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Add regions bed and nf-test to glnexus (#6888)
Add regions and nf-test to glnexus Co-authored-by: Sateesh_Peri <[email protected]>
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,97 @@ | ||
nextflow_process { | ||
|
||
name "Test Process GLNEXUS" | ||
script "../main.nf" | ||
process "GLNEXUS" | ||
|
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tag "modules" | ||
tag "modules_nfcore" | ||
tag "glnexus" | ||
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test("vcfs, []") { | ||
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when { | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test' ], | ||
[ | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), | ||
] | ||
]) | ||
input[1] = [[],[]] | ||
""" | ||
} | ||
} | ||
|
||
then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
|
||
} | ||
|
||
test("vcfs, bed") { | ||
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when { | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test' ], | ||
[ | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), | ||
] | ||
]) | ||
input[1] = [ | ||
[ id:'region' ], | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), | ||
] | ||
""" | ||
} | ||
} | ||
|
||
then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
|
||
} | ||
|
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test("vcfs, bed - stub") { | ||
|
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options "-stub" | ||
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when { | ||
process { | ||
""" | ||
input[0] = Channel.of([ | ||
[ id:'test' ], | ||
[ | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test.genome.vcf.gz', checkIfExists: true), | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/gvcf/test2.genome.vcf.gz', checkIfExists: true), | ||
] | ||
]) | ||
input[1] = [ | ||
[ id:'region' ], | ||
file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.bed', checkIfExists: true), | ||
] | ||
""" | ||
} | ||
} | ||
|
||
then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
|
||
} | ||
|
||
} |
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Original file line number | Diff line number | Diff line change |
---|---|---|
@@ -0,0 +1,101 @@ | ||
{ | ||
"vcfs, bed - stub": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
] | ||
], | ||
"1": [ | ||
"versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" | ||
], | ||
"bcf": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"test.bcf:md5,d41d8cd98f00b204e9800998ecf8427e" | ||
] | ||
], | ||
"versions": [ | ||
"versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" | ||
] | ||
} | ||
], | ||
"meta": { | ||
"nf-test": "0.9.0", | ||
"nextflow": "24.04.4" | ||
}, | ||
"timestamp": "2024-10-29T12:17:01.253378301" | ||
}, | ||
"vcfs, bed": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" | ||
] | ||
], | ||
"1": [ | ||
"versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" | ||
], | ||
"bcf": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" | ||
] | ||
], | ||
"versions": [ | ||
"versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" | ||
] | ||
} | ||
], | ||
"meta": { | ||
"nf-test": "0.9.0", | ||
"nextflow": "24.04.4" | ||
}, | ||
"timestamp": "2024-10-29T12:16:53.859544065" | ||
}, | ||
"vcfs, []": { | ||
"content": [ | ||
{ | ||
"0": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" | ||
] | ||
], | ||
"1": [ | ||
"versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" | ||
], | ||
"bcf": [ | ||
[ | ||
{ | ||
"id": "test" | ||
}, | ||
"test.bcf:md5,62b2cea9c1b92ac63645cb031eea46fc" | ||
] | ||
], | ||
"versions": [ | ||
"versions.yml:md5,dfeeb7f12f37cbef54a798614b83ffb0" | ||
] | ||
} | ||
], | ||
"meta": { | ||
"nf-test": "0.9.0", | ||
"nextflow": "24.04.4" | ||
}, | ||
"timestamp": "2024-10-29T12:13:03.068397129" | ||
} | ||
} |
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