new module: PARSNP

[chrisgulvik]

Is there an existing module for this?

• [x] I have searched for the existing module

Is there an open PR for this?

• [x] I have searched for existing PRs

Is there an open issue for this?

• [x] I have searched for existing issues

Further Information

I'd like to request parsnp be added in as a nf-core module. It already has a bioconda recipe here and corresponding container here.

Version print

parsnp -V 2>&1 | tail -n 1 yields parsnp 2.1.3

Help print

parsnp --help

Test example (runtime < 10 sec with 4 G ram, 2 CPU)

• Note: this is in cwd of the github repo

git clone [email protected]:marbl/parsnp.git
cd parsnp
parsnp \
  -r examples/mers_virus/ref/England1.fna \
  -d examples/mers_virus/genomes/ \
  -o OUTDIR
du -sh OUTDIR/parsnp.ggr OUTDIR/parsnp.tree
    # 20K       OUTDIR/parsnp.ggr
    # 4.0K      OUTDIR/parsnp.tree

Are you going to work on this?

• [ ] If I'm planning to work on this module, I added myself to the Assignees to facilitate tracking who is working on the module