Skip to content
GitLab
Menu
Projects
Groups
Snippets
Help
Help
Support
Community forum
Keyboard shortcuts
?
Submit feedback
Contribute to GitLab
Sign in
Toggle navigation
Menu
Open sidebar
genotoul-bioinfo
metagWGS
Commits
ac61682d
Commit
ac61682d
authored
Feb 25, 2021
by
Joanna Fourquet
Browse files
update help for --step
parent
fffb4ee3
Changes
1
Hide whitespace changes
Inline
Side-by-side
main.nf
View file @
ac61682d
...
...
@@ -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.
...
...
Write
Preview
Markdown
is supported
0%
Try again
or
attach a new file
.
Attach a file
Cancel
You are about to add
0
people
to the discussion. Proceed with caution.
Finish editing this message first!
Cancel
Please
register
or
sign in
to comment