millironx/nf-core_modules
1
0
Fork 0
mirror of https://github.com/MillironX/nf-core_modules.git synced 2024-12-22 19:18:17 +00:00
Code Issues Releases Packages Activity

seacr | PR review changes

Browse source
This commit is contained in:
Chris Cheshire 2021-01-05 09:50:47 +00:00
parent 7e9cbfc8d1
commit 9c00d1722c
1 changed files with 5 additions and 4 deletions
Show stats Download patch file Download diff file Expand all files Collapse all files

9
software/seacr/callpeak/main.nf
View file

@ -4,6 +4,8 @@ include { initOptions; saveFiles; getSoftwareName } from './functions'
params.options = [:] params.options = [:]
def options = initOptions(params.options) def options = initOptions(params.options)
def VERSION = '1.3'
process SEACR_CALLPEAK { process SEACR_CALLPEAK {
tag "$meta.id" tag "$meta.id"
label 'process_medium' label 'process_medium'
@ -11,8 +13,7 @@ process SEACR_CALLPEAK {
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::seacr=1.3" : null) conda (params.enable_conda ? "bioconda::seacr=1.3 conda-forge::r-base=4.0.2 bioconda::bedtools=2.29.2" : 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/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0" container "https://depot.galaxyproject.org/singularity/mulled-v2-03bfeb32fe80910c231f630d4262b83677c8c0f4:5bb5ed4307a8187a7f34730b00431de93688fa59-0"
} else { } else {
@ -30,12 +31,12 @@ process SEACR_CALLPEAK {
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}"
""" """
SEACR_1.3.sh \\ SEACR_1.3.sh \\
$bedgraph \\ $bedgraph \\
$ctrlbedgraph \\ $ctrlbedgraph \\
$options.args \\ $options.args \\
$prefix $prefix
echo 1.3 > ${software}.version.txt echo $VERSION > ${software}.version.txt
""" """
} }