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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
8 stars 1 forks source link

[DEV ] Adding a qc report report workflow #56

Closed Mxrcon closed 2 years ago

Mxrcon commented 2 years ago

Hey there :wave:,

As requested on #55, I took some time to add the fastqc and multiqc modules and also implement them in a way that respect user choices. I considered 3 possibilities:

  1. The user uses the workflow as normal, so the program runs qc report by default
  2. The user uses the workflow but doesn't want qc report, so should use --skip_qc true on CLI or modify the standard param on the config file.
  3. The user only wants to run qc_report, so it can use -entry QUALITY_CONTROL on CLI command

A param based decision looked the most intuitive and user-friendly option, but we can discuss the implementation as the base work (module addition and configuration) is already done!

Feel free to discuss those changes with me, I'm available to make any requested change and listen your thoughts about it!

Hope we have a merge! Kindly, Davi

abhi18av commented 2 years ago

Oh, one thing that remains is to update the README for information from https://github.com/mtb-bioinformatics/mtbseq-nf/pull/56#issue-1108414021

Mxrcon commented 2 years ago

yes sure, I'll update the dag as well