Skip to content

Commit

Permalink
Update commonoptions.md
Browse files Browse the repository at this point in the history
  • Loading branch information
pdimens authored Jul 31, 2024
1 parent a4c6fec commit a89aac1
Showing 1 changed file with 1 addition and 2 deletions.
3 changes: 1 addition & 2 deletions commonoptions.md
Original file line number Diff line number Diff line change
Expand Up @@ -14,8 +14,7 @@ where `module` is something like [!badge corners="pill" text="impute"](Modules/i
which can include things like an input `--vcf` file, `--molecule-distance`, etc. After the options
is where you provide the input files/directories without flags and following standard BASH expansion
rules (e.g. wildcards). You can mix and match entire directories, individual files, and wildcard expansions.
In most cases, you can provide an unlimited amount of input arguments, which Harpy will parse and symlink
into the `*/workflow/input` folder, leaving the original files unmodified. In practice, that can look like:
In most cases, you can provide an unlimited amount of input arguments. In practice, that can look like:
```bash
harpy align bwa -t 5 -g genome.fasta data/pop1 data/pop2/trimmed*gz data/pop3/sample{1,2}* data/pop4/sample{2..5}*gz
```
Expand Down

0 comments on commit a89aac1

Please sign in to comment.