Commit ac61682d authored by Joanna Fourquet's avatar Joanna Fourquet
Browse files

update help for --step

parent fffb4ee3
......@@ -27,9 +27,20 @@
Options:
--step Choose one step into: "01_clean_qc", "02_assembly", "03_filtering", "04_structural_annot", "05_alignment", "06_func_annot", "07_taxo_affi", "08_binning".
Only exception: "03_filtering" step can be associated with coma to "04_structural_annot", "05_alignment", "06_func_annot", "07_taxo_affi" and "08_binning".
--step Choose step(s) into: "01_clean_qc", "02_assembly", "03_filtering",
"04_structural_annot", "05_alignment", "06_func_annot", "07_taxo_affi", "08_binning".
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".
iii. 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_second_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.
01_clean_qc options:
--skip_01_clean_qc Skip 01_clean_qc step.
--adapter1 Sequence of adapter 1. Default: Illumina TruSeq adapter.
......
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