first version for the GUI with snakemake. features:
user can input sra
user can input fastq files
can only execute one workflow task at a time, can be cleared/reset
all other options are hardcoded n snakemake: GATK and GRCh38
some things to know for the user:
if any, fastq files must be located in user defined analysis directory
others folders generated by snakemake e.g.data and SnpEff are located in user's current directory (in Debug mode this would be /Spritz/GUI/bin/Debug)
user must have Powershell and docker installed
some things to know for us:
docker is currently pulling an image from rinaibrhm/spritz docker hub
image has to be rebuilt and pushed to docker hub for any edits/changes to snakemake rules/scripts/etc
i didn't really touch all the code for the toolkit wrappers but i don't think we need it anymore.
anyway, i feel like this still needs testing on your end. :)
first version for the GUI with snakemake. features:
GATK
andGRCh38
some things to know for the user:
data
andSnpEff
are located in user's current directory (in Debug mode this would be/Spritz/GUI/bin/Debug
)docker
installedsome things to know for us:
rinaibrhm/spritz
docker hubi didn't really touch all the code for the toolkit wrappers but i don't think we need it anymore. anyway, i feel like this still needs testing on your end. :)