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CDCgov / phoenix

🔥🐦🔥PHoeNIx: A short-read pipeline for healthcare-associated and antimicrobial resistant pathogens
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[New Feature Request] - Why don't fastp, quast, and potentially other tools make it to the multiqc report? #128

Closed jfnjdoh closed 6 months ago

jfnjdoh commented 7 months ago

When running the test sample or my own samples, reports from tool like fastp, QUAST, and potentially others, don't make it into the multiqc report. Both fastp and QUAST are supported by multiqc and the files that it uses (fastp json and QUAST report.tsv) exist. Could this be an issue of which directory multiqc is run on or when the multiqc process is called in the nextflow workflow?

jvhagey commented 6 months ago

Hi @jfnjdoh, this isn't a bug we didn't configure to do this yet. I think it would be helpful for users review so we will work to add this in v2.2.0 as v2.1.0 should be out by the end of the month and I don't want it delayed for this. Thanks for your suggestion, I will leave the issue open until fixed.

jvhagey commented 6 months ago

Fixed with commit . Will be out in the next release of phx. Please reopen if it is not as expected.