simonlevine / fainhd Goto Github PK

Test data is single ended (apparently). Need to support single-ended viral sequence by default.

This should be pretty simple, just steal the way they do it in the STAR wrapper: https://snakemake-wrappers.readthedocs.io/en/stable/wrappers/star/align.html#code

Any rule that uses a wrapper handles its own conda dependencies. Therefore, most of the dependencies listed are unneeded

One at the root and one in docs directory.

Which is actually used? I think its the one in the root. We should delete the other

Need some way to handle something like:

sequence_files_R1: 
- "data/raw/reads/lib1_R1.fastq"
- "data/raw/reads/lib2_R1.fastq"
sequence_files_R2: 
- "data/raw/reads/lib1_R2.fastq"
- "data/raw/reads/lib2_R2.fastq"

Currently, this would crash...

https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html#log-files

Duplicating code/docs is bad. You can do something like this in the toc tree:
.. include:: ../../README.md
@simonlevine

Instead of using a data download script, have snakemake do the dirty work: https://snakemake.readthedocs.io/en/stable/snakefiles/remote_files.html