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@@ -6,7 +6,7 @@ repos: | |
additional_dependencies: | ||
- [email protected] | ||
- repo: https://github.com/python-jsonschema/check-jsonschema | ||
rev: 0.29.3 | ||
rev: 0.29.4 | ||
hooks: | ||
- id: check-jsonschema | ||
# match meta.ymls in one of the subdirectories of modules/nf-core | ||
|
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--- | ||
# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json | ||
channels: | ||
- conda-forge | ||
- bioconda | ||
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dependencies: | ||
- bioconda::arriba=2.4.0 |
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nextflow_process { | ||
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name "Test Process ARRIBA_ARRIBA" | ||
script "../main.nf" | ||
process "ARRIBA_ARRIBA" | ||
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tag "modules" | ||
tag "modules_nfcore" | ||
tag "arriba" | ||
tag "arriba/arriba" | ||
tag "arriba/download" | ||
tag "star/genomegenerate" | ||
tag "star/align" | ||
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setup { | ||
config "./nextflow.config" | ||
options "-stub" | ||
run("ARRIBA_DOWNLOAD") { | ||
script "../../../arriba/download/main.nf" | ||
process { | ||
""" | ||
input[0] = 'GRCh38' | ||
""" | ||
} | ||
} | ||
run("STAR_GENOMEGENERATE") { | ||
script "../../../star/genomegenerate/main.nf" | ||
options "-stub" | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test_fasta' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] | ||
]) | ||
input[1] = Channel.of([ | ||
[ id:'test_gtf' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
]) | ||
""" | ||
} | ||
} | ||
run("STAR_ALIGN") { | ||
script "../../../star/align/main.nf" | ||
options "-stub" | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test', single_end:false ], // meta map | ||
[ | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_1.fastq.gz', checkIfExists: true), | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/fastq/test_rnaseq_2.fastq.gz', checkIfExists: true) | ||
] | ||
]) | ||
input[1] = STAR_GENOMEGENERATE.out.index | ||
input[2] = Channel.of([ | ||
[ id:'test_gtf' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
]) | ||
input[3] = false | ||
input[4] = 'illumina' | ||
input[5] = false | ||
""" | ||
} | ||
} | ||
} | ||
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test("homo_sapiens - paired_end - stub") { | ||
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options "-stub" | ||
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when { | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test', single_end:false ], // meta map | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.rna.paired_end.sorted.bam', checkIfExists: true) ] | ||
]) | ||
input[1] = Channel.of([ | ||
[ id:'test_fasta' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true) ] | ||
]) | ||
input[2] = Channel.of([ | ||
[ id:'test_gtf' ], | ||
[ file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.gtf', checkIfExists: true) ] | ||
]) | ||
input[3] = [] | ||
input[4] = [] | ||
input[5] = [] | ||
input[6] = [] | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
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} | ||
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} |
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{ | ||
"homo_sapiens - paired_end - stub": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
[ | ||
{ | ||
"id": "test", | ||
"single_end": false | ||
}, | ||
"test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" | ||
] | ||
], | ||
"1": [ | ||
[ | ||
{ | ||
"id": "test", | ||
"single_end": false | ||
}, | ||
"test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" | ||
] | ||
], | ||
"2": [ | ||
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" | ||
], | ||
"fusions": [ | ||
[ | ||
{ | ||
"id": "test", | ||
"single_end": false | ||
}, | ||
"test.fusions.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" | ||
] | ||
], | ||
"fusions_fail": [ | ||
[ | ||
{ | ||
"id": "test", | ||
"single_end": false | ||
}, | ||
"test.fusions.discarded.tsv:md5,f50b84b1db4b83ba62ec1deacc69c260" | ||
] | ||
], | ||
"versions": [ | ||
"versions.yml:md5,d323796555db4a58fe4c6bc08d1dec30" | ||
] | ||
} | ||
], | ||
"meta": { | ||
"nf-test": "0.9.0", | ||
"nextflow": "24.04.4" | ||
}, | ||
"timestamp": "2024-10-08T15:41:23.945072" | ||
} | ||
} |
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5
...les/nf-core/arriba/arriba/nextflow.config → ...-core/arriba/arriba/tests/nextflow.config
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process { | ||
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publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" } | ||
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withName: STAR_GENOMEGENERATE { | ||
ext.args = '--genomeSAindexNbases 11' | ||
} | ||
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withName: STAR_ALIGN { | ||
ext.args = '--readFilesCommand zcat --outSAMtype BAM Unsorted --outSAMunmapped Within --outBAMcompression 0 --outFilterMultimapNmax 50 --peOverlapNbasesMin 10 --alignSplicedMateMapLminOverLmate 0.5 --alignSJstitchMismatchNmax 5 -1 5 5 --chimSegmentMin 10 --chimOutType WithinBAM HardClip --chimJunctionOverhangMin 10 --chimScoreDropMax 30 --chimScoreJunctionNonGTAG 0 --chimScoreSeparation 1 --chimSegmentReadGapMax 3 --chimMultimapNmax 50' | ||
} | ||
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} |
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