   files:
     - 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
+- name: tabix tabix gff
+  command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_gff -c tests/config/nextflow.config
   tags:
-    - htslib
-    - htslib_tabix
+    - tabix
+    - tabix_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
+- name: tabix tabix vcf
+  command: nextflow run ./tests/software/tabix/tabix -entry test_tabix_tabix_vcf -c tests/config/nextflow.config
   tags:
-    - htslib
-    - htslib_tabix
+    - tabix
+    - tabix_tabix
     - vcf
   files:
     - path: output/tabix/test.vcf.gz.tbi
-      md5sum: a03f56d3e968f32256ffb9f6b7d01812
+      md5sum: a03f56d3e968f32256ffb9f6b7d01812