Fixed images, genomecov

This commit is contained in:
sruthipsuresh 2021-01-28 08:24:33 -06:00
parent e3bbbb48fc
commit e360617ac6
5 changed files with 21 additions and 18 deletions

View file

@ -13,23 +13,28 @@ process BEDTOOLS_GENOMECOV {
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {
container "quay.io/biocontainers/bedtools:bedtools:2.30.0--hc088bd4_0"
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
}
input:
tuple val(meta), path(bams), path (sizes)
tuple val(meta), path(bams)
output:
tuple val(meta), path("*.bed"), emit: coverage
path "*.version.txt", emit: version
tuple val(meta), path("*.bed"), emit: coverage
path "*.version.txt", emit: version
script:
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bedtools genomecov -ibam $bams -g $sizes ${options.args} > ${prefix}.bed
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
def software = getSoftwareName(task.process)
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
"""
bedtools \\
genomecov \\
-ibam $bams \\
$options.args \\
> ${prefix}.bed
bedtools --version | sed -e "s/bedtools v//g" > ${software}.version.txt
"""
}

View file

@ -36,7 +36,7 @@ input:
- bam:
type: file
description: List of bam files
pattern: "*.{bed}"
pattern: "*.{bam}"
output:
- meta:
type: map
@ -45,7 +45,7 @@ output:
e.g. [ id:'test', single_end:false ]
- bed:
type: file
description: Computed bed file
description: Computed genomecov bed file
pattern: "*.{bed}"
- version:

View file

@ -13,7 +13,7 @@ process BEDTOOLS_SLOP {
conda (params.enable_conda ? "bioconda::bedtools=2.30.0" : null)
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
container "https://depot.galaxyproject.org/singularity/bedtools:bedtools:2.30.0--hc088bd4_0"
container "https://depot.galaxyproject.org/singularity/bedtools:2.30.0--hc088bd4_0"
} else {
container "quay.io/biocontainers/bedtools:2.30.0--hc088bd4_0"
}

View file

@ -64,7 +64,7 @@ output:
- bed:
type: file
description: Edited bed file
pattern: "*.{slopbed}"
pattern: "*.{slop.bed}"
- version:
type: file

View file

@ -22,8 +22,7 @@ workflow test_bedtools_complement {
workflow test_bedtools_genomecov {
def input = []
input = [ [ id:'test'],
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true),
file("${launchDir}/tests/data/bed/genome.sizes", checkIfExists: true) ] //metamap
file("${launchDir}/tests/data/bam/test.paired_end.sorted.bam", checkIfExists: true) ]
BEDTOOLS_GENOMECOV( input )
}
@ -38,7 +37,6 @@ workflow test_bedtools_intersect {
}
// TODO use output of sort module
workflow test_bedtools_merge {
def input = []
input = [ [ id:'test' ], // meta map