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BIMSBbioinfo / pigx_rnaseq

Bulk RNA-seq Data Processing, Quality Control, and Downstream Analysis Pipeline
GNU General Public License v3.0
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idea how to print instruction to directly set paths to reproduce analysis #116

Closed smoe closed 2 years ago

smoe commented 2 years ago

This PR is meant as a request for discussion in an attempt to address issue https://github.com/BIMSBbioinfo/pigx_rnaseq/issues/115 .

smoe commented 2 years ago

The runs with that last version have completed and I find this looks fine. The "problem" is that this is now redundant with the table. The table imho is less important (albeit nicer) to have a functional reproducibility of the whole code, hence maybe the the table should go.

You may want to add additional explanations how to reproduce all the figures. And maybe you also present the versions of all the tools that have contributed to the analysis and then call the section "Methods" or "Provenance" instead of "Input Selection", maybe all written in a way that your users can copy parts of it for their publication. Patch?

borauyar commented 2 years ago

@smoe yes, this should help with the debugging purposes. Thank you!