Add checks for uniqueness of sample ids #1902
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| [meta.patient, meta.subMap('sample', 'status')] | ||
| } | ||
| .unique() | ||
| .groupTuple() |
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let's double check here that we are not collapsing out lane
maxulysse
reviewed
May 26, 2025
| @@ -39,7 +59,7 @@ nextflow_pipeline { | |||
| assert workflow.failed | |||
| assertAll( | |||
| { assert snapshot( | |||
| workflow.stderr.toString().replace("[", "").replace("]", "").split(",")[0] | |||
| workflow.stderr.toString().contains("Patient [test] has more than one sample [2] with normal status [0] and one sample with tumor status [1].") | |||
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for me this was inconsitent across the nextflow versions so that I always got a mismatch
maxulysse
reviewed
May 26, 2025
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| [ | ||
| "\u001b0;31mThe following invalid input values have been detected:", | ||
| " ", | ||
| " \t-> Entry 2: Error for field 'sample' (test 2): \"test 2\" does not match regular expression ^\\S+$ (Sample ID must be provided", | ||
| " cannot contain spaces and must be a string value)", | ||
| " \u001b0m" | ||
| ] |
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I liked that we were capturing the stderr 😢
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for me this was inconsitent across the nextflow versions so that I always got a mismatch
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PR checklist
Closes #1674
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).