mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 02:58:17 +00:00
Macs2 calllpeak (#1038)
* Add tests and yml file for macs2/callpeak * add format option for macs2 * update macs2/callpeak to accept format argument * update test.yml * update the container version. * try to fix the issue in conda container. * Update conda and containers * Going back to previous container versions Co-authored-by: JoseEspinosa <kadomu@gmail.com>
This commit is contained in:
JIANHONG OU
GitHub
parent
3426834744
commit
4398056204
5 changed files with 146 additions and 3 deletions
|
|
@ -13,9 +13,9 @@ process MACS2_CALLPEAK {
|
|||
|
||||
conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
|
||||
if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
|
||||
container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h0213d0e_1"
|
||||
container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3"
|
||||
} else {
|
||||
container "quay.io/biocontainers/macs2:2.2.7.1--py38h0213d0e_1"
|
||||
container "quay.io/biocontainers/macs2:2.2.7.1--py38h4a8c8d9_3"
|
||||
}
|
||||
|
||||
input:
|
||||
|
|
@ -33,12 +33,19 @@ process MACS2_CALLPEAK {
|
|||
|
||||
script:
|
||||
def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
|
||||
def args = options.args.tokenize()
|
||||
def format = meta.single_end ? 'BAM' : 'BAMPE'
|
||||
def control = controlbam ? "--control $controlbam" : ''
|
||||
if(args.contains('--format')){
|
||||
def id = args.findIndexOf{it=='--format'}
|
||||
format = args[id+1]
|
||||
args.remove(id+1)
|
||||
args.remove(id)
|
||||
}
|
||||
"""
|
||||
macs2 \\
|
||||
callpeak \\
|
||||
$options.args \\
|
||||
${args.join(' ')} \\
|
||||
--gsize $macs2_gsize \\
|
||||
--format $format \\
|
||||
--name $prefix \\
|
||||
|
|
|
|||
63
modules/macs2/callpeak/meta.yml
Normal file
63
modules/macs2/callpeak/meta.yml
Normal file
|
|
@ -0,0 +1,63 @@
|
|||
name: macs2_callpeak
|
||||
description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
|
||||
keywords:
|
||||
- alignment
|
||||
- atac-seq
|
||||
- chip-seq
|
||||
- peak-calling
|
||||
tools:
|
||||
- macs2:
|
||||
description: Model Based Analysis for ChIP-Seq data
|
||||
homepage: None
|
||||
documentation: https://docs.csc.fi/apps/macs2/
|
||||
tool_dev_url: https://github.com/macs3-project/MACS
|
||||
doi: "https://doi.org/10.1101/496521"
|
||||
licence: ['BSD']
|
||||
|
||||
input:
|
||||
- meta:
|
||||
type: map
|
||||
description: |
|
||||
Groovy Map containing sample information
|
||||
e.g. [ id:'test', single_end:false ]
|
||||
- ipbam:
|
||||
type: file
|
||||
description: The ChIP-seq treatment file
|
||||
- controlbam:
|
||||
type: file
|
||||
description: The control file
|
||||
- macs2_gsize:
|
||||
type: string
|
||||
description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
|
||||
'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)
|
||||
|
||||
output:
|
||||
- versions:
|
||||
type: file
|
||||
description: File containing software version
|
||||
pattern: "versions.yml"
|
||||
- peak:
|
||||
type: file
|
||||
description: BED file containing annotated peaks
|
||||
pattern: "*.gappedPeak,*.narrowPeak}"
|
||||
- xls:
|
||||
type: file
|
||||
description: xls file containing annotated peaks
|
||||
pattern: "*.xls"
|
||||
- gapped:
|
||||
type: file
|
||||
description: Optional BED file containing gapped peak
|
||||
pattern: "*.gappedPeak"
|
||||
- bed:
|
||||
type: file
|
||||
description: Optional BED file containing peak summits locations for every peak
|
||||
pattern: "*.bed"
|
||||
- bdg:
|
||||
type: file
|
||||
description: Optional bedGraph files for input and treatment input samples
|
||||
pattern: "*.bdg"
|
||||
|
||||
authors:
|
||||
- "@ntoda03"
|
||||
- "@JoseEspinosa"
|
||||
- "@jianhong"
|
||||
|
|
@ -778,6 +778,10 @@ lofreq/indelqual:
|
|||
- modules/lofreq/indelqual/**
|
||||
- tests/modules/lofreq/indelqual/**
|
||||
|
||||
macs2/callpeak:
|
||||
- modules/macs2/callpeak/**
|
||||
- tests/modules/macs2/callpeak/**
|
||||
|
||||
malt/build:
|
||||
- modules/malt/build/**
|
||||
- tests/modules/malt/build_test/**
|
||||
|
|
|
|||
31
tests/modules/macs2/callpeak/main.nf
Normal file
31
tests/modules/macs2/callpeak/main.nf
Normal file
|
|
@ -0,0 +1,31 @@
|
|||
#!/usr/bin/env nextflow
|
||||
|
||||
nextflow.enable.dsl = 2
|
||||
|
||||
include { MACS2_CALLPEAK } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--qval 0.1"] )
|
||||
include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--qval 0.1"] )
|
||||
include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--format BED --qval 1 --nomodel --extsize 200"] )
|
||||
|
||||
workflow test_macs2_callpeak_bed {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file( params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true)],
|
||||
[]]
|
||||
|
||||
MACS2_CALLPEAK_BED ( input, 4000 )
|
||||
}
|
||||
|
||||
workflow test_macs2_callpeak {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
|
||||
[]]
|
||||
|
||||
MACS2_CALLPEAK ( input, 40000 )
|
||||
}
|
||||
|
||||
workflow test_macs2_callpeak_ctrl {
|
||||
input = [ [ id:'test', single_end:false ], // meta map
|
||||
[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
|
||||
[ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
|
||||
|
||||
MACS2_CALLPEAK_CTRL ( input, 40000 )
|
||||
}
|
||||
38
tests/modules/macs2/callpeak/test.yml
Normal file
38
tests/modules/macs2/callpeak/test.yml
Normal file
|
|
@ -0,0 +1,38 @@
|
|||
- name: macs2 callpeak test_macs2_callpeak_bed
|
||||
command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak_bed -c tests/config/nextflow.config
|
||||
tags:
|
||||
- macs2
|
||||
- macs2/callpeak
|
||||
files:
|
||||
- path: output/macs2/test_peaks.narrowPeak
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
- path: output/macs2/test_peaks.xls
|
||||
md5sum: 762383e3a35e1f9ac3834fd6b2926092
|
||||
- path: output/macs2/test_summits.bed
|
||||
md5sum: d41d8cd98f00b204e9800998ecf8427e
|
||||
|
||||
- name: macs2 callpeak test_macs2_callpeak
|
||||
command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak -c tests/config/nextflow.config
|
||||
tags:
|
||||
- macs2
|
||||
- macs2/callpeak
|
||||
files:
|
||||
- path: output/macs2/test_peaks.narrowPeak
|
||||
md5sum: 2e4da1c1704595e12aaf99cc715ad70c
|
||||
- path: output/macs2/test_peaks.xls
|
||||
md5sum: 5d65cb3dbd5421ea3bb5b490a100e9a4
|
||||
- path: output/macs2/test_summits.bed
|
||||
md5sum: 26f0f97b6c14dbca129e947a58067c82
|
||||
|
||||
- name: macs2 callpeak test_macs2_callpeak_ctrl
|
||||
command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak_ctrl -c tests/config/nextflow.config
|
||||
tags:
|
||||
- macs2
|
||||
- macs2/callpeak
|
||||
files:
|
||||
- path: output/macs2/test_peaks.narrowPeak
|
||||
md5sum: 653e1108cc57ca07d0f60fc0f4fb8ba3
|
||||
- path: output/macs2/test_peaks.xls
|
||||
md5sum: bf86546faa7b581b5209c29b22046a0a
|
||||
- path: output/macs2/test_summits.bed
|
||||
md5sum: 4f3c7c53a1d730d90d1b3dd9d3197af4
|
||||
Loading…
Reference in a new issue