Speed-ups, additional input method, change in batches for binning and added raw read QC

arumugamlab / MIntO

Pipeline for Reproducible and Scalable Integration of Metagenomic and Metatranscriptomic Data

MIT License

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Closed jszarvas closed 3 weeks ago

jszarvas commented 3 weeks ago

Details:

prevent fastANI overthreading by restricting default OMP thread usage,
switch batching for binning preparation by sample amounts to available RAM for BWA Index (conservative method),
replaced hmmersearch by its implementation using pyhmmer for dbCAN (4-5x speedup),
added FastQC to QC_1 with multiQC output in the output folder,
expanded the metadata column-name variable input method to work with sub-folder structure as well.

jszarvas commented 3 weeks ago

Test outputs are identical.

jszarvas commented 3 weeks ago

Testing is done 👍