Add snakemake wrapper

[KristinaGagalova]

Hi Lauren,

Given the growing community of snakemake and also its broad application I suggest adding longstitch to a wrapper so it's easier to run it in a snakefile. So far it's a bit awkward.

Some more details here: https://snakemake.readthedocs.io/en/latest/snakefiles/modularization.html?highlight=wrapper

Cheers
Kristina

[lcoombe]

Hi Kristina,

Sure, I'm happy to look into that! Just so I know (I'm less familiar with snakefiles), could you explain what's awkward right now about calling the longstitch makefile itself within a rule in a snakefile?

Thanks!
Lauren

[KristinaGagalova]

Its mostly the fact of running longstitch from the current directory (create symlinks and move the output to another directory). I am processing multiple samples with snakemake and I am trying to keep all the sample files under separate dir.

[lcoombe]

Just documenting our Slack conversation here!

For running LongStitch in a given directory, -C dir option of makefiles is useful. I'm going to look into adding another rule to the LongStitch make_links or similar that can take in the paths to the input files, and create soft-links in the working directory (or directory specified by -C)

[KristinaGagalova]

This finally worked out

rules my_rule:
....
shell:
    """
    mkdir -p out_dir/{wildcards.sample} && \
    longstitch make_links -C {params.cur_dir}/out_dir/{wildcards.sample} reads_path={params.cur_dir}/{input.fastq} 
    draft_path={params.cur_dir}/{input.assembly} && \
    longstitch run -C {params.cur_dir}/out_dir/{wildcards.sample} out_prefix={wildcards.sample} draft={wildcards.sample} reads 
    {wildcards.sample}
    """

• Anything after -C needs to be always full path
• longstitch make_links requires full path for reads_path and draft_path
• longstitch run doesn't require a full path for reads and draft

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