GitHub - jaredslosberg/get_SRA_fastqs: Snakemake workflow to grab raw fastqs from SRA from SRR, SRX, SRP, or PJRNA accession numbers

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Snakemake workflow to grab raw fastqs from SRA from SRR, SRX, SRP, or PJRNA accession numbers

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Name		Name	Last commit message	Last commit date
Latest commit History 11 Commits
config		config
scripts		scripts
.gitignore		.gitignore
README.txt		README.txt
SRA_project_snake.sh		SRA_project_snake.sh
Snakefile		Snakefile

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WARNING: in development

Snakemake workflow to go from NCBI accessions to fastqs.

Input: could be SRR, SRX, or SRP ids
	-recommended to be SRP ids, directories are named based on this
note: smallest resolution that can be returned is SRX. if a SRR is input, it will grab metadata and fastqs for the entire SRX it resides in

Output:
	-writes fastqs from fasterq-dump to any directory specified in config file
	-appends [project_id]/[experiment_id] to that specified directory to organize fastqs
	-status file in ./output/[project_id]/[experiment_id] that records date of most recent download

TODO: make clear which yaml is parameters vs conda env
Test in isolated (singularity) environment
Where does prefetch go
Write metadata and fastqs to same location


First time running:
#will create conda environment to call snakemake helper scripts with
$ bash ./scripts/config.sh
#may need to configure (https://github.com/ncbi/sra-tools/wiki/03.-Quick-Toolkit-Configuration)

Call SRA_project_snake with:
$ bash SRA_project_snake.sh [SRP-accession-id]