added CONTRIBUTING.md (modeled after Ryan Wick's Badread contributing.md)
updated README with TOC (w/ links), edited for clarity, added section for usage of gpu-basecalling scripts
gpu-basecalling script changes:
adjusted gpu-basecalling scripts to not be specific to pjx8, any user can run them
USAGE echo statements fixed and edited for visibility on cmdline
added third positional argument to run_01_basecall-w-gpu.sh to require setting fast or hac for different Guppy basecalling modes/models. Added checks to make sure either fast or hac is specified with error echo statment
after demultiplexing w qcat, fastq files are now gzipped (removes need for the prep_samples script)
I'd like to make a release, perhaps v0.2? So that folks can download that release for their usage of the scripts, rather than git cloneing the most recent developments
This PR has the following edits/contributions
run_01_basecall-w-gpu.shto require settingfastorhacfor different Guppy basecalling modes/models. Added checks to make sure eitherfastorhacis specified with error echo statmentqcat, fastq files are now gzipped (removes need for the prep_samples script)I'd like to make a release, perhaps v0.2? So that folks can download that release for their usage of the scripts, rather than
git cloneing the most recent developments