mirror of
https://github.com/MillironX/nf-core_modules.git
synced 2024-12-22 11:08:17 +00:00
Merge pull request #1693 from matthdsm/update/mosdepth
mosdepth: cram compatiblility
This commit is contained in:
Harshil Patel
GitHub
commit
2c0b0df088
5 changed files with 166 additions and 77 deletions
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@ -10,13 +10,13 @@ process MOSDEPTH {
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input:
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tuple val(meta), path(bam), path(bai)
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path bed
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val window_size
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path fasta
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output:
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tuple val(meta), path('*.global.dist.txt') , emit: global_txt
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tuple val(meta), path('*.region.dist.txt') , emit: regions_txt , optional:true
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tuple val(meta), path('*.summary.txt') , emit: summary_txt
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tuple val(meta), path('*.per-base.d4') , emit: d4 , optional:true
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tuple val(meta), path('*.per-base.d4') , emit: per_base_d4 , optional:true
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tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed, optional:true
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tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi, optional:true
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tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed , optional:true
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@ -29,19 +29,21 @@ process MOSDEPTH {
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script:
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def args = task.ext.args ?: ''
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def prefix = task.ext.prefix ?: "${meta.id}"
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if (window_size) {
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interval = "--by ${window_size}"
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} else if ( bed ) {
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interval = "--by ${bed}"
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} else {
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interval = ""
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def reference = fasta ? "--fasta ${fasta}" : ""
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def interval = bed ? "--by ${bed}" : ""
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if (bed && args.contains("--by")) {
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exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition"
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}
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"""
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mosdepth \\
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--threads ${task.cpus} \\
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$interval \\
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$reference \\
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$args \\
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$prefix \\
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$bam
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cat <<-END_VERSIONS > versions.yml
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"${task.process}":
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mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//')
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@ -30,10 +30,10 @@ input:
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type: file
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description: BED file with intersected intervals
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pattern: "*.{bed}"
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- window_size:
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type: integer
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description: Window size
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pattern: "[0-9]+"
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- fasta:
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type: file
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description: Reference genome FASTA file
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pattern: "*.{fa,fasta}"
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output:
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- meta:
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type: map
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@ -60,6 +60,10 @@ output:
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type: file
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description: Index file for BED file with per-base coverage
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pattern: "*.{per-base.bed.gz.csi}"
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- per_base_d4:
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type: file
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description: D4 file with per-base coverage
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pattern: "*.{per-base.d4}"
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- regions_bed:
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type: file
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description: BED file with per-region coverage
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@ -76,3 +80,4 @@ authors:
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- "@joseespinosa"
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- "@drpatelh"
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- "@ramprasadn"
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- "@matthdsm"
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@ -2,35 +2,72 @@
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nextflow.enable.dsl = 2
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include { MOSDEPTH } from '../../../modules/mosdepth/main.nf'
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include { MOSDEPTH } from '../../../modules/mosdepth/main.nf'
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include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/mosdepth/main.nf'
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include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/mosdepth/main.nf'
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workflow test_mosdepth {
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input = [ [ id:'test', single_end:true ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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input = [
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[ id:'test', single_end:true ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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MOSDEPTH ( input, [], [] )
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}
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workflow test_mosdepth_window {
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input = [ [ id:'test', single_end:true ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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window = 100
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MOSDEPTH ( input, [], window )
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}
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workflow test_mosdepth_bed {
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input = [ [ id:'test', single_end:true ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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bed = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ]
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input = [
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[ id:'test', single_end:true ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
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MOSDEPTH ( input, bed, [] )
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}
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workflow test_mosdepth_cram {
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input = [
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[ id:'test', single_end:true ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
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]
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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MOSDEPTH ( input, [], fasta )
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}
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workflow test_mosdepth_cram_bed {
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input = [
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[ id:'test', single_end:true ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ]
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]
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bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
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fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ]
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MOSDEPTH ( input, bed, fasta )
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}
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workflow test_mosdepth_window {
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input = [
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[ id:'test', single_end:true ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
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MOSDEPTH_WINDOW ( input, [], [] )
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}
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workflow test_mosdepth_fail {
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input = [
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[ id:'test', single_end:true ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ],
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[ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ]
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]
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bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ]
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MOSDEPTH_FAIL ( input, bed, [] )
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}
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@ -1,5 +1,10 @@
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process {
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
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withName: MOSDEPTH_FAIL {
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ext.args = "--by 100"
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}
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withName: MOSDEPTH_WINDOW {
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ext.args = "--by 100"
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}
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}
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@ -1,53 +1,93 @@
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- name: mosdepth
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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- name: mosdepth test_mosdepth
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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tags:
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- mosdepth
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files:
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- path: ./output/mosdepth/test.per-base.bed.gz.csi
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md5sum: b2aad62c41a7146680d31df505fcc8c5
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- path: ./output/mosdepth/test.per-base.bed.gz
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md5sum: 11b3f649072c2c7453febb085b1a9c33
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- path: ./output/mosdepth/test.mosdepth.global.dist.txt
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md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
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- path: ./output/mosdepth/test.mosdepth.summary.txt
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md5sum: 7b249dd3b3e58cc122fbd25ea84aa25d
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- path: output/mosdepth/test.mosdepth.global.dist.txt
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md5sum: e82e90c7d508a135b5a8a7cd6933452e
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- path: output/mosdepth/test.mosdepth.summary.txt
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md5sum: 4f0d231060cbde4efdd673863bd2fb59
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- path: output/mosdepth/test.per-base.bed.gz
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md5sum: bc1df47d46f818fee5275975925d769a
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- path: output/mosdepth/test.per-base.bed.gz.csi
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md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
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- name: mosdepth window
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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- name: mosdepth test_mosdepth_bed
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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tags:
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- mosdepth
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files:
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- path: ./output/mosdepth/test.per-base.bed.gz.csi
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md5sum: b2aad62c41a7146680d31df505fcc8c5
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- path: ./output/mosdepth/test.per-base.bed.gz
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md5sum: 11b3f649072c2c7453febb085b1a9c33
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- path: ./output/mosdepth/test.mosdepth.global.dist.txt
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md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
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- path: ./output/mosdepth/test.regions.bed.gz
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md5sum: 64e1ced01c4443d7c1796ef553992f0c
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- path: ./output/mosdepth/test.regions.bed.gz.csi
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md5sum: 9e312b4b0784bd46dfbd23b3a8afed6a
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- path: ./output/mosdepth/test.mosdepth.region.dist.txt
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md5sum: 65fbc824c4212c6884354d8ac72ad37e
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- path: ./output/mosdepth/test.mosdepth.summary.txt
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md5sum: 11804907dab069ddb99ca97bf2698572
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- path: output/mosdepth/test.mosdepth.global.dist.txt
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md5sum: e82e90c7d508a135b5a8a7cd6933452e
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- path: output/mosdepth/test.mosdepth.region.dist.txt
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md5sum: e82e90c7d508a135b5a8a7cd6933452e
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- path: output/mosdepth/test.mosdepth.summary.txt
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md5sum: 96c037f769974b904beb53edc4f56d82
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- path: output/mosdepth/test.per-base.bed.gz
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md5sum: bc1df47d46f818fee5275975925d769a
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- path: output/mosdepth/test.per-base.bed.gz.csi
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md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
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- path: output/mosdepth/test.regions.bed.gz
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md5sum: 5d398caf7171ec4406278e2add3009ae
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- path: output/mosdepth/test.regions.bed.gz.csi
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md5sum: 47669cfe41f3e222e74d81e1b1be191f
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- name: mosdepth bed
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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- name: mosdepth test_mosdepth_cram
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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tags:
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- mosdepth
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files:
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- path: ./output/mosdepth/test.per-base.bed.gz.csi
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md5sum: b2aad62c41a7146680d31df505fcc8c5
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- path: ./output/mosdepth/test.per-base.bed.gz
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md5sum: 11b3f649072c2c7453febb085b1a9c33
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- path: ./output/mosdepth/test.mosdepth.global.dist.txt
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md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a
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- path: ./output/mosdepth/test.regions.bed.gz
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md5sum: 347f877700d1dc42c95157199eff25d5
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- path: ./output/mosdepth/test.regions.bed.gz.csi
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md5sum: ed5fbf46e3bdcbf60094df295bc40356
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- path: ./output/mosdepth/test.mosdepth.region.dist.txt
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md5sum: 295564628113d2ec0ca34d7f661cfea8
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- path: ./output/mosdepth/test.mosdepth.summary.txt
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md5sum: b07817412fd17819c14541e63bc4926c
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- path: output/mosdepth/test.mosdepth.global.dist.txt
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md5sum: e82e90c7d508a135b5a8a7cd6933452e
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- path: output/mosdepth/test.mosdepth.summary.txt
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md5sum: 4f0d231060cbde4efdd673863bd2fb59
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- path: output/mosdepth/test.per-base.bed.gz
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md5sum: bc1df47d46f818fee5275975925d769a
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- path: output/mosdepth/test.per-base.bed.gz.csi
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md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
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- name: mosdepth test_mosdepth_cram_bed
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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tags:
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- mosdepth
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files:
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- path: output/mosdepth/test.mosdepth.global.dist.txt
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md5sum: e82e90c7d508a135b5a8a7cd6933452e
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- path: output/mosdepth/test.mosdepth.region.dist.txt
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md5sum: e82e90c7d508a135b5a8a7cd6933452e
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- path: output/mosdepth/test.mosdepth.summary.txt
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md5sum: 96c037f769974b904beb53edc4f56d82
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- path: output/mosdepth/test.per-base.bed.gz
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md5sum: bc1df47d46f818fee5275975925d769a
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- path: output/mosdepth/test.per-base.bed.gz.csi
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md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
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- path: output/mosdepth/test.regions.bed.gz
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md5sum: 5d398caf7171ec4406278e2add3009ae
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- path: output/mosdepth/test.regions.bed.gz.csi
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md5sum: 47669cfe41f3e222e74d81e1b1be191f
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- name: mosdepth test_mosdepth_window
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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tags:
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- mosdepth
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files:
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- path: output/mosdepth/test.mosdepth.global.dist.txt
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md5sum: e82e90c7d508a135b5a8a7cd6933452e
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- path: output/mosdepth/test.mosdepth.region.dist.txt
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md5sum: 39e0e707ec32feb5176fd20a95f1f468
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- path: output/mosdepth/test.mosdepth.summary.txt
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md5sum: 96c037f769974b904beb53edc4f56d82
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- path: output/mosdepth/test.per-base.bed.gz
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md5sum: bc1df47d46f818fee5275975925d769a
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- path: output/mosdepth/test.per-base.bed.gz.csi
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md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4
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- path: output/mosdepth/test.regions.bed.gz
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md5sum: f02e2cb49cc050e13d76942d6960827a
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- path: output/mosdepth/test.regions.bed.gz.csi
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md5sum: 257d67678136963d9dd904330079609d
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- name: mosdepth test_mosdepth_fail
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command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_fail -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config
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tags:
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- mosdepth
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exit_code: 1
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