This is adopted from StaG-mwc, a shotgun sequencing processing snakemake pipeline

Add-on features:

1. Add kneaddata module in workflow/rules/preproc/read_quality.smk
2. Add a script workflow/scripts/kneaddata_summary.py to summarise pre-processing statistics for kneadata and modify workflow/rules/preproc/preprocessing_summary.smk to incoporate kneaddata summary.
3. Modify workflow/rules/taxonomic_profiling/strainphlan.smk to allow parallel run of StrainPhlAn on all available clades based on pre-specified prevalence in the sample batch.
4. Add profiles/sge and profiles/pbs to enable running on sge and pbs clusters. The sge cluster module was modified from https://github.com/Snakemake-Profiles/sge

Check https://github.com/ctmrbio/stag-mwc for the latest git repo for stag-mwc

Check https://stag-mwc.readthedocs.io for the full documentation of the lastest stag-mwc git repo

Citing

If you find StaG-mwc useful in your research, please cite the Zenodo DOI: https://zenodo.org/badge/latestdoi/125840716