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Welcome to the Twist_DNA_Solid wiki!

Detailed documentation can be found in this google document:
[GMS Solid documentation](https://docs.google.com/document/d/1ht0VzB976dCdLEm9H1YfMJeiLJdIqW6wEWNhXj78P6o/edit#heading=h.tdceox13op5c)

Example of how to run the pipeline in Uppsala

git clone https://github.com/genomic-medicine-sweden/Twist_Solid.git .
git checkout v0.2.3-alpha
python3.9 -m venv ~/Snakemake/venv/
source ~/Snakemake/venv/bin/activate
pip install -r requirements.txt
pip install hydra_genetics

#Generate sample and unit files (modify tumor content values in samples.tsv after creation)
hydra-genetics create-input-files -d path/dir1 -d path/dir2

#Run the pipeline
module add snakemake singularity slurm-drmaa
snakemake --notemp --profile profiles/uppsala/ -s workflow/Snakefile

Modification needed if not run in Uppsala

#Modify file paths in config/config.yaml
#Make your own profile
#Modify start command
#Download reference files

Key components of the pipeline

• workflow/Snakefile - Imports selected modules from hydra-genetics
• workflow/rules/common.smk - Specifies the output files that we want to keep
• workflow/rules/results_files.smk - Rules that copy output files (specified in common.smk) from the output of the pipeline to the results folder structure of your choice
• config/config.yaml - Specification of where all the prerequisite files are, of containers and of pipeline specific parameters.
• config/resources.yaml - Specification of default resources used on the cluster and rules using non-standard values (i.e. extra cores or time)
• slurm/config.yaml - Slurm profile