From 01fb8851c3e778052d342059736ecc09abab2e0d Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 24 May 2022 11:47:58 +0200 Subject: [PATCH 1/7] mosdept: cram compatiblility --- modules/mosdepth/main.nf | 33 +++-------- modules/mosdepth/meta.yml | 13 +++-- tests/modules/mosdepth/main.nf | 55 +++++++++++------- tests/modules/mosdepth/test.yml | 98 +++++++++++++++++++-------------- 4 files changed, 106 insertions(+), 93 deletions(-) diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index ff91e06f..894df1ae 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -10,13 +10,13 @@ process MOSDEPTH { input: tuple val(meta), path(bam), path(bai) path bed - val window_size + path fasta output: tuple val(meta), path('*.global.dist.txt') , emit: global_txt tuple val(meta), path('*.region.dist.txt') , emit: regions_txt , optional:true tuple val(meta), path('*.summary.txt') , emit: summary_txt - tuple val(meta), path('*.per-base.d4') , emit: d4 , optional:true + tuple val(meta), path('*.per-base.d4') , emit: per_base_d4 , optional:true tuple val(meta), path('*.per-base.bed.gz') , emit: per_base_bed, optional:true tuple val(meta), path('*.per-base.bed.gz.csi'), emit: per_base_csi, optional:true tuple val(meta), path('*.regions.bed.gz') , emit: regions_bed , optional:true @@ -29,36 +29,17 @@ process MOSDEPTH { script: def args = task.ext.args ?: '' def prefix = task.ext.prefix ?: "${meta.id}" - if (window_size) { - interval = "--by ${window_size}" - } else if ( bed ) { - interval = "--by ${bed}" - } else { - interval = "" - } + def reference = fasta ? "--fasta ${fasta}" : "" + def interval = bed ? "--by ${bed}" : "" + """ mosdepth \\ + --threads ${task.cpus} \\ $interval \\ + $reference \\ $args \\ $prefix \\ $bam - cat <<-END_VERSIONS > versions.yml - "${task.process}": - mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.global.dist.txt - touch ${prefix}.region.dist.txt - touch ${prefix}.summary.txt - touch ${prefix}.per-base.d4 - touch ${prefix}.per-base.bed.gz - touch ${prefix}.per-base.bed.gz.csi - touch ${prefix}.regions.bed.gz - touch ${prefix}.regions.bed.gz.csi cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/mosdepth/meta.yml b/modules/mosdepth/meta.yml index 636e966b..6e9e34c9 100644 --- a/modules/mosdepth/meta.yml +++ b/modules/mosdepth/meta.yml @@ -30,10 +30,10 @@ input: type: file description: BED file with intersected intervals pattern: "*.{bed}" - - window_size: - type: integer - description: Window size - pattern: "[0-9]+" + - fasta: + type: file + description: Reference genome FASTA file + pattern: "*.{fa,fasta}" output: - meta: type: map @@ -60,6 +60,10 @@ output: type: file description: Index file for BED file with per-base coverage pattern: "*.{per-base.bed.gz.csi}" + - per_base_d4: + type: file + description: D4 file with per-base coverage + pattern: "*.{per-base.d4}" - regions_bed: type: file description: BED file with per-region coverage @@ -76,3 +80,4 @@ authors: - "@joseespinosa" - "@drpatelh" - "@ramprasadn" + - "@matthdsm" diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf index ddd68129..86ca0e86 100644 --- a/tests/modules/mosdepth/main.nf +++ b/tests/modules/mosdepth/main.nf @@ -5,32 +5,45 @@ nextflow.enable.dsl = 2 include { MOSDEPTH } from '../../../modules/mosdepth/main.nf' workflow test_mosdepth { - input = [ [ id:'test', single_end:true ], - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] + input = [ + [ id:'test', single_end:true ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] + ] MOSDEPTH ( input, [], [] ) } - -workflow test_mosdepth_window { - input = [ [ id:'test', single_end:true ], - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] - window = 100 - - MOSDEPTH ( input, [], window ) -} - - workflow test_mosdepth_bed { - input = [ [ id:'test', single_end:true ], - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], - [ file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] - ] - bed = [ file(params.test_data['sarscov2']['genome']['test_bed'], checkIfExists: true) ] + input = [ + [ id:'test', single_end:true ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] + ] + bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] MOSDEPTH ( input, bed, [] ) } + +workflow test_mosdepth_cram { + input = [ + [ id:'test', single_end:true ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ] + ] + fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] + + MOSDEPTH ( input, [], fasta ) +} + +workflow test_mosdepth_cram_bed { + input = [ + [ id:'test', single_end:true ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_cram_crai'], checkIfExists: true) ] + ] + bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] + fasta = [ file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) ] + + MOSDEPTH ( input, bed, fasta ) +} diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml index c66e0b89..2cacb185 100644 --- a/tests/modules/mosdepth/test.yml +++ b/tests/modules/mosdepth/test.yml @@ -1,53 +1,67 @@ -- name: mosdepth - command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config +- name: mosdepth test_mosdepth + command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config tags: - mosdepth files: - - path: ./output/mosdepth/test.per-base.bed.gz.csi - md5sum: b2aad62c41a7146680d31df505fcc8c5 - - path: ./output/mosdepth/test.per-base.bed.gz - md5sum: 11b3f649072c2c7453febb085b1a9c33 - - path: ./output/mosdepth/test.mosdepth.global.dist.txt - md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a - - path: ./output/mosdepth/test.mosdepth.summary.txt - md5sum: 7b249dd3b3e58cc122fbd25ea84aa25d + - path: output/mosdepth/test.mosdepth.global.dist.txt + md5sum: e82e90c7d508a135b5a8a7cd6933452e + - path: output/mosdepth/test.mosdepth.summary.txt + md5sum: 4f0d231060cbde4efdd673863bd2fb59 + - path: output/mosdepth/test.per-base.bed.gz + md5sum: bc1df47d46f818fee5275975925d769a + - path: output/mosdepth/test.per-base.bed.gz.csi + md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 -- name: mosdepth window - command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config +- name: mosdepth test_mosdepth_bed + command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config tags: - mosdepth files: - - path: ./output/mosdepth/test.per-base.bed.gz.csi - md5sum: b2aad62c41a7146680d31df505fcc8c5 - - path: ./output/mosdepth/test.per-base.bed.gz - md5sum: 11b3f649072c2c7453febb085b1a9c33 - - path: ./output/mosdepth/test.mosdepth.global.dist.txt - md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a - - path: ./output/mosdepth/test.regions.bed.gz - md5sum: 64e1ced01c4443d7c1796ef553992f0c - - path: ./output/mosdepth/test.regions.bed.gz.csi - md5sum: 9e312b4b0784bd46dfbd23b3a8afed6a - - path: ./output/mosdepth/test.mosdepth.region.dist.txt - md5sum: 65fbc824c4212c6884354d8ac72ad37e - - path: ./output/mosdepth/test.mosdepth.summary.txt - md5sum: 11804907dab069ddb99ca97bf2698572 + - path: output/mosdepth/test.mosdepth.global.dist.txt + md5sum: e82e90c7d508a135b5a8a7cd6933452e + - path: output/mosdepth/test.mosdepth.region.dist.txt + md5sum: e82e90c7d508a135b5a8a7cd6933452e + - path: output/mosdepth/test.mosdepth.summary.txt + md5sum: 96c037f769974b904beb53edc4f56d82 + - path: output/mosdepth/test.per-base.bed.gz + md5sum: bc1df47d46f818fee5275975925d769a + - path: output/mosdepth/test.per-base.bed.gz.csi + md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 + - path: output/mosdepth/test.regions.bed.gz + md5sum: 5d398caf7171ec4406278e2add3009ae + - path: output/mosdepth/test.regions.bed.gz.csi + md5sum: 47669cfe41f3e222e74d81e1b1be191f -- name: mosdepth bed - command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config +- name: mosdepth test_mosdepth_cram + command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config tags: - mosdepth files: - - path: ./output/mosdepth/test.per-base.bed.gz.csi - md5sum: b2aad62c41a7146680d31df505fcc8c5 - - path: ./output/mosdepth/test.per-base.bed.gz - md5sum: 11b3f649072c2c7453febb085b1a9c33 - - path: ./output/mosdepth/test.mosdepth.global.dist.txt - md5sum: 2a1de1b0ecc361a21cd296ec4e1efd6a - - path: ./output/mosdepth/test.regions.bed.gz - md5sum: 347f877700d1dc42c95157199eff25d5 - - path: ./output/mosdepth/test.regions.bed.gz.csi - md5sum: ed5fbf46e3bdcbf60094df295bc40356 - - path: ./output/mosdepth/test.mosdepth.region.dist.txt - md5sum: 295564628113d2ec0ca34d7f661cfea8 - - path: ./output/mosdepth/test.mosdepth.summary.txt - md5sum: b07817412fd17819c14541e63bc4926c + - path: output/mosdepth/test.mosdepth.global.dist.txt + md5sum: e82e90c7d508a135b5a8a7cd6933452e + - path: output/mosdepth/test.mosdepth.summary.txt + md5sum: 4f0d231060cbde4efdd673863bd2fb59 + - path: output/mosdepth/test.per-base.bed.gz + md5sum: bc1df47d46f818fee5275975925d769a + - path: output/mosdepth/test.per-base.bed.gz.csi + md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 + +- name: mosdepth test_mosdepth_cram_bed + command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_cram_bed -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config + tags: + - mosdepth + files: + - path: output/mosdepth/test.mosdepth.global.dist.txt + md5sum: e82e90c7d508a135b5a8a7cd6933452e + - path: output/mosdepth/test.mosdepth.region.dist.txt + md5sum: e82e90c7d508a135b5a8a7cd6933452e + - path: output/mosdepth/test.mosdepth.summary.txt + md5sum: 96c037f769974b904beb53edc4f56d82 + - path: output/mosdepth/test.per-base.bed.gz + md5sum: bc1df47d46f818fee5275975925d769a + - path: output/mosdepth/test.per-base.bed.gz.csi + md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 + - path: output/mosdepth/test.regions.bed.gz + md5sum: 5d398caf7171ec4406278e2add3009ae + - path: output/mosdepth/test.regions.bed.gz.csi + md5sum: 47669cfe41f3e222e74d81e1b1be191f From b5850fd47157627b43fe6c80fd9defb097df893e Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 24 May 2022 12:16:03 +0200 Subject: [PATCH 2/7] add stub --- modules/mosdepth/main.nf | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index 894df1ae..1f503c6b 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -46,4 +46,22 @@ process MOSDEPTH { mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') END_VERSIONS """ + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + """ + touch ${prefix}.global.dist.txt + touch ${prefix}.region.dist.txt + touch ${prefix}.summary.txt + touch ${prefix}.per-base.d4 + touch ${prefix}.per-base.bed.gz + touch ${prefix}.per-base.bed.gz.csi + touch ${prefix}.regions.bed.gz + touch ${prefix}.regions.bed.gz.csi + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + mosdepth: \$(mosdepth --version 2>&1 | sed 's/^.*mosdepth //; s/ .*\$//') + END_VERSIONS + """ } From 7e777c6626064d7463ecbf91c2c599db85eec647 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 24 May 2022 12:25:31 +0200 Subject: [PATCH 3/7] add error is is provided twice --- modules/mosdepth/main.nf | 3 +++ 1 file changed, 3 insertions(+) diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index 1f503c6b..a5218286 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -31,6 +31,9 @@ process MOSDEPTH { def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--fasta ${fasta}" : "" def interval = bed ? "--by ${bed}" : "" + if (bed && ext.args.contains("--by")) { + exit 1, "--by can only be specified once." + } """ mosdepth \\ From 858cbe80c67093a39486bbb545b91c95077615bd Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 24 May 2022 12:43:49 +0200 Subject: [PATCH 4/7] add must fail test --- modules/mosdepth/main.nf | 2 +- tests/modules/mosdepth/main.nf | 14 +++++++++++++- tests/modules/mosdepth/nextflow.config | 4 +++- tests/modules/mosdepth/test.yml | 6 ++++++ 4 files changed, 23 insertions(+), 3 deletions(-) diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index a5218286..39586797 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -31,7 +31,7 @@ process MOSDEPTH { def prefix = task.ext.prefix ?: "${meta.id}" def reference = fasta ? "--fasta ${fasta}" : "" def interval = bed ? "--by ${bed}" : "" - if (bed && ext.args.contains("--by")) { + if (bed && args.contains("--by")) { exit 1, "--by can only be specified once." } diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf index 86ca0e86..eab47e89 100644 --- a/tests/modules/mosdepth/main.nf +++ b/tests/modules/mosdepth/main.nf @@ -2,7 +2,8 @@ nextflow.enable.dsl = 2 -include { MOSDEPTH } from '../../../modules/mosdepth/main.nf' +include { MOSDEPTH } from '../../../modules/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/mosdepth/main.nf' workflow test_mosdepth { input = [ @@ -47,3 +48,14 @@ workflow test_mosdepth_cram_bed { MOSDEPTH ( input, bed, fasta ) } + +workflow test_mosdepth_fail { + input = [ + [ id:'test', single_end:true ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] + ] + bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] + + MOSDEPTH_FAIL ( input, bed, [] ) +} diff --git a/tests/modules/mosdepth/nextflow.config b/tests/modules/mosdepth/nextflow.config index 8730f1c4..85674a3c 100644 --- a/tests/modules/mosdepth/nextflow.config +++ b/tests/modules/mosdepth/nextflow.config @@ -1,5 +1,7 @@ process { publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } - + withName: MOSDEPTH_FAIL { + ext.args = "--by 100" + } } diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml index 2cacb185..4eaf9bf1 100644 --- a/tests/modules/mosdepth/test.yml +++ b/tests/modules/mosdepth/test.yml @@ -65,3 +65,9 @@ md5sum: 5d398caf7171ec4406278e2add3009ae - path: output/mosdepth/test.regions.bed.gz.csi md5sum: 47669cfe41f3e222e74d81e1b1be191f + +- name: mosdepth test_mosdepth_fail + command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_fail -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config + tags: + - mosdepth + exitcode: 1 From 5bc2d419a94ec8b916739205961c115f62eec9c6 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 24 May 2022 13:23:00 +0200 Subject: [PATCH 5/7] fix fail test --- tests/modules/mosdepth/test.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml index 4eaf9bf1..a927396c 100644 --- a/tests/modules/mosdepth/test.yml +++ b/tests/modules/mosdepth/test.yml @@ -70,4 +70,4 @@ command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_fail -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config tags: - mosdepth - exitcode: 1 + exit_code: 1 From a2a8e09762a5aec8985f0d93125eafe3a6d2d365 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 24 May 2022 13:45:52 +0200 Subject: [PATCH 6/7] Update modules/mosdepth/main.nf Co-authored-by: Harshil Patel --- modules/mosdepth/main.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/mosdepth/main.nf b/modules/mosdepth/main.nf index 39586797..5f6538e7 100644 --- a/modules/mosdepth/main.nf +++ b/modules/mosdepth/main.nf @@ -32,7 +32,7 @@ process MOSDEPTH { def reference = fasta ? "--fasta ${fasta}" : "" def interval = bed ? "--by ${bed}" : "" if (bed && args.contains("--by")) { - exit 1, "--by can only be specified once." + exit 1, "'--by' can only be specified once when running mosdepth! Either remove input BED file definition or remove '--by' from 'ext.args' definition" } """ From 8381a5e5dd73228b3fe744e51f1964d62c28c1e5 Mon Sep 17 00:00:00 2001 From: Matthias De Smet <11850640+matthdsm@users.noreply.github.com> Date: Tue, 24 May 2022 14:43:40 +0200 Subject: [PATCH 7/7] add window test --- tests/modules/mosdepth/main.nf | 16 ++++++++++++++-- tests/modules/mosdepth/nextflow.config | 3 +++ tests/modules/mosdepth/test.yml | 20 ++++++++++++++++++++ 3 files changed, 37 insertions(+), 2 deletions(-) diff --git a/tests/modules/mosdepth/main.nf b/tests/modules/mosdepth/main.nf index eab47e89..96a9ef20 100644 --- a/tests/modules/mosdepth/main.nf +++ b/tests/modules/mosdepth/main.nf @@ -2,8 +2,9 @@ nextflow.enable.dsl = 2 -include { MOSDEPTH } from '../../../modules/mosdepth/main.nf' -include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/mosdepth/main.nf' +include { MOSDEPTH } from '../../../modules/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_FAIL } from '../../../modules/mosdepth/main.nf' +include { MOSDEPTH as MOSDEPTH_WINDOW } from '../../../modules/mosdepth/main.nf' workflow test_mosdepth { input = [ @@ -49,6 +50,17 @@ workflow test_mosdepth_cram_bed { MOSDEPTH ( input, bed, fasta ) } +workflow test_mosdepth_window { + input = [ + [ id:'test', single_end:true ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) ], + [ file(params.test_data['homo_sapiens']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true) ] + ] + bed = [ file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) ] + + MOSDEPTH_WINDOW ( input, [], [] ) +} + workflow test_mosdepth_fail { input = [ [ id:'test', single_end:true ], diff --git a/tests/modules/mosdepth/nextflow.config b/tests/modules/mosdepth/nextflow.config index 85674a3c..4a6153e6 100644 --- a/tests/modules/mosdepth/nextflow.config +++ b/tests/modules/mosdepth/nextflow.config @@ -4,4 +4,7 @@ process { withName: MOSDEPTH_FAIL { ext.args = "--by 100" } + withName: MOSDEPTH_WINDOW { + ext.args = "--by 100" + } } diff --git a/tests/modules/mosdepth/test.yml b/tests/modules/mosdepth/test.yml index a927396c..a3115d6e 100644 --- a/tests/modules/mosdepth/test.yml +++ b/tests/modules/mosdepth/test.yml @@ -66,6 +66,26 @@ - path: output/mosdepth/test.regions.bed.gz.csi md5sum: 47669cfe41f3e222e74d81e1b1be191f +- name: mosdepth test_mosdepth_window + command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_window -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config + tags: + - mosdepth + files: + - path: output/mosdepth/test.mosdepth.global.dist.txt + md5sum: e82e90c7d508a135b5a8a7cd6933452e + - path: output/mosdepth/test.mosdepth.region.dist.txt + md5sum: 39e0e707ec32feb5176fd20a95f1f468 + - path: output/mosdepth/test.mosdepth.summary.txt + md5sum: 96c037f769974b904beb53edc4f56d82 + - path: output/mosdepth/test.per-base.bed.gz + md5sum: bc1df47d46f818fee5275975925d769a + - path: output/mosdepth/test.per-base.bed.gz.csi + md5sum: 9e649ac749ff6c6073bef5ab63e8aaa4 + - path: output/mosdepth/test.regions.bed.gz + md5sum: f02e2cb49cc050e13d76942d6960827a + - path: output/mosdepth/test.regions.bed.gz.csi + md5sum: 257d67678136963d9dd904330079609d + - name: mosdepth test_mosdepth_fail command: nextflow run ./tests/modules/mosdepth -entry test_mosdepth_fail -c ./tests/config/nextflow.config -c ./tests/modules/mosdepth/nextflow.config tags: