search

KwanLab / Autometa

Autometa: Automated Extraction of Genomes from Shotgun Metagenomes
https://autometa.readthedocs.io
Other
40 stars 15 forks source link

Create nextflow process to hmmpress marker hmms #171

Open chasemc opened 3 years ago

chasemc commented 3 years ago

One thing I wanted to note is that currently this only works with docker as executor (ie not with conda only) because the MARKERS process requires hmmpress'ed files. @Sidduppal This also needs to be addressed in the installation documentation https://github.com/Sidduppal/Autometa/blob/documentation/docs/source/install.rst

Reference on why docker works and conda alone doesn't: https://github.com/KwanLab/Autometa/blob/50f7a60c329acfa9e705b4cf343dfdcc21ade0ec/Dockerfile#L36-L41

Originally posted by @chasemc in https://github.com/KwanLab/Autometa/pull/157#issuecomment-838836484

chasemc commented 2 years ago

Nextflow module will need to be changed (is Docker image specific): https://github.com/KwanLab/Autometa/blob/36d52b18425d765a804a09f020bc2bda8374094c/modules/local/markers.nf#L44-L45