mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-31 03:32:10 -05:00
Merge pull request #151 from drpatelh/bedtools
Follow up fixes for bedtools modules added in #79
This commit is contained in:
Harshil Patel
GitHub
commit
46e5df2cf7
25 changed files with 158 additions and 161 deletions
2
.github/workflows/pytest-workflow.yml
vendored
2
.github/workflows/pytest-workflow.yml
vendored
|
|
@ -25,7 +25,7 @@ jobs:
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matrix:
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nxf_version: ['20.11.0-edge']
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tags: ['${{ fromJson(needs.changes.outputs.modules) }}']
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profile: ['docker', 'singularity'] ## 'conda'
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profile: ['docker', 'singularity', 'conda']
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env:
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NXF_ANSI_LOG: false
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steps:
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|
|
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Binary file not shown.
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Before Width: | Height: | Size: 15 KiB After Width: | Height: | Size: 34 KiB |
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@ -11,7 +11,7 @@ process BEDTOOLS_COMPLEMENT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
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} else {
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@ -19,11 +19,12 @@ process BEDTOOLS_COMPLEMENT {
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}
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input:
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tuple val(meta), path(beds), path(sizes)
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tuple val(meta), path(bed)
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path sizes
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output:
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tuple val(meta), path('*.complement.bed'), emit: bed
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path '*.version.txt' , emit: version
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tuple val(meta), path('*.bed'), emit: bed
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path '*.version.txt' , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -31,10 +32,10 @@ process BEDTOOLS_COMPLEMENT {
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"""
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bedtools \\
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complement \\
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-i $beds \\
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-i $bed \\
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-g $sizes \\
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$options.args \\
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> ${prefix}.complement.bed
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> ${prefix}.bed
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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|
|
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|||
|
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@ -24,22 +24,25 @@ params:
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|||
description: |
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||||
Run the module with Conda using the software specified
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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:
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- meta:
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type: map
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description: |
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Groovy Map containing sample information
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e.g. [ id:'test', single_end:false ]
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- beds:
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- bed:
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type: file
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description: List of bed files
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description: Input BED file
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pattern: "*.{bed}"
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- sizes:
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type: file
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description: File which defines the chromosome lengths for a given genome
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pattern: "*.{sizes}"
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output:
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- meta:
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type: map
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@ -49,11 +52,12 @@ output:
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- bed:
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type: file
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description: Bed file with all genomic intervals that are not covered by at least one record from the input file.
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pattern: "*.{complement.bed}"
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pattern: "*.{bed}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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-"@Emiller88"
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-"@sruthipsuresh"
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- "@Emiller88"
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- "@sruthipsuresh"
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- "@drpatelh"
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|
|
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@ -11,7 +11,7 @@ process BEDTOOLS_GENOMECOV {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
|
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
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} else {
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|
|
@ -19,11 +19,11 @@ process BEDTOOLS_GENOMECOV {
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}
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input:
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tuple val(meta), path(bams)
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tuple val(meta), path(bam)
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output:
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tuple val(meta), path("*.bed"), emit: coverage
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path "*.version.txt", emit: version
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tuple val(meta), path("*.bed"), emit: bed
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path "*.version.txt" , emit: version
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script:
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def software = getSoftwareName(task.process)
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@ -31,7 +31,7 @@ process BEDTOOLS_GENOMECOV {
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"""
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bedtools \\
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genomecov \\
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-ibam $bams \\
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-ibam $bam \\
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$options.args \\
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> ${prefix}.bed
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|
|
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|
|
@ -9,7 +9,6 @@ tools:
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description: |
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A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
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documentation: https://bedtools.readthedocs.io/en/latest/content/tools/genomecov.html
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params:
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- outdir:
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type: string
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|
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@ -26,7 +25,11 @@ params:
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|||
description: |
|
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Run the module with Conda using the software specified
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via the `conda` directive
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|
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- singularity_pull_docker_container:
|
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type: boolean
|
||||
description: |
|
||||
Instead of directly downloading Singularity images for use with Singularity,
|
||||
force the workflow to pull and convert Docker containers instead.
|
||||
input:
|
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- meta:
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type: map
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@ -35,7 +38,7 @@ input:
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e.g. [ id:'test', single_end:false ]
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- bam:
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type: file
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description: List of bam files
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description: Input BAM file
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pattern: "*.{bam}"
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output:
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- meta:
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@ -47,12 +50,11 @@ output:
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type: file
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description: Computed genomecov bed file
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pattern: "*.{bed}"
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- version:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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|
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authors:
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-"@Emiller88"
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-"@sruthipsuresh"
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- "@Emiller88"
|
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- "@sruthipsuresh"
|
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- "@drpatelh"
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|
|
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|
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@ -11,7 +11,7 @@ process BEDTOOLS_INTERSECT {
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mode: params.publish_dir_mode,
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saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:meta.id) }
|
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|
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
|
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conda (params.enable_conda ? "bioconda::bedtools=2.30.0=hc088bd4_0" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
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} else {
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|
|
@ -22,8 +22,8 @@ process BEDTOOLS_INTERSECT {
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tuple val(meta), path(bed1), path(bed2)
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output:
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tuple val(meta), path('*.intersect.bed'), emit: bed
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path '*.version.txt' , emit: version
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||||
tuple val(meta), path('*.bed'), emit: bed
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||||
path '*.version.txt' , emit: version
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||||
|
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script:
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def software = getSoftwareName(task.process)
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|
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@ -31,10 +31,10 @@ process BEDTOOLS_INTERSECT {
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"""
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bedtools \\
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intersect \\
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-a ${bed1} \\
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-b ${bed2} \\
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-a $bed1 \\
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-b $bed2 \\
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$options.args \\
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> ${prefix}.intersect.bed
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> ${prefix}.bed
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bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
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"""
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||||
|
|
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|||
|
|
@ -24,7 +24,11 @@ params:
|
|||
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
|
||||
|
|
@ -33,13 +37,12 @@ input:
|
|||
e.g. [ id:'test', single_end:false ]
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- bed1:
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type: file
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description: Bed file, each feature in 1 is compared to 2 in search of overlaps
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description: BED file, each feature in 1 is compared to 2 in search of overlaps
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pattern: "*.{bed}"
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- bed2:
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type: file
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description: Second bed file, used to compare to 1.
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description: Second bed file, used to compare to first BED file
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pattern: "*.{bed}"
|
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|
||||
output:
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||||
- meta:
|
||||
type: map
|
||||
|
|
@ -48,12 +51,13 @@ output:
|
|||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
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type: file
|
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description: Overlapped bed file
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pattern: "*.{intersect.bed}"
|
||||
description: BED file with intersected intervals
|
||||
pattern: "*.{bed}"
|
||||
- version:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "*.{version.txt}"
|
||||
authors:
|
||||
-"@Emiller88"
|
||||
-"@sruthipsuresh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -9,9 +9,9 @@ process BEDTOOLS_MERGE {
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label 'process_medium'
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publishDir "${params.outdir}",
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mode: params.publish_dir_mode,
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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::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) {
|
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container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
|
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} else {
|
||||
|
|
@ -19,11 +19,11 @@ process BEDTOOLS_MERGE {
|
|||
}
|
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|
||||
input:
|
||||
tuple val(meta), path(beds)
|
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tuple val(meta), path(bed)
|
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|
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output:
|
||||
tuple val(meta), path('*.merged.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)
|
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|
|
@ -31,9 +31,9 @@ process BEDTOOLS_MERGE {
|
|||
"""
|
||||
bedtools \\
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merge \\
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-i $beds \\
|
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-i $bed \\
|
||||
$options.args \\
|
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> ${prefix}.merged.bed
|
||||
> ${prefix}.bed
|
||||
|
||||
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -24,7 +24,11 @@ params:
|
|||
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
|
||||
|
|
@ -33,9 +37,8 @@ input:
|
|||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Presorted interval bed file
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
@ -45,11 +48,12 @@ output:
|
|||
- bed:
|
||||
type: file
|
||||
description: Overlapped bed file with combined features
|
||||
pattern: "*.{merged.bed}"
|
||||
pattern: "*.{bed}"
|
||||
- version:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "*.{version.txt}"
|
||||
authors:
|
||||
-"@Emiller88"
|
||||
-"@sruthipsuresh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -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" > ${software}.version.txt
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -1,75 +1,59 @@
|
|||
name: bedtools_slop
|
||||
description: Adds a specified number of bases in each direction (unique values may be specified for either -l or -r)
|
||||
keywords:
|
||||
- bed
|
||||
- slopBed
|
||||
- bed
|
||||
- slopBed
|
||||
tools:
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
|
||||
|
||||
- bedtools:
|
||||
description: |
|
||||
A set of tools for genomic analysis tasks, specifically enabling genome arithmetic (merge, count, complement) on various file types.
|
||||
documentation: https://bedtools.readthedocs.io/en/latest/content/tools/slop.html
|
||||
params:
|
||||
- l:
|
||||
type: integer
|
||||
description: The number of base pairs to subtract from the start coordinate
|
||||
- r:
|
||||
type: integer
|
||||
description: The number of base pairs to add to the end coordinate
|
||||
- b:
|
||||
type: integer
|
||||
description: Increases the entry by the same number base pairs in each direction
|
||||
- pct:
|
||||
type: boolean
|
||||
description: |
|
||||
Define -l and -r as a fraction of the feature’s length. E.g. if used on a 1000bp feature, -l 0.50, will add 500 bp “upstream”. By default this is set to false.
|
||||
|
||||
- header:
|
||||
type: boolean
|
||||
description: |
|
||||
Print the header from the input file prior to results.
|
||||
|
||||
- outdir:
|
||||
type: string
|
||||
description: |
|
||||
The pipeline's output directory. By default, the module will
|
||||
output files into `$params.outdir/<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
|
||||
|
||||
- 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 ]
|
||||
- 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"
|
||||
|
|
|
|||
|
|
@ -11,7 +11,7 @@ process BEDTOOLS_SORT {
|
|||
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 {
|
||||
|
|
@ -19,11 +19,11 @@ process BEDTOOLS_SORT {
|
|||
}
|
||||
|
||||
input:
|
||||
tuple val(meta), path(beds)
|
||||
tuple val(meta), path(bed)
|
||||
|
||||
output:
|
||||
tuple val(meta), path('*.sort.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)
|
||||
|
|
@ -31,9 +31,9 @@ process BEDTOOLS_SORT {
|
|||
"""
|
||||
bedtools \\
|
||||
sort \\
|
||||
-i $beds \\
|
||||
-i $bed \\
|
||||
$options.args \\
|
||||
> ${prefix}.sort.bed
|
||||
> ${prefix}.bed
|
||||
|
||||
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
|
||||
"""
|
||||
|
|
|
|||
|
|
@ -24,18 +24,21 @@ params:
|
|||
description: |
|
||||
Run the module with Conda using the software specified
|
||||
via the `conda` directive
|
||||
|
||||
- singularity_pull_docker_container:
|
||||
type: boolean
|
||||
description: |
|
||||
Instead of directly downloading Singularity images for use with Singularity,
|
||||
force the workflow to pull and convert Docker containers instead.
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- beds:
|
||||
- bed:
|
||||
type: file
|
||||
description: List of bed files
|
||||
description: Input BED file
|
||||
pattern: "*.{bed}"
|
||||
|
||||
output:
|
||||
- meta:
|
||||
type: map
|
||||
|
|
@ -44,14 +47,13 @@ output:
|
|||
e.g. [ id:'test', single_end:false ]
|
||||
- bed:
|
||||
type: file
|
||||
description: Sorted bed file
|
||||
pattern: "*.{sort.bed}"
|
||||
|
||||
description: Sorted BED file
|
||||
pattern: "*.{bed}"
|
||||
- version:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "*.{version.txt}"
|
||||
|
||||
authors:
|
||||
-"@Emiller88"
|
||||
-"@sruthipsuresh"
|
||||
- "@Emiller88"
|
||||
- "@sruthipsuresh"
|
||||
- "@drpatelh"
|
||||
|
|
|
|||
|
|
@ -7,8 +7,7 @@ include { BEDTOOLS_COMPLEMENT } from '../../../../software/bedtools/complement/m
|
|||
workflow test_bedtools_complement {
|
||||
def input = []
|
||||
input = [ [ id:'test'],
|
||||
file("${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_COMPLEMENT( input )
|
||||
BEDTOOLS_COMPLEMENT ( input, file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,5 +4,5 @@
|
|||
- bedtools
|
||||
- bedtools_complement
|
||||
files:
|
||||
- path: output/bedtools/test.complement.bed
|
||||
- path: output/bedtools/test.bed
|
||||
md5sum: 55a43973abb1a08ac57290ff44f6c502
|
||||
|
|
|
|||
|
|
@ -4,12 +4,11 @@ nextflow.enable.dsl = 2
|
|||
|
||||
include { BEDTOOLS_GENOMECOV } from '../../../../software/bedtools/genomecov/main.nf' addParams( options: [:] )
|
||||
|
||||
|
||||
workflow test_bedtools_genomecov {
|
||||
def input = []
|
||||
input = [ [ id:'test'],
|
||||
file("${launchDir}/tests/data/bam/test.paired_end.name.sorted.bam", checkIfExists: true) ]
|
||||
|
||||
BEDTOOLS_GENOMECOV( input )
|
||||
BEDTOOLS_GENOMECOV ( input )
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -10,5 +10,5 @@ workflow test_bedtools_intersect {
|
|||
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true),
|
||||
file("${launchDir}/tests/data/bed/B.bed", checkIfExists: true) ]
|
||||
|
||||
BEDTOOLS_INTERSECT( input )
|
||||
BEDTOOLS_INTERSECT ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,5 +4,5 @@
|
|||
- bedtools
|
||||
- bedtools_intersect
|
||||
files:
|
||||
- path: output/bedtools/test.intersect.bed
|
||||
- path: output/bedtools/test.bed
|
||||
md5sum: cc1bb317886e7df0a942b56f8a320d9c
|
||||
|
|
|
|||
|
|
@ -9,6 +9,6 @@ workflow test_bedtools_merge {
|
|||
input = [ [ id:'test'],
|
||||
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
|
||||
|
||||
BEDTOOLS_MERGE( input )
|
||||
BEDTOOLS_MERGE ( input )
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -4,5 +4,5 @@
|
|||
- bedtools
|
||||
- bedtools_merge
|
||||
files:
|
||||
- path: output/bedtools/test.merged.bed
|
||||
- path: output/bedtools/test.bed
|
||||
md5sum: 13e5a3b254fac35fe0da0c92cbaf1761
|
||||
|
|
|
|||
|
|
@ -7,9 +7,8 @@ include { BEDTOOLS_SLOP } from '../../../../software/bedtools/slop/main.nf' addP
|
|||
workflow test_bedtools_slop {
|
||||
def input = []
|
||||
input = [ [ id:'test'],
|
||||
file("${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("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) )
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -4,5 +4,5 @@
|
|||
- bedtools
|
||||
- bedtools_slop
|
||||
files:
|
||||
- path: output/bedtools/test.slop.bed
|
||||
- path: output/bedtools/test.bed
|
||||
md5sum: 5f6ecc3e3cc6cee9537a1d088b02abec
|
||||
|
|
|
|||
|
|
@ -9,6 +9,5 @@ workflow test_bedtools_sort {
|
|||
input = [ [ id:'test'],
|
||||
file("${launchDir}/tests/data/bed/A.bed", checkIfExists: true) ]
|
||||
|
||||
BEDTOOLS_SORT( input )
|
||||
|
||||
BEDTOOLS_SORT ( input )
|
||||
}
|
||||
|
|
|
|||
|
|
@ -4,5 +4,5 @@
|
|||
- bedtools
|
||||
- bedtools_sort
|
||||
files:
|
||||
- path: output/bedtools/test.sort.bed
|
||||
- path: output/bedtools/test.bed
|
||||
md5sum: 4279202e33fcce3d19f420f1b27fddee
|
||||
|
|
|
|||
Loading…
Reference in a new issue