update

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