diff --git a/software/bedtools/slop/main.nf b/software/bedtools/slop/main.nf index cd13fae3..1e18b388 100644 --- a/software/bedtools/slop/main.nf +++ b/software/bedtools/slop/main.nf @@ -11,20 +11,20 @@ process BEDTOOLS_SLOP { 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::bedtools=2.30.0" : null) + conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null) if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) { container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0" } else { container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0" } - input: - tuple val(meta), path(beds), path (sizes) + tuple val(meta), path(bed) + path sizes output: - tuple val(meta), path("*.slop.bed"), emit: bed - path "*.version.txt", emit: version + tuple val(meta), path("*.bed"), emit: bed + path "*.version.txt" , emit: version script: def software = getSoftwareName(task.process) @@ -32,10 +32,10 @@ process BEDTOOLS_SLOP { """ bedtools \\ slop \\ - -i $beds \\ + -i $bed \\ -g $sizes \\ $options.args \\ - > ${prefix}.slop.bed + > ${prefix}.bed bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt """ diff --git a/software/bedtools/slop/meta.yml b/software/bedtools/slop/meta.yml index 1484d02c..2318802e 100644 --- a/software/bedtools/slop/meta.yml +++ b/software/bedtools/slop/meta.yml @@ -1,75 +1,59 @@ name: bedtools_slop description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r) keywords: - - bed - - slopBed + - bed + - slopBed tools: - - bedtools: - description: | - A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. - documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html - + - bedtools: + description: | + A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types. + documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html params: - - l: - type: integer - description: The number of base pairs to subtract from the start coordinate - - r: - type: integer - description: The number of base pairs to add to the end coordinate - - b: - type: integer - description: Increases the entry by the same number base pairs in each direction - - pct: - type: boolean - description: | - Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. By default this is set to false. - - - header: - type: boolean - description: | - Print the header from the input file prior to results. - - - outdir: - type: string - description: | - The pipeline's output directory. By default, the module will - output files into `$params.outdir/` - - 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 - + - outdir: + type: string + description: | + The pipeline's output directory. By default, the module will + output files into `$params.outdir/` + - 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 ] - - bed: - type: file - description: List of bed files - pattern: "*.{bed}" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Input BED file + pattern: "*.{bed}" output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - bed: - type: file - description: Edited bed file - pattern: "*.{slop.bed}" - - - version: - type: file - description: File containing software version - pattern: "*.{version.txt}" - -authors: -"@Emiller88" - -"@sruthipsuresh" + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - bed: + type: file + description: Slopped BED file + pattern: "*.{bed}" + - version: + type: file + description: File containing software version + pattern: "*.{version.txt}" +authors: + - "@Emiller88" + - "@sruthipsuresh" + - "@drpatelh" diff --git a/tests/software/bedtools/slop/main.nf b/tests/software/bedtools/slop/main.nf index 821cf030..fb2ccb38 100644 --- a/tests/software/bedtools/slop/main.nf +++ b/tests/software/bedtools/slop/main.nf @@ -7,9 +7,8 @@ include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addP workflow test_bedtools_slop { def input = [] input = [ [ id:'test'], - file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true), - file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] + file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ] - BEDTOOLS_SLOP( input ) + BEDTOOLS_SLOP ( input, file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ) } diff --git a/tests/software/bedtools/slop/test.yml b/tests/software/bedtools/slop/test.yml index 6b31bfd2..6af4f522 100644 --- a/tests/software/bedtools/slop/test.yml +++ b/tests/software/bedtools/slop/test.yml @@ -4,5 +4,5 @@ - bedtools - bedtools_slop files: - - path: output/bedtools/test.slop.bed + - path: output/bedtools/test.bed md5sum: 5f6ecc3e3cc6cee9537a1d088b02abec