Skip to content
Snippets Groups Projects

QuaC - First major review

Merged Manavalan Gajapathy requested to merge make_it_production_ready into master
All threads resolved!
2 files
+ 5
4
Compare changes
  • Side-by-side
  • Inline
Files
2
+ 4
2
@@ -11,15 +11,17 @@ module reset
@@ -11,15 +11,17 @@ module reset
module load Anaconda3/2020.02
module load Anaconda3/2020.02
module load snakemake/5.9.1-foss-2018b-Python-3.6.6
module load snakemake/5.9.1-foss-2018b-Python-3.6.6
MODULES="all"
PROJECT_NAME="CF_CFF_PFarrell"
PROJECT_NAME="CF_CFF_PFarrell"
PEDIGREE_FPATH="data/raw/ped/${PROJECT_NAME}.ped"
PEDIGREE_FPATH="data/raw/ped/${PROJECT_NAME}.ped"
 
OUT_DIR="data/processed/${PROJECT_NAME}"
 
 
MODULES="all"
EXTRA_ARGS="-n -q"
EXTRA_ARGS="-n -q"
# EXTRA_ARGS=""
# EXTRA_ARGS=""
snakemake \
snakemake \
--snakefile "workflow/Snakefile" \
--snakefile "workflow/Snakefile" \
--config modules="${MODULES}" project_name="${PROJECT_NAME}" ped="${PEDIGREE_FPATH}" \
--config modules="${MODULES}" project_name="${PROJECT_NAME}" ped="${PEDIGREE_FPATH}" out_dir="${OUT_DIR}" \
--use-conda \
--use-conda \
--profile 'configs/snakemake_slurm_profile/{{cookiecutter.profile_name}}' \
--profile 'configs/snakemake_slurm_profile/{{cookiecutter.profile_name}}' \
--cluster-config 'configs/cluster_config.json' \
--cluster-config 'configs/cluster_config.json' \
Loading