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nf-test for pilon #5293
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nf-test for pilon #5293
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nextflow_process { | ||
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name "Test Process PILON" | ||
script "../main.nf" | ||
process "PILON" | ||
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tag "modules" | ||
tag "modules_nfcore" | ||
tag "pilon" | ||
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test("Test PILON") { | ||
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when { | ||
process { | ||
""" | ||
input[0] = [ [ id:'test', single_end:false ], // meta map | ||
file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true) | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Apparently the new guideline is to use URLs instead of the test_data object, so please change the tests accordingly There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Hi, I just started so can you point to the guidelines? I found some info (but not technical details) here? There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Refer to #5281 for an example, I believe it's not documented yet, but the documentation team is working on it There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. Changing to the test-data path is not required currently, just optional. |
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] | ||
input[1] = [ [ 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[2] = "bam" | ||
""" | ||
} | ||
} | ||
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then { | ||
assertAll( | ||
{ assert process.success }, | ||
{ assert snapshot(process.out).match() } | ||
) | ||
} | ||
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} | ||
There was a problem hiding this comment. Choose a reason for hiding this commentThe reason will be displayed to describe this comment to others. Learn more. I see that the module has multiple modes, is it possible to add tests for the others? And a stub test as well, although I see the module currently lacks a stub |
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} |
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pilon: | ||
- "modules/nf-core/pilon/**" |
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Change test name to something more specific, there is no standard (yet) but something like
pilon - bam - paired
should do