diff --git a/.github/filters.yml b/.github/filters.yml index 9fe5cdb9..c462d603 100644 --- a/.github/filters.yml +++ b/.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/** diff --git a/software/bcftools/bgzip/functions.nf b/software/tabix/bgzip/functions.nf similarity index 100% rename from software/bcftools/bgzip/functions.nf rename to software/tabix/bgzip/functions.nf diff --git a/software/bcftools/bgzip/main.nf b/software/tabix/bgzip/main.nf similarity index 68% rename from software/bcftools/bgzip/main.nf rename to software/tabix/bgzip/main.nf index 3e6e72e6..aa469e22 100644 --- a/software/bcftools/bgzip/main.nf +++ b/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 """ } diff --git a/software/bcftools/bgzip/meta.yml b/software/tabix/bgzip/meta.yml similarity index 84% rename from software/bcftools/bgzip/meta.yml rename to software/tabix/bgzip/meta.yml index c2f9e548..2bdb2a0f 100644 --- a/software/bcftools/bgzip/meta.yml +++ b/software/tabix/bgzip/meta.yml @@ -1,14 +1,14 @@ -name: bcftools_bgzip -description: Compresses VCF files +name: tabix_bgzip +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 - pattern: "*.{vcf}" + description: Output compressed file + pattern: "*.{gz}" - version: type: file description: File containing software version @@ -58,3 +58,4 @@ output: authors: - "@joseespinosa" - "@drpatelh" + - "@maxulysse" diff --git a/tests/software/bcftools/bgzip/test.yml b/tests/software/bcftools/bgzip/test.yml deleted file mode 100644 index b8b69258..00000000 --- a/tests/software/bcftools/bgzip/test.yml +++ /dev/null @@ -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 diff --git a/tests/software/bcftools/bgzip/main.nf b/tests/software/tabix/bgzip/main.nf similarity index 54% rename from tests/software/bcftools/bgzip/main.nf rename to tests/software/tabix/bgzip/main.nf index 02fc80d2..ba6a3912 100644 --- a/tests/software/bcftools/bgzip/main.nf +++ b/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 ) } diff --git a/tests/software/tabix/bgzip/test.yml b/tests/software/tabix/bgzip/test.yml new file mode 100644 index 00000000..f935668d --- /dev/null +++ b/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