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Add found_in tag to call repeat expansions
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99 changes: 99 additions & 0 deletions
99
subworkflows/local/call_repeat_expansions/tests/main.nf.test
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,99 @@ | ||
| nextflow_workflow { | ||
|
|
||
| name "Test Workflow CALL_REPEAT_EXPANSIONS" | ||
| script "../main.nf" | ||
| config "./nextflow.config" | ||
| workflow "CALL_REPEAT_EXPANSIONS" | ||
|
|
||
| setup { | ||
| run("GUNZIP") { | ||
| script "../../../../modules/nf-core/gunzip/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = [ | ||
| [ id:'test' ], | ||
| file(params.pipelines_testdata_base_path + 'reference/hg38.test.fa.gz', checkIfExists: true) | ||
| ] | ||
| """ | ||
| } | ||
|
|
||
| } | ||
|
|
||
| run("SAMTOOLS_FAIDX") { | ||
| script "../../../../modules/nf-core/samtools/faidx/main.nf" | ||
| process { | ||
| """ | ||
| input[0] = GUNZIP.out.gunzip | ||
| input[1] = [[],[]] | ||
| """ | ||
| } | ||
|
|
||
| } | ||
| } | ||
|
|
||
| test("[bam, bai], fasta, fai, bed") { | ||
|
|
||
| when { | ||
| workflow { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false, project: 'project', sex: 1 ], // meta map | ||
| file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true), | ||
| file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true) | ||
| ]) | ||
| input[1] = GUNZIP.out.gunzip | ||
| input[2] = SAMTOOLS_FAIDX.out.fai | ||
| input[3] = Channel.of([ | ||
| [ id: 'pathogenic_repeats' ], | ||
| file(params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed') | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert workflow.out.sample_bai.get(0).get(1).endsWith(".bai") }, | ||
| { assert snapshot( | ||
| path(workflow.out.sample_vcf.get(0).get(1)).vcf.variantsMD5, | ||
| path(workflow.out.project_vcf.get(0).get(1)).vcf.variantsMD5, | ||
| bam(workflow.out.sample_bam.get(0).get(1), stringency: 'silent').getReadsMD5(), | ||
| workflow.out.versions, | ||
| ).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
|
|
||
| test("[bam, bai], fasta, fai, bed - stub") { | ||
|
|
||
| options "-stub" | ||
|
|
||
| when { | ||
| workflow { | ||
| """ | ||
| input[0] = Channel.of([ | ||
| [ id:'test', single_end:false, project: 'project', sex: 1 ], // meta map | ||
| file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam', checkIfExists: true), | ||
| file(params.pipelines_testdata_base_path + 'testdata/HG002_PacBio_Revio.bam.bai', checkIfExists: true) | ||
| ]) | ||
| input[1] = GUNZIP.out.gunzip | ||
| input[2] = SAMTOOLS_FAIDX.out.fai | ||
| input[3] = Channel.of([ | ||
| [ id: 'pathogenic_repeats' ], | ||
| file(params.pipelines_testdata_base_path + 'reference/pathogenic_repeats.hg38.bed') | ||
| ]) | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert workflow.success }, | ||
| { assert snapshot(workflow.out).match() } | ||
| ) | ||
| } | ||
|
|
||
| } | ||
| } |
128 changes: 128 additions & 0 deletions
128
subworkflows/local/call_repeat_expansions/tests/main.nf.test.snap
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,128 @@ | ||
| { | ||
| "[bam, bai], fasta, fai, bed": { | ||
| "content": [ | ||
| "502b7befd528ce70b8269a8e4b9281df", | ||
| "1de84bd070a82b37e6fac25d19ae604e", | ||
| "65999ab8f2bc7841de8172468bf23ab6", | ||
| [ | ||
| "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070", | ||
| "versions.yml:md5,6576546ea5cf2a0cb6438b4c6758fd1e", | ||
| "versions.yml:md5,799b136592e7434ff7eb9ddcc70e7e41", | ||
| "versions.yml:md5,8a4b29c3089d4b00cfe6c5c39b88d1ab", | ||
| "versions.yml:md5,b9424dde80b33e84164cc956a14aa459" | ||
| ] | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-10-29T10:47:08.425030144" | ||
| }, | ||
| "[bam, bai], fasta, fai, bed - stub": { | ||
| "content": [ | ||
| { | ||
| "0": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false, | ||
| "project": "project", | ||
| "sex": 1 | ||
| }, | ||
| "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" | ||
| ] | ||
| ], | ||
| "1": [ | ||
| [ | ||
| { | ||
| "id": "project" | ||
| }, | ||
| "project.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" | ||
| ] | ||
| ], | ||
| "2": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false, | ||
| "project": "project", | ||
| "sex": 1 | ||
| }, | ||
| "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "3": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false, | ||
| "project": "project", | ||
| "sex": 1 | ||
| }, | ||
| "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "4": [ | ||
| "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070", | ||
| "versions.yml:md5,6576546ea5cf2a0cb6438b4c6758fd1e", | ||
| "versions.yml:md5,799b136592e7434ff7eb9ddcc70e7e41", | ||
| "versions.yml:md5,8a4b29c3089d4b00cfe6c5c39b88d1ab", | ||
| "versions.yml:md5,b9424dde80b33e84164cc956a14aa459" | ||
| ], | ||
| "project_vcf": [ | ||
| [ | ||
| { | ||
| "id": "project" | ||
| }, | ||
| "project.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" | ||
| ] | ||
| ], | ||
| "sample_bai": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false, | ||
| "project": "project", | ||
| "sex": 1 | ||
| }, | ||
| "test.bam.bai:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "sample_bam": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false, | ||
| "project": "project", | ||
| "sex": 1 | ||
| }, | ||
| "test.bam:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
| ] | ||
| ], | ||
| "sample_vcf": [ | ||
| [ | ||
| { | ||
| "id": "test", | ||
| "single_end": false, | ||
| "project": "project", | ||
| "sex": 1 | ||
| }, | ||
| "test.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940" | ||
| ] | ||
| ], | ||
| "versions": [ | ||
| "versions.yml:md5,52272b464e62cb9e5d41622ea76cd070", | ||
| "versions.yml:md5,6576546ea5cf2a0cb6438b4c6758fd1e", | ||
| "versions.yml:md5,799b136592e7434ff7eb9ddcc70e7e41", | ||
| "versions.yml:md5,8a4b29c3089d4b00cfe6c5c39b88d1ab", | ||
| "versions.yml:md5,b9424dde80b33e84164cc956a14aa459" | ||
| ] | ||
| } | ||
| ], | ||
| "meta": { | ||
| "nf-test": "0.9.0", | ||
| "nextflow": "24.04.4" | ||
| }, | ||
| "timestamp": "2024-10-29T15:35:39.127660234" | ||
| } | ||
| } |
16 changes: 16 additions & 0 deletions
16
subworkflows/local/call_repeat_expansions/tests/nextflow.config
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,16 @@ | ||
| process { | ||
| withName: 'CALL_REPEAT_EXPANSIONS:ADD_FOUND_IN_TAG' { | ||
| ext.prefix = { "${meta.id}_found_in" } | ||
| ext.args = '--no-version' | ||
| ext.args2 = '--output-type b --no-version' | ||
| } | ||
| withName: 'CALL_REPEAT_EXPANSIONS:BCFTOOLS_MERGE' { | ||
| ext.args = '--output-type z --force-single --no-version' | ||
| } | ||
| withName: 'CALL_REPEAT_EXPANSIONS:BCFTOOLS_SORT_TRGT' { | ||
| ext.args = '--output-type z --write-index=tbi' | ||
| } | ||
| withName: 'CALL_REPEAT_EXPANSIONS:TRGT' { | ||
| ext.args = { "--sample-name ${meta.id}" } | ||
| } | ||
| } |
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