louiejtaylor/hisss

Snakemake workflow to download and/or align reads to targets and produce useful outputs.

hisss's Issues

Use grabseqs

Allow downloading of reads only

Natively support downloading from MG-RAST

Allow for data directories outside of root dir

Different behavior for relative vs. absolute paths?

Downloaded fastq files are too big for the storage

Bug where single-end section printed even if no single-end samples

Change logic in list-SRA.py

Summarize coverage depth, breadth, and read counts after alignment

SRA Rule targets need to be fastq.gz

fastq-dump uses --gzip now but the rule targets still end in ".fastq". They'll need to be ".fastq.gz" so Snakemake sees the output show up as it expects it.

Build bowtie2 index upstream of alignment

• rule build_index
• Add index as input to rule align_reads

Use fasterq-dump instead of fastq-dump!

Command-line specification of things to exclude (i.e. splitting paired and unpaired, include v. exclude amplicons)

for list_SRA.py

Handle downloading from SRA

Is it possible to run the snakemake command line in any folder?

R is not included in requirements.txt

For completeness, R/Rscript should be included as an explicit dependency.

Also, this issue serves as a reminder to check for any other missing dependencies by running a test on a fresh server :D

Sleep IFF fastq-dump fails before retrying