diff --git a/software/ucsc/bedgraphtobigwig/functions.nf b/software/ucsc/bedgraphtobigwig/functions.nf new file mode 120000 index 00000000..5e1a8e03 --- /dev/null +++ b/software/ucsc/bedgraphtobigwig/functions.nf @@ -0,0 +1 @@ +../../lib/functions.nf \ No newline at end of file diff --git a/software/ucsc/bedgraphtobigwig/main.nf b/software/ucsc/bedgraphtobigwig/main.nf new file mode 100644 index 00000000..4da63fe1 --- /dev/null +++ b/software/ucsc/bedgraphtobigwig/main.nf @@ -0,0 +1,35 @@ +// Import generic module functions +include { initOptions; saveFiles; getSoftwareName } from './functions' + +def VERSION = '377' + +process UCSC_BEDRAPHTOBIGWIG { + tag "$meta.id" + label 'process_medium' + publishDir "${params.outdir}", + mode: params.publish_dir_mode, + saveAs: { filename -> saveFiles(filename:filename, options:options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } + + container "quay.io/biocontainers/ucsc-bedgraphtobigwig:377--h446ed27_1" + //container "https://depot.galaxyproject.org/singularity/ucsc-bedgraphtobigwig:377--h446ed27_1" + + conda (params.conda ? "bioconda::ucsc-bedgraphtobigwig=377" : null) + + input: + tuple val(meta), path(bedgraph) + path sizes + val options + + output: + tuple val(meta), path("*.bigWig"), emit: bigwig + path "*.version.txt", emit: version + + script: + def software = getSoftwareName(task.process) + def ioptions = initOptions(options) + def prefix = ioptions.suffix ? "${meta.id}${ioptions.suffix}" : "${meta.id}" + """ + bedGraphToBigWig $bedgraph $sizes ${prefix}.bigWig + echo $VERSION > ${software}.version.txt + """ +}