Add athena-meta pipeline

[johnne]

The meta branch now contains snakemake rules to run athena-meta. To try it out

• update your environment to install megahit and bwa
• run the test script (bash tests/run.sh) to generate the trimmed files and barcode cluster file
• run the metagenomic part:

snakemake -s src/blr/rules/meta.smk --use-conda -np outdir/athena.done (remove the '-n' to trigger the actual run)

All seems to work fine (on linux) up until the Flye step of athena-meta. Here it crashes with something seemingly related to this issue. Note: running with just one thread does not fix the problem. Also, running with the athena-meta-flye-docker docker image does not work either.

I'll try to look into the problem further.

[FrickTobias]

Looks really good to me!

Could you make a PR for now excluding Flye? I am about to fix the macOS compatibility issue with the .environment.yml file, so I thought we could try and avoid merge conflicts, since I see you've worked on the same file.

[FrickTobias]

I went ahead and pushed to master, shouldn't be too hard to manually fix the conflict since it is only two rows (as I understand at least) so go ahead and wait until Flye works.

[johnne]

When I update flye to the latest version (2.4.2) it works. Oddly enough that upgrade forces a downgrade of athena-meta from version 1.3 to 1.2 (because the developer had listed flye at v. 2.4 in the original conda recipe, but then changed it to 2.3.1 for some reason).