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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
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@ -13,9 +13,9 @@ process MACS2_CALLPEAK {
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conda (params.enable_conda ? "bioconda::macs2=2.2.7.1" : null)
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if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
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container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h0213d0e_1"
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container "https://depot.galaxyproject.org/singularity/macs2:2.2.7.1--py38h4a8c8d9_3"
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} else {
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container "quay.io/biocontainers/macs2:2.2.7.1--py38h0213d0e_1"
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container "quay.io/biocontainers/macs2:2.2.7.1--py38h4a8c8d9_3"
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}
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input:
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@ -33,12 +33,19 @@ process MACS2_CALLPEAK {
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def args = options.args.tokenize()
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def format = meta.single_end ? 'BAM' : 'BAMPE'
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def control = controlbam ? "--control $controlbam" : ''
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if(args.contains('--format')){
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def id = args.findIndexOf{it=='--format'}
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format = args[id+1]
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args.remove(id+1)
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args.remove(id)
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}
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"""
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macs2 \\
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callpeak \\
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$options.args \\
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${args.join(' ')} \\
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--gsize $macs2_gsize \\
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--format $format \\
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--name $prefix \\
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63
modules/macs2/callpeak/meta.yml
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63
modules/macs2/callpeak/meta.yml
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@ -0,0 +1,63 @@
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name: macs2_callpeak
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description: Peak calling of enriched genomic regions of ChIP-seq and ATAC-seq experiments
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keywords:
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- alignment
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- atac-seq
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- chip-seq
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- peak-calling
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tools:
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- macs2:
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description: Model Based Analysis for ChIP-Seq data
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homepage: None
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documentation: https://docs.csc.fi/apps/macs2/
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tool_dev_url: https://github.com/macs3-project/MACS
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doi: "https://doi.org/10.1101/496521"
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licence: ['BSD']
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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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- ipbam:
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type: file
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description: The ChIP-seq treatment file
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- controlbam:
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type: file
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description: The control file
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- macs2_gsize:
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type: string
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description: Effective genome size. It can be 1.0e+9 or 1000000000, or shortcuts:'hs' for human (2.7e9),
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'mm' for mouse (1.87e9), 'ce' for C. elegans (9e7) and 'dm' for fruitfly (1.2e8)
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output:
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- versions:
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type: file
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description: File containing software version
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pattern: "versions.yml"
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- peak:
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type: file
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description: BED file containing annotated peaks
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pattern: "*.gappedPeak,*.narrowPeak}"
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- xls:
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type: file
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description: xls file containing annotated peaks
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pattern: "*.xls"
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- gapped:
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type: file
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description: Optional BED file containing gapped peak
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pattern: "*.gappedPeak"
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- bed:
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type: file
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description: Optional BED file containing peak summits locations for every peak
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pattern: "*.bed"
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- bdg:
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type: file
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description: Optional bedGraph files for input and treatment input samples
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pattern: "*.bdg"
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authors:
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- "@ntoda03"
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- "@JoseEspinosa"
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- "@jianhong"
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@ -778,6 +778,10 @@ lofreq/indelqual:
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- modules/lofreq/indelqual/**
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- tests/modules/lofreq/indelqual/**
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macs2/callpeak:
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- modules/macs2/callpeak/**
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- tests/modules/macs2/callpeak/**
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malt/build:
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- modules/malt/build/**
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- tests/modules/malt/build_test/**
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31
tests/modules/macs2/callpeak/main.nf
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31
tests/modules/macs2/callpeak/main.nf
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@ -0,0 +1,31 @@
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#!/usr/bin/env nextflow
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nextflow.enable.dsl = 2
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include { MACS2_CALLPEAK } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--qval 0.1"] )
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include { MACS2_CALLPEAK as MACS2_CALLPEAK_CTRL } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--qval 0.1"] )
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include { MACS2_CALLPEAK as MACS2_CALLPEAK_BED } from '../../../../modules/macs2/callpeak/main.nf' addParams( options: ["args": "--format BED --qval 1 --nomodel --extsize 200"] )
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workflow test_macs2_callpeak_bed {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file( params.test_data['homo_sapiens']['pacbio']['genemodel1'], checkIfExists: true)],
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[]]
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MACS2_CALLPEAK_BED ( input, 4000 )
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}
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workflow test_macs2_callpeak {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
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[]]
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MACS2_CALLPEAK ( input, 40000 )
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}
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workflow test_macs2_callpeak_ctrl {
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input = [ [ id:'test', single_end:false ], // meta map
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[ file( params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true) ],
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[ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]]
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MACS2_CALLPEAK_CTRL ( input, 40000 )
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}
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38
tests/modules/macs2/callpeak/test.yml
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38
tests/modules/macs2/callpeak/test.yml
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@ -0,0 +1,38 @@
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- name: macs2 callpeak test_macs2_callpeak_bed
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command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak_bed -c tests/config/nextflow.config
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tags:
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- macs2
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- macs2/callpeak
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files:
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- path: output/macs2/test_peaks.narrowPeak
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/macs2/test_peaks.xls
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md5sum: 762383e3a35e1f9ac3834fd6b2926092
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- path: output/macs2/test_summits.bed
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- name: macs2 callpeak test_macs2_callpeak
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command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak -c tests/config/nextflow.config
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tags:
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- macs2
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- macs2/callpeak
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files:
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- path: output/macs2/test_peaks.narrowPeak
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md5sum: 2e4da1c1704595e12aaf99cc715ad70c
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- path: output/macs2/test_peaks.xls
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md5sum: 5d65cb3dbd5421ea3bb5b490a100e9a4
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- path: output/macs2/test_summits.bed
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md5sum: 26f0f97b6c14dbca129e947a58067c82
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- name: macs2 callpeak test_macs2_callpeak_ctrl
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command: nextflow run tests/modules/macs2/callpeak -entry test_macs2_callpeak_ctrl -c tests/config/nextflow.config
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tags:
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- macs2
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- macs2/callpeak
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files:
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- path: output/macs2/test_peaks.narrowPeak
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md5sum: 653e1108cc57ca07d0f60fc0f4fb8ba3
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- path: output/macs2/test_peaks.xls
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md5sum: bf86546faa7b581b5209c29b22046a0a
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- path: output/macs2/test_summits.bed
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md5sum: 4f3c7c53a1d730d90d1b3dd9d3197af4
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