diff --git a/README.md b/README.md index ebe4620..c8dee01 100644 --- a/README.md +++ b/README.md @@ -16,7 +16,7 @@ The module contiains -SYNTAX: snakemakeslurm [--debug] [snakemake flags] +SYNTAX: snakemakeslurm [--debug] [--use] [snakemake flags] EXAMPLE: ``` @@ -34,8 +34,10 @@ CMD: snakemake \ --error {cluster.error} --output {cluster.output} \ -p all ``` + * --debug prints snakemake commandline, but does NOT invoke snakemake. + * --use adds --use-conda and/or --use-singularity if those directives are present in Snakefile -Notice: +Notes: * it has defined (mostly 1-to-1) name mappings for SLURM attributes to keys in the cluster.json file * it has populated "--mail-user $USER@uab.edu" * it has mapped rule.threads to SLURM:--cpus-per-task