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Refactor genrich to avoid params in main (#981)
* Refactor genrich to avoid params in main * Missed to commit test.yml file
This commit is contained in:
Jose Espinosa-Carrasco
GitHub
parent
a4943a9e57
commit
0a7368aa6f
4 changed files with 81 additions and 26 deletions
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@ -22,6 +22,10 @@ process GENRICH {
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tuple val(meta), path(treatment_bam)
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path control_bam
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path blacklist_bed
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val save_pvalues
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val save_pileup
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val save_bed
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val save_duplicates
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output:
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tuple val(meta), path("*narrowPeak") , emit: peaks
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@ -33,13 +37,13 @@ process GENRICH {
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script:
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def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
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def control = params.control_bam ? "-c $control_bam" : ''
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def pvalues = params.pvalues ? "-f ${prefix}.pvalues.bedGraph" : ""
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def pileup = params.pileup ? "-k ${prefix}.pileup.bedGraph" : ""
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def bed = params.bed ? "-b ${prefix}.intervals.bed" : ""
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def blacklist = params.blacklist_bed ? "-E $blacklist_bed" : ""
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def control = control_bam ? "-c $control_bam" : ''
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def blacklist = blacklist_bed ? "-E $blacklist_bed" : ""
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def pvalues = save_pvalues ? "-f ${prefix}.pvalues.bedGraph" : ""
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def pileup = save_pileup ? "-k ${prefix}.pileup.bedGraph" : ""
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def bed = save_bed ? "-b ${prefix}.intervals.bed" : ""
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def duplicates = ""
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if (params.save_duplicates) {
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if (save_duplicates) {
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if (options.args.contains('-r')) {
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duplicates = "-R ${prefix}.duplicates.txt"
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} else {
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@ -58,7 +62,6 @@ process GENRICH {
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$pileup \\
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$bed \\
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$duplicates \\
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$blacklist \\
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$control
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cat <<-END_VERSIONS > versions.yml
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@ -15,7 +15,6 @@ tools:
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tool_dev_url: https://github.com/jsh58/Genrich
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doi: ""
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licence: ['MIT']
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input:
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- meta:
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type: map
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@ -34,7 +33,18 @@ input:
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type: file
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description: Bed file containing genomic intervals to exclude from the analysis
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pattern: "*.{bed}"
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- save_pvalues:
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type: boolean
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description: Create bedgraph-ish file for p/q-values file
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- save_pileup:
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type: boolean
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description: Create bedgraph-ish file for pileups and p-values
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- save_bed:
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type: boolean
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description: Create BED file for reads/fragments/intervals
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- save_duplicates:
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type: boolean
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description: Create PCR duplicates file (only works if -r option is set)
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output:
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- meta:
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type: map
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@ -65,7 +75,6 @@ output:
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type: file
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description: File containing software version
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pattern: "*.{version.txt}"
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authors:
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- "@JoseEspinosa"
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@ -2,10 +2,10 @@
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nextflow.enable.dsl = 2
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include { GENRICH } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:false, save_duplicates:false, options: ["args": "-p 0.1"] )
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include { GENRICH as GENRICH_BLACKLIST } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:true, save_duplicates:false, options: ["args": "-p 0.1"] )
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include { GENRICH as GENRICH_ALL_OUTPUTS } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: true, pileup:true, bed:true, blacklist_bed:false, save_duplicates:true, options: ["args": "-r -p 0.1"] )
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include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf' addParams( control_bam: false, pvalues: false, pileup:false, bed:false, blacklist_bed:false, save_duplicates:false, options: ["args": "-j -p 0.1"] )
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include { GENRICH } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-p 0.1"] )
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include { GENRICH as GENRICH_CTRL } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-p 0.9"] )
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include { GENRICH as GENRICH_ALL } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-r -p 0.1"] )
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include { GENRICH as GENRICH_ATACSEQ } from '../../../modules/genrich/main.nf' addParams( options: ["args": "-j -p 0.1"] )
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workflow test_genrich {
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input = [ [ id:'test', single_end:false ], // meta map
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@ -13,7 +13,12 @@ workflow test_genrich {
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control = [ ]
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blacklist = [ ]
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GENRICH ( input, control, blacklist )
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save_pvalues = false
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save_pileup = false
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save_bed = false
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save_duplicates = false
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GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
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}
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workflow test_genrich_ctrl {
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@ -22,7 +27,12 @@ workflow test_genrich_ctrl {
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control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
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blacklist = [ ]
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GENRICH ( input, control, blacklist )
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save_pvalues = false
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save_pileup = false
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save_bed = false
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save_duplicates = false
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GENRICH_CTRL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
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}
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workflow test_genrich_all_outputs {
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@ -31,14 +41,39 @@ workflow test_genrich_all_outputs {
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control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
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blacklist = [ ]
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GENRICH_ALL_OUTPUTS ( input, control, blacklist )
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save_pvalues = true
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save_pileup = true
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save_bed = true
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save_duplicates = true
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GENRICH_ALL ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
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}
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workflow test_genrich_blacklist {
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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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control = [ ]
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blacklist = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true)]
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save_pvalues = false
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save_pileup = false
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save_bed = false
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save_duplicates = false
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GENRICH ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
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}
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workflow test_genrich_atacseq {
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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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control = [ file( params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true) ]
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control = [ ]
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blacklist = [ ]
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GENRICH_ATACSEQ ( input, control, blacklist )
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save_pvalues = false
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save_pileup = false
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save_bed = false
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save_duplicates = false
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GENRICH_ATACSEQ ( input, control, blacklist, save_pvalues, save_pileup, save_bed, save_duplicates )
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}
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@ -12,7 +12,7 @@
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- genrich
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files:
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- path: output/genrich/test.narrowPeak
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md5sum: 6afabdd3f691c7c84c66ff8a23984681
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md5sum: 2fcc392360b317f5ebee88cdbc149e05
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- name: genrich test_genrich_all_outputs
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command: nextflow run tests/modules/genrich -entry test_genrich_all_outputs -c tests/config/nextflow.config
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@ -20,15 +20,23 @@
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- genrich
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files:
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- path: output/genrich/test.duplicates.txt
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md5sum: a92893f905fd8b3751bc6a960fbfe7ba
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md5sum: 159d557af7c23bc3cfb802d87fa96c34
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- path: output/genrich/test.intervals.bed
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md5sum: 52edf47e6641c0cc03f9cca7324f7eaa
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md5sum: 4bea65caa3f4043d703af4b57161112e
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- path: output/genrich/test.narrowPeak
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md5sum: e45eb7d000387975050c2e85c164e5be
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md5sum: d41d8cd98f00b204e9800998ecf8427e
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- path: output/genrich/test.pileup.bedGraph
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md5sum: e4f7fa664cd4ed2cf3a1a3a9eb415e71
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md5sum: 03e53848de695b5794f32f15b2709203
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- path: output/genrich/test.pvalues.bedGraph
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md5sum: 564859953704983393d4b7d6317060cd
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md5sum: b14feef34b6d2379a173a734ca963cde
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- name: genrich test_genrich_blacklist
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command: nextflow run tests/modules/genrich -entry test_genrich_blacklist -c tests/config/nextflow.config
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tags:
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- genrich
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files:
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- path: output/genrich/test.narrowPeak
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md5sum: 6afabdd3f691c7c84c66ff8a23984681
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- name: genrich test_genrich_atacseq
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command: nextflow run tests/modules/genrich -entry test_genrich_atacseq -c tests/config/nextflow.config
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