Commit d1616ad0 authored by Joanna Fourquet's avatar Joanna Fourquet
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Update usage.md

parent c06f62f2
......@@ -143,6 +143,7 @@ The next parameters can be used when you run metagWGS.
`--step "your_step"`: indicate the step of the pipeline you want to run. The steps available are described in the [`README`](https://forgemia.inra.fr/genotoul-bioinfo/metagwgs/-/tree/dev#metagwgs-steps) (`01_clean_qc`, `02_assembly`, `03_filtering`, `04_structural_annot`, `05_alignment`, `06_func_annot`, `07_taxo_affi` and `08_binning`).
**NOTES:**
**i. You can directly indicate the final step that is important to you. For example, if you are interested in binning (and the taxonomic affiliation of bins), just use `--step "08_binning"`. It runs the previous steps automatically (except `03_filtering`, see ii).**
**ii. `03_filtering` is automatically skipped for the next steps `04_structural_annot`, `05_alignment`, `06_func_annot`, `07_taxo_affi` and `08_binning`. If you want to filter your assembly before doing one of these steps, you must use `--step "03_filtering,the_step"`, for example `--step "03_filtering,04_structural_annot"`.**
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