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sgsutcliffe
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Mar 20, 2026
| def species = meta.Species ?: "Unknown" | ||
| def qc_status = meta.QCStatus ?: "Unknown" | ||
| def has_file = mikro_file && mikro_file.size() > 0 ? "--has_mikro_file" : "" | ||
| def has_file = (mikro_file && mikro_file.name != 'NO_FILE') ? "--has_mikro_file" : "" |
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I believe the issue is with the path.size() when there is a single path in nextflow version 25 where it actually gives a 0/null
I noticed that the --has_mikro_file was not working in this version of nextflow so I am proposing an alternative approach.
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A much better approach!
sgsutcliffe
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Mar 20, 2026
tests/pipelines/main.nf.test
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| then { | ||
| assert workflow.failed | ||
| assert workflow.stdout.contains("ERROR ~ Argument of `file` function cannot be empty") | ||
| assert workflow.stdout.any { it =~ /ERROR ~ Argument of `file\(\)?` function cannot be empty/ } |
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Made the error message flexible as depending on the nextflow version it can be file() or file in the error message.
sgsutcliffe
commented
Mar 20, 2026
| then { | ||
| assert workflow.failed | ||
| assert workflow.stdout.contains("ERROR ~ Argument of `file` function cannot be empty") | ||
| assert workflow.stdout.any { it =~ /Argument of .* function cannot be empty/ } |
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Made it more flexible because regex was not working for both scenarios
kylacochrane
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Mar 20, 2026
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Thanks so much for getting typingQC aligned with nextflow v.25.10.4 Steven!
This all looks great!
| def species = meta.Species ?: "Unknown" | ||
| def qc_status = meta.QCStatus ?: "Unknown" | ||
| def has_file = mikro_file && mikro_file.size() > 0 ? "--has_mikro_file" : "" | ||
| def has_file = (mikro_file && mikro_file.name != 'NO_FILE') ? "--has_mikro_file" : "" |
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A much better approach!
kylacochrane
approved these changes
Mar 20, 2026
kylacochrane
approved these changes
Mar 20, 2026
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