Example 1 (simple)

snakemake \
  --profile profile/local `# sets up where and how jobs are submitted` \
  --config \
    env="fiberseq-smk" `# sets the conda env for the jobs, always the same` \
    test=.test/ccs.bam `# path to the ccs reads with HiFi kinetics, and the key sets the sample name` \
    ref=.test/ref.fa `# reference to align results to`  

If you find this too verbose you can instead include the config options in a configuration file:

snakemake --profile profile/local --configfile config.yaml 

See config/config.yml for an example configuration file.

Example 2 (multiple inputs)

snakemake \
  --profile profile/local \
  --config \
    env="fiberseq-smk" \
    sample_name_2=/path/to/ccs.1.bam \
    sample_name_1=/path/to/ccs.2.bam \
    ref=.test/ref.fa

Example 3 (subread inputs)

snakemake \
  --profile profile/local \
  --config \
    env="fiberseq-smk" \
    input_type="subreads" \
    sample_name=/path/to/subreads.bam \
    ref=.test/ref.fa

Example 4 (make bed files)

snakemake \
  --profile profile/local \
  --config \
    env="fiberseq-smk" \
    make_bed=True \
    sample_name=/path/to/fiberseq.bam `# path to a bam generated by fiberseq-smk` \
    ref=.test/ref.fa

Example 5 use ipdSummary with subread inputs (required)

snakemake \
  --profile profile/local \
  --config \
    env="fiberseq-smk" \
    ipdsummary=True \
    input_type="subreads" \
    sample_name=/path/to/subreads.bam \
    ref=.test/ref.fa