chores: replace bcftools/bgzip by tabix/bgzip cf #179

.github/filters.yml

@@ -2,10 +2,6 @@ bandage_image:
   - software/bandage/image/**
   - tests/software/bandage/image/**
 
-bcftools_bgzip:
-  - software/bcftools/bgzip/**
-  - tests/software/bcftools/bgzip/**
-
 bcftools_consensus:
   - software/bcftools/consensus/**
   - tests/software/bcftools/consensus/**
@@ -233,6 +229,10 @@ stringtie:
   - software/stringtie/**
   - tests/software/stringtie/**
 
+tabix_bgzip:
+  - software/tabix/bgzip/**
+  - tests/software/tabix/bgzip/**
+
 tool_subtool:
   - software/TOOL/SUBTOOL/**
   - tests/software/TOOL/SUBTOOL/**

software/tabix/bgzip/main.nf

@@ -4,31 +4,31 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 def options    = initOptions(params.options)
 
-process BCFTOOLS_BGZIP {
+process TABIX_BGZIP {
     tag "$meta.id"
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
         saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
-    conda (params.enable_conda ? "bioconda::bcftools=1.11=h7c999a4_0" : null)
+    conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
+        container "https://depot.galaxyproject.org/singularity/tabix:0.2.6--ha92aebf_0"
     } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
+        container "quay.io/biocontainers/tabix:0.2.6--ha92aebf_0"
     }
 
     input:
-    tuple val(meta), path(vcf)
+    tuple val(meta), path(file)
 
     output:
-    tuple val(meta), path("*.gz"), emit: vcf
+    tuple val(meta), path("*.gz"), emit: file
     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 $vcf > ${prefix}.vcf.gz
+    bgzip -c $options.args $file > ${prefix}.${file.getExtension()}.gz
     echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
     """
 }

software/tabix/bgzip/meta.yml

@@ -1,14 +1,14 @@
-name: bcftools_bgzip
+name: tabix_bgzip
-description: Compresses VCF files
+description: Compresses files
 keywords:
-    - variant calling
     - compress
-    - VCF
+    - bgzip
+    - tabix
 tools:
     - bgzip:
         description: |
           Bgzip compresses files in a similar manner to, and compatible with, gzip.
-        homepage: http://samtools.github.io/bcftools/bcftools.html
+        homepage: https://www.htslib.org/doc/tabix.html
         documentation: http://www.htslib.org/doc/bgzip.html
         doi: 10.1093/bioinformatics/btp352
 params:
@@ -38,19 +38,19 @@ input:
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - vcf:
+    - file:
         type: file
-        description: VCF text file
+        description: text file
 output:
     - meta:
         type: map
         description: |
           Groovy Map containing sample information
           e.g. [ id:'test', single_end:false ]
-    - vcf:
+    - file:
         type: file
-        description: Output compressed VCF file
+        description: Output compressed file
-        pattern: "*.{vcf}"
+        pattern: "*.{gz}"
     - version:
         type: file
         description: File containing software version
@@ -58,3 +58,4 @@ output:
 authors:
     - "@joseespinosa"
     - "@drpatelh"
+    - "@maxulysse"

tests/software/bcftools/bgzip/test.yml

@@ -1,8 +0,0 @@
-- name: bcftools bgzip
-  command: nextflow run ./tests/software/bcftools/bgzip -entry test_bcftools_bgzip -c tests/config/nextflow.config
-  tags:
-    - bcftools
-    - bcftools_bgzip
-  files:
-    - path: output/bcftools/test.vcf.gz
-      md5sum: eb75ae1f08a1884f8edc59ed423471a2

tests/software/tabix/bgzip/main.nf

@@ -2,13 +2,13 @@
 
 nextflow.enable.dsl = 2
 
-include { BCFTOOLS_BGZIP } from '../../../../software/bcftools/bgzip/main.nf' addParams( options: [:] )
+include { TABIX_BGZIP as BGZIP_VCF } from '../../../../software/tabix/bgzip/main.nf' addParams( options: [:] )
 
-workflow test_bcftools_bgzip {
+workflow test_tabix_bgzip_vcf {
 
     def input = []
     input = [ [ id:'test' ], // meta map
               [ file("${launchDir}/tests/data/vcf/test.vcf", checkIfExists: true) ]]
 
-    BCFTOOLS_BGZIP ( input )
+    BGZIP_VCF ( input )
 }

tests/software/tabix/bgzip/test.yml

@@ -0,0 +1,8 @@
+- name: tabix bgzip
+  command: nextflow run ./tests/software/tabix/bgzip -entry test_tabix_bgzip_vcf -c tests/config/nextflow.config
+  tags:
+    - tabix
+    - tabix_bgzip
+  files:
+    - path: output/bgzip/test.vcf.gz
+      md5sum: 40419fb7562475d1c8ec4ab725796de2