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

software/bcftools/tabix/functions.nf

@@ -1,60 +0,0 @@
-
-/*
- * -----------------------------------------------------
- *  Utility functions used in nf-core DSL2 module files
- * -----------------------------------------------------
- */
-
-/*
- * Extract name of software tool from process name using $task.process
- */
-def getSoftwareName(task_process) {
-    return task_process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()
-}
-
-/*
- * Function to initialise default values and to generate a Groovy Map of available options for nf-core modules
- */
-def initOptions(Map args) {
-    def Map options = [:]
-    options.args          = args.args ?: ''
-    options.args2         = args.args2 ?: ''
-    options.publish_by_id = args.publish_by_id ?: false
-    options.publish_dir   = args.publish_dir ?: ''
-    options.publish_files = args.publish_files
-    options.suffix        = args.suffix ?: ''
-    return options
-}
-
-/*
- * Tidy up and join elements of a list to return a path string
- */
-def getPathFromList(path_list) {
-    def paths = path_list.findAll { item -> !item?.trim().isEmpty() }  // Remove empty entries
-    paths = paths.collect { it.trim().replaceAll("^[/]+|[/]+\$", '') } // Trim whitespace and trailing slashes
-    return paths.join('/')
-}
-
-/*
- * Function to save/publish module results
- */
-def saveFiles(Map args) {
-    if (!args.filename.endsWith('.version.txt')) {
-        def ioptions = initOptions(args.options)
-        def path_list = [ ioptions.publish_dir ?: args.publish_dir ]
-        if (ioptions.publish_by_id) {
-            path_list.add(args.publish_id)
-        }
-        if (ioptions.publish_files instanceof Map) {
-            for (ext in ioptions.publish_files) {
-                if (args.filename.endsWith(ext.key)) {
-                    def ext_list = path_list.collect()
-                    ext_list.add(ext.value)
-                    return "${getPathFromList(ext_list)}/$args.filename"
-                }
-            }
-        } else if (ioptions.publish_files == null) {
-            return "${getPathFromList(path_list)}/$args.filename"
-        }
-    }
-}

software/bcftools/tabix/main.nf

@@ -1,33 +0,0 @@
-// Import generic module functions
-include { initOptions; saveFiles; getSoftwareName } from './functions'
-
-params.options = [:]
-def options    = initOptions(params.options)
-
-process BCFTOOLS_TABIX {
-    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)
-    if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/bcftools:1.11--h7c999a4_0"
-    } else {
-        container "quay.io/biocontainers/bcftools:1.11--h7c999a4_0"
-    }
-
-    input:
-    tuple val(meta), path(vcf)
-
-    output:
-    tuple val(meta), path("*.tbi"), emit: tbi
-    path  "*.version.txt"         , emit: version
-
-    script:
-    def software = getSoftwareName(task.process)
-    """
-    tabix $options.args $vcf
-    echo \$(bcftools --version 2>&1) | sed 's/^.*bcftools //; s/ .*\$//' > ${software}.version.txt
-    """
-}

software/bcftools/tabix/meta.yml

@@ -1,63 +0,0 @@
-name: bcftools_tabix
-description: Index GFF/BED/SAM/VCF file
-keywords:
-    - index
-    - vcf
-    - bed
-    - sam
-    - gff
-tools:
-    - stats:
-        description: |
-          Indexes a TAB-delimited genome position file.
-        homepage: http://samtools.github.io/bcftools/bcftools.html
-        documentation: http://www.htslib.org/doc/bcftools.html
-        doi: 10.1093/bioinformatics/btp352
-params:
-    - outdir:
-        type: string
-        description: |
-          The pipeline's output directory. By default, the module will
-          output files into `$params.outdir/<SOFTWARE>`
-    - publish_dir_mode:
-        type: string
-        description: |
-          Value for the Nextflow `publishDir` mode parameter.
-          Available: symlink, rellink, link, copy, copyNoFollow, move.
-    - enable_conda:
-        type: boolean
-        description: |
-          Run the module with Conda using the software specified
-          via the `conda` directive
-    - singularity_pull_docker_container:
-        type: boolean
-        description: |
-          Instead of directly downloading Singularity images for use with Singularity,
-          force the workflow to pull and convert Docker containers instead.
-input:
-    - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - vcf:
-        type: file
-        description: TAB-delimited genome position file compressed with bgzip
-        pattern: "*.{vcf.gz,bed.gz,sam.gz,gff.gz}"
-output:
-    - meta:
-        type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
-    - tbi:
-        type: file
-        description:  Index file
-        pattern: "*.{tbi}"
-    - version:
-        type: file
-        description: File containing software version
-        pattern: "*.{version.txt}"
-authors:
-    - "@joseespinosa"
-    - "@drpatelh"

software/tabix/tabix/main.nf

@@ -4,12 +4,12 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
 params.options = [:]
 def options    = initOptions(params.options)
 
-process HTSLIB_TABIX {
-    tag "$tab"
+process TABIX_TABIX {
+    tag "$meta.id"
     label 'process_medium'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
-        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
+        saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
 
     conda (params.enable_conda ? "bioconda::tabix=0.2.6" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
@@ -19,10 +19,10 @@ process HTSLIB_TABIX {
     }
 
     input:
-    path tab
+    tuple val(meta), path(tab)
 
     output:
-    path("*.tbi")        , emit: tbi
+    tuple val(meta), path("*.tbi"), emit: tbi
     path  "*.version.txt"         , emit: version
 
     script:

software/tabix/tabix/meta.yml

@@ -1,5 +1,5 @@
-name: htslib_tabix
-description: create tabix index from a sorted bgzip vcf file
+name: tabix_tabix
+description: create tabix index from a sorted bgzip tab-delimited genome file
 keywords:
     - index
     - tabix
@@ -7,7 +7,7 @@ keywords:
 tools:
     - tabix:
         description: Generic indexer for TAB-delimited genome position files.
-        homepage: https://www.htslib.org/
+        homepage: https://www.htslib.org/doc/tabix.html
         documentation: https://www.htslib.org/doc/tabix.1.html
         doi: 10.1093/bioinformatics/btq671
 params:
@@ -32,11 +32,21 @@ params:
             Instead of directly downloading Singularity images for use with Singularity,
             force the workflow to pull and convert Docker containers instead.
 input:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
     - tab:
         type: file
-        description: TAB-delimited genome file
-        pattern: "*"
+        description: TAB-delimited genome position file compressed with bgzip
+        pattern: "*.{bed.gz,gff.gz,sam.gz,vcf.gz}"
 output:
+    - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test', single_end:false ]
     - tbi:
         type: file
         description: tabix index file
@@ -46,4 +56,6 @@ output:
         description: File containing software version
         pattern: "*.{version.txt}"
 authors:
+    - "@joseespinosa"
+    - "@drpatelh"
     - "@maxulysse"