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License: The Unlicense
Home Page: https://fainhd.readthedocs.io/en/latest/
License: The Unlicense
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...
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
Feb 17 15:53:00 ..... started STAR run
Feb 17 15:53:00 ..... loading genome
EXITING because of FATAL ERROR: Genome version: 2.7.1a is INCOMPATIBLE with running STAR version: 2.7.5c
SOLUTION: please re-generate genome from scratch with running version of STAR, or with version: 2.7.4a
Feb 17 15:53:00 ...... FATAL ERROR, exiting
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