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CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
Apache License 2.0
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[BUG] - input filename collision #100

Closed erinyoung closed 1 year ago

erinyoung commented 1 year ago

Describe the bug I don't know if you want to do anything about this, but right now there's no check in the sample sheet to see if two samples are named the same thing.

This is a user-generated error caused by the end user, which was me.

Impact Fails at multiqc step.

To Reproduce Have two samples named the same thing

Expected behavior It failed at the last step, I don't know if you want it to fail before the workflow starts.

Screenshots

Workflow execution completed unsuccessfully
Error executing process > 'PHOENIX:PHOENIX_EXTERNAL:MULTIQC'

Caused by:
  Process `PHOENIX:PHOENIX_EXTERNAL:MULTIQC` input file name collision -- There are multiple input files for each of the following file names: 1326569_2_fastqc.zip, 1326569_1_fastqc.zip

Tip: you can replicate the issue by changing to the process work dir and entering the command `bash .command.run`

Logs

Additional context I still think this is a user error, but I thought I would let you know.

jvhagey commented 1 year ago

Thanks for reporting this, probably best to address it so resources aren't wasted due to typos. Added a check for duplicate sample id and fastq files in commit fd6127f. Change will be in next release (v1.2.0).