Improve input validation for FASTQ - Githubissues

nf-core / oncoanalyser

A comprehensive cancer DNA/RNA analysis and reporting pipeline

https://nf-co.re/oncoanalyser

MIT License

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Improve input validation for FASTQ #91

Open scwatts opened 2 weeks ago

scwatts commented 2 weeks ago

Description of feature

Validation of input FASTQ files should be improved:

certain unsupported samplesheet FASTQ input rows produce non-descript errors
- see here for an example: https://nfcore.slack.com/archives/C04CQ1LK7U1/p1724454431405079
all file inputs including FASTQ should be init as Nextflow.File objects and checked to exist (w/ stub mode exception):

https://github.com/nf-core/oncoanalyser/blob/4227bc1083209d79c8735d32e6c75f762a640006/lib/Utils.groovy#L127-L133

This work may also relate to:

https://github.com/nf-core/oncoanalyser/issues/51