diff --git a/snakemake.md b/snakemake.md index eaca95981..4272e9a25 100644 --- a/snakemake.md +++ b/snakemake.md @@ -13,9 +13,11 @@ all sorts of things necessary for Snakemake to do its magic. However, as a convenience, Harpy workflows will also create a copy of the Snakemake workflow log (all those things that print on screen when Harpy is running) in a workflow's output directory. These logs are found in `OUTDIR/logs/snakemake` -and are named `DATE-TIME.snakelog`. As an example, using the default +and are named `workflow.runX.DATE.snakelog`, where `workflow` is the harpy workflow +(qc, sv_naibr, etc.), `runX` is the attempt number (given by `X`, e.g. `run4`), and +`DATE` is given as `MONTH_DAY_YEAR`. As an example, using the default settings of `harpy qc`, you will find a copy of your workflow's log in -`QC/logs/snakemake/5_13_2024-11_59_22.snakelog`. The name of this log will +`QC/logs/snakemake/qc.run1.5_13_2024.snakelog`. The name of this log will **not** match the official log Snakemake creates in `.snakemake/logs`, but the contents will be identical. This naming convention exists to allow multiple runs in a single output directory, which usually happens because something went wrong. @@ -37,17 +39,18 @@ harpy qc --snakemake "--dry-run --debug --shadow-prefix /scratch" rawseq !!!danger reserved/forbidden arguments Harpy calls Snakemake with a given set of arguments, meaning you cannot append these again to the internal command line call. Well, you can, but Snakemake will -error and exit. [Everything else](https://snakemake.readthedocs.io/en/stable/executing/cli.html#all-options) +complain or behave unexpectedly. [Everything else](https://snakemake.readthedocs.io/en/stable/executing/cli.html#all-options) is allowed. The reserved (**forbidden**) arguments are: -- `--directory` -- `--cores` -- `--snakefile` +- `--conda-prefix` - `--configfile` -- `--rerun-incomplete` +- `--cores` +- `--directory` - `--nolock` -- `--conda-prefix` +- `--rerun-incomplete` +- `--rerun-triggers` +- `--show-failed-logs` - `--software-deployment-method` -- `--rerun-triggers` +- `--snakefile` !!! ### Common use cases