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mycobactopia-org / MTBseq-nf

MTBSeq made simple and easy using Nextflow and nf-core standard.
https://doi.org/10.5281/zenodo.5498063
MIT License
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[Fix] Preventing workflows from caching the `samples.tsv` for cohort steps #66

Closed Mxrcon closed 2 years ago

Mxrcon commented 2 years ago

Hey :wave:, on my latest runs I firstly run 3 samples completely and after a successful run I started a new run with 71 samples using -resume, Interestingly the samples.tsv was kept the same and the cohort only run for 3 samples.

The samples.tsv for 3 samples only had information for 3 samples, and after resuming the sample sample.tsv was used, so the other 68 samples where ignored by mtbseq as they weren't mentioned on the samples.tsv file.

As a solution for this, I added cache: false to the collectFile operator, so the file will be generated again on every run.

Feel free to add your thoughts on the comments session, I'm available to discuss and make any requested modification.

Kindly, Davi

Mxrcon commented 2 years ago

@abhi18av if you resume, it'll rerun only the cohort steps, the per sample steps seems to be cached normally accordingly to my tests.

abhi18av commented 2 years ago

Perfect, merging this one then - muito obrigado!

Mxrcon commented 2 years ago

;) always happy to contribute