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port htseq count pytest to nf-test (#5194)
* port htseq count pytest to nf-test * rename yml file * add extra line * fix tag.yml * fix meta.yml * fix meta.yml --------- Co-authored-by: zxBIB Grochowalski,Lukasz (GCBDS) EXTERNAL <[email protected]> Co-authored-by: Mauro Saporita <[email protected]>
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nextflow_process { | ||
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name "Test Process HTSEQ_COUNT" | ||
script "../main.nf" | ||
process "HTSEQ_COUNT" | ||
tag "modules" | ||
tag "modules_nfcore" | ||
tag "htseq" | ||
tag "htseq/count" | ||
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test("bam input") { | ||
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when { | ||
process { | ||
""" | ||
input[0] = [ | ||
[ id:'test', single_end:false ], // meta map | ||
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) | ||
] | ||
input[1] = [ | ||
[ id:'test2'], // meta map | ||
file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) | ||
] | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll ( | ||
{ assert process.success }, | ||
{ assert process.out.txt.get(0).get(1) ==~ ".*.txt" }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
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} | ||
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} | ||
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test("cram input") { | ||
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when { | ||
process { | ||
""" | ||
input[0] = [ | ||
[ id:'test', single_end:false ], // meta map | ||
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) | ||
] | ||
input[1] = [ | ||
[ id:'test2'], // meta map | ||
file(params.test_data['homo_sapiens']['genome']['genome_gtf'], checkIfExists: true) | ||
] | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll ( | ||
{ assert process.success }, | ||
{ assert process.out.txt.get(0).get(1) ==~ ".*.txt" }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
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} | ||
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} | ||
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} |
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Original file line number | Diff line number | Diff line change |
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htseq/count: | ||
- "modules/nf-core/htseq/count/**" |
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