diff --git a/commonoptions.md b/commonoptions.md index 10a0c6a40..39ea3addf 100644 --- a/commonoptions.md +++ b/commonoptions.md @@ -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 ```