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Fix bedtools complement module

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drpatelh 2021-02-07 20:55:12 +00:00
parent e4adb8ab53
commit a9102c329c
2 changed files with 13 additions and 13 deletions
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13
software/bedtools/complement/main.nf
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@ -11,7 +11,7 @@ process BEDTOOLS_COMPLEMENT {
mode: params.publish_dir_mode, mode: params.publish_dir_mode,
saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) } 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) { if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0" container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else { } else {
@ -19,11 +19,12 @@ process BEDTOOLS_COMPLEMENT {
} }
input: input:
tuple val(meta), path(beds), path(sizes) tuple val(meta), path(bed)
path sizes
output: output:
tuple val(meta), path('*.complement.bed'), emit: bed tuple val(meta), path('*.bed'), emit: bed
path '*.version.txt' , emit: version path '*.version.txt' , emit: version
script: script:
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
@ -31,10 +32,10 @@ process BEDTOOLS_COMPLEMENT {
""" """
bedtools \\ bedtools \\
complement \\ complement \\
-i $beds \\ -i $bed \\
-g $sizes \\ -g $sizes \\
$options.args \\ $options.args \\
> ${prefix}.complement.bed > ${prefix}.bed
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
""" """

13
software/bedtools/complement/meta.yml
View file

@ -24,22 +24,20 @@ params:
description: | description: |
Run the module with Conda using the software specified Run the module with Conda using the software specified
via the `conda` directive via the `conda` directive
input: input:
- meta: - meta:
type: map type: map
description: | description: |
Groovy Map containing sample information Groovy Map containing sample information
e.g. [ id:'test', single_end:false ] e.g. [ id:'test', single_end:false ]
- beds: - bed:
type: file type: file
description: List of bed files description: Input BED file
pattern: "*.{bed}" pattern: "*.bed"
- sizes: - sizes:
type: file type: file
description: File which defines the chromosome lengths for a given genome description: File which defines the chromosome lengths for a given genome
pattern: "*.{sizes}" pattern: "*.sizes"
output: output:
- meta: - meta:
type: map type: map
@ -49,7 +47,7 @@ output:
- bed: - bed:
type: file type: file
description: Bed file with all genomic intervals that are not covered by at least one record from the input file. description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
pattern: "*.{complement.bed}" pattern: "*.bed"
- version: - version:
type: file type: file
description: File containing software version description: File containing software version
@ -57,3 +55,4 @@ output:
authors: authors:
-"@Emiller88" -"@Emiller88"
-"@sruthipsuresh" -"@sruthipsuresh"
-"@drpatelh"