Commit 407373a7 authored by Joanna Fourquet's avatar Joanna Fourquet
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Update usage.md

parent 55777e67
...@@ -142,7 +142,7 @@ The next parameters can be used when you run metagWGS. ...@@ -142,7 +142,7 @@ 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`). `--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`).
**NOTE:** you must indicate only **one** step when you run the pipeline. It runs previous steps automatically. The **only exception** to this rule is the combination of the step `03_filtering` with the next steps `04_structural_annot`, `05_alignment`, `06_func_annot`, `07_taxo_affi` and `08_binning`. `03_filtering` is automatically skipped for the 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,one_of_these_steps"`, for example `--step "03_filtering,04_structural_annot"`. **NOTE:** 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. However, `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"`. When you run one of the three steps `06_func_annot`, `07_taxo_affi` or `08_binning` during a first analysis and then another of these steps interests you and you run metagWGS again to get the result of this other step, you have to indicate `--step "the_first_step,the_new_step"`. This will allow you to have a final MultiQC html report that will take into account the metrics of both analyses performed. If the third of these steps interests you and you run again metagWGS for this step, you also have to indicate `--step "the_first_step,the_second_step,the_third,step"` for the same reasons.
When you want to run a particular step, you just need to specify its name: When you want to run a particular step, you just need to specify its name:
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