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Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
This commit is contained in:
sruthipsuresh 2021-02-01 19:28:03 -06:00 committed by sruthipsuresh
parent e5c21d15a3
commit fc8cdde2b4
6 changed files with 41 additions and 29 deletions
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3
software/bedtools/complement/meta.yml
View file

@ -32,7 +32,7 @@ input:
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 ]
- bed: - beds:
type: file type: file
description: List of bed files description: List of bed files
pattern: "*.{bed}" pattern: "*.{bed}"
@ -46,7 +46,6 @@ output:
type: file type: file
description: Edited bed file description: Edited bed file
pattern: "*.{complement.bed}" pattern: "*.{complement.bed}"
- version: - version:
type: file type: file
description: File containing software version description: File containing software version

9
software/bedtools/genomecov/main.nf
View file

@ -1,6 +1,7 @@
// Import generic module functions // Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions' include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
process BEDTOOLS_GENOMECOV { process BEDTOOLS_GENOMECOV {
@ -10,11 +11,11 @@ process BEDTOOLS_GENOMECOV {
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 =2.29.2" : null) conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : 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:2.29.2--hc088bd4_0" container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
} else { } else {
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
} }
input: input:
@ -29,6 +30,6 @@ process BEDTOOLS_GENOMECOV {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
bedtools genomecov -ibam $bams -g $sizes ${options.args} > ${prefix}.bed bedtools genomecov -ibam $bams -g $sizes ${options.args} > ${prefix}.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
""" """
} }

22
software/bedtools/intersect/main.nf
View file

@ -1,6 +1,7 @@
// Import generic module functions // Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions' include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
process BEDTOOLS_INTERSECT { process BEDTOOLS_INTERSECT {
@ -10,24 +11,31 @@ process BEDTOOLS_INTERSECT {
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 =2.29.2" : null) conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : 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:2.29.2--hc088bd4_0" container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
} else { } else {
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
} }
input: input:
tuple val(meta), path(bedfile1), path(bedfile2) tuple val(meta), path(bed1), path(bed2)
output: output:
tuple val(meta), path("*.intersect.bed"), emit: intersect tuple val(meta), path("*.intersect.bed"), emit: bed
path "*.version.txt", emit: version path "*.version.txt", emit: version
script: // TODO change script to account for multiple possible intersections script: // TODO change script to account for multiple possible intersections
def software = getSoftwareName(task.process) def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
bedtools intersect -a ${bedfile1} -b ${bedfile2} ${options.args} > ${prefix}.intersect.bed bedtools \\
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt intersect \\
-a ${bed1} \\
-b ${bed2} \\
$options.args \\
> ${prefix}.intersect.bed
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
""" """
} }

14
software/bedtools/merge/main.nf
View file

@ -1,6 +1,7 @@
// Import generic module functions // Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions' include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
process BEDTOOLS_MERGE { process BEDTOOLS_MERGE {
@ -10,23 +11,24 @@ process BEDTOOLS_MERGE {
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:'') } saveAs: { filename -> saveFiles(filename:filename, options:params.options, publish_dir:getSoftwareName(task.process), publish_id:'') }
conda (params.enable_conda ? "bioconda::bedtools =2.29.2" : null) conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : 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:2.29.2--hc088bd4_0" container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
} else { } else {
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
} }
input: input:
tuple val(meta), path(sort) tuple val(meta), path(bed)
output: output:
path("*.merged.bed"), emit: merge path("*.merged.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)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
bedtools merge -i ${sort} ${options.args} > ${prefix}.merged.bed bedtools merge -i ${sort} ${options.args} > ${prefix}.merged.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
""" """
} }

11
software/bedtools/slop/main.nf
View file

@ -1,5 +1,6 @@
// Import generic module functions // Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions' include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:] params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
@ -10,11 +11,11 @@ process BEDTOOLS_SLOP {
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 =2.29.2" : null) conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : 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:2.29.2--hc088bd4_0" container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
} else { } else {
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
} }
@ -22,7 +23,7 @@ process BEDTOOLS_SLOP {
tuple val(meta), path(beds), path (sizes) tuple val(meta), path(beds), path (sizes)
output: output:
tuple val(meta), path("*.slop.bed"), emit: slopbed tuple val(meta), path("*.slop.bed"), emit: bed
path "*.version.txt", emit: version path "*.version.txt", emit: version
script: script:
@ -41,7 +42,7 @@ process BEDTOOLS_SLOP {
} else { } else {
""" """
slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed slopBed -i $beds -g $sizes -l $params.l -r $params.r $header $pct $options.args> ${prefix}.slop.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
""" """
} }
} }

11
software/bedtools/sort/main.nf
View file

@ -1,6 +1,7 @@
// Import generic module functions // Import generic module functions
include { initOptions; saveFiles; getSoftwareName } from './functions' include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
process BEDTOOLS_SORT { process BEDTOOLS_SORT {
@ -10,18 +11,18 @@ process BEDTOOLS_SORT {
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 =2.29.2" : null) conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : 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:2.29.2--hc088bd4_0" container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
} else { } else {
container "quay.io/biocontainers/bedtools:2.29.2--hc088bd4_0" container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
} }
input: input:
tuple val(meta), path(beds) tuple val(meta), path(beds)
output: output:
tuple val(meta), path("*.sort.bed"), emit: sort tuple val(meta), path("*.sort.bed"), emit: bed
path "*.version.txt", emit: version path "*.version.txt", emit: version
script: script:
@ -29,6 +30,6 @@ process BEDTOOLS_SORT {
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}" def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
""" """
bedtools sort -i $beds ${options.args} > ${prefix}.sort.bed bedtools sort -i $beds ${options.args} > ${prefix}.sort.bed
bedtools --version | sed -e "s/Bedtools v//g" > ${software}.version.txt bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
""" """
} }