snakemake --profile profiles/checkpoint --config m64076_221108_005936=/mmfs1/gscratch/stergachislab/data-store/PacBio-archive/m64076_221108_005936/m64076_221108_005936.subreads.bam --dry-runAfter --config you can list one or more subread bam file(s) each as a key value pair, where the key is the movie name and the value is the full path. Right now this example shows a --dry-run, remove that to run the pipeline.
Dependencies are managed with conda. If you are in the Stergachis lab be sure to include the following in your .bashrc if you want to use the pre-computed conda env.
export SNAKEMAKE_CONDA_PREFIX=/mmfs1/gscratch/stergachislab/snakemake-conda-envs