diff --git a/snakemake.md b/snakemake.md index c451d6733..b9aff8ae7 100644 --- a/snakemake.md +++ b/snakemake.md @@ -29,8 +29,9 @@ and deletes the original Snakemake logfile that you would expect to find in `.sn Harpy relies on Snakemake under the hood to handle file and job dependencies. Most of these details have been abstracted away from the end-user, but most Harpy modules have an optional flag `--snakemake` that you can use to augment -the Snakemake workflow if necessary. Whenever you use this flag, your argument -must be enclosed in quotation marks, for example: +the Snakemake workflow if necessary. [The full list of Snakemake command line +options can be found here](https://snakemake.readthedocs.io/en/stable/executing/cli.html). +Whenever you use this flag, your argument must be enclosed in quotation marks, for example: ```bash harpy qc --snakemake "--dry-run" rawseq ```