Visualization of pipeline
Visualization of the pipeline based on
the test datasets are available in directory ./pipeline_visualized/
. Commands used to
create this visualization:
# For Cheaha users only. Open interactive node
srun --ntasks=1 --cpus-per-task=1 --mem-per-cpu=4096 --partition=express --pty /bin/bash
# For Cheaha users only. Set up environment.
module reset
module load Anaconda3/2020.02
module load Singularity/3.5.2-GCC-5.4.0-2.26
# activate conda env
conda activate quac
PROJECT_CONFIG="project_2samples"
PRIOR_QC_STATUS="include_priorQC"
DAG_DIR="pipeline_visualized"
###### WGS mode ######
# DAG
python src/run_quac.py \
--sample_config ".test/configs/${PRIOR_QC_STATUS}/sample_config/${PROJECT_CONFIG}_wgs.tsv" \
--pedigree ".test/configs/${PRIOR_QC_STATUS}/pedigree/${PROJECT_CONFIG}.ped" \
--quac_watch_config "configs/quac_watch/wgs_quac_watch_config.yaml" \
--include_prior_qc \
--extra_args "--dag -F | dot -Tpng > ${DAG_DIR}/wgs_dag.png"
# Rulegraph - less informative than DAG at sample level but less dense than DAG makes this easier to skim
python src/run_quac.py \
--sample_config ".test/configs/${PRIOR_QC_STATUS}/sample_config/${PROJECT_CONFIG}_wgs.tsv" \
--pedigree ".test/configs/${PRIOR_QC_STATUS}/pedigree/${PROJECT_CONFIG}.ped" \
--quac_watch_config "configs/quac_watch/wgs_quac_watch_config.yaml" \
--include_prior_qc \
--extra_args "--rulegraph -F | dot -Tpng > ${DAG_DIR}/wgs_rulegraph.png"
###### Exome mode ######
# DAG
python src/run_quac.py \
--sample_config ".test/configs/${PRIOR_QC_STATUS}/sample_config/${PROJECT_CONFIG}_exome.tsv" \
--pedigree ".test/configs/${PRIOR_QC_STATUS}/pedigree/${PROJECT_CONFIG}.ped" \
--quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \
--include_prior_qc \
--exome \
--extra_args "--dag -F | dot -Tpng > ${DAG_DIR}/exome_dag.png"
# Rulegraph - less informative than DAG at sample level but less dense than DAG makes this easier to skim
python src/run_quac.py \
--sample_config ".test/configs/${PRIOR_QC_STATUS}/sample_config/${PROJECT_CONFIG}_exome.tsv" \
--pedigree ".test/configs/${PRIOR_QC_STATUS}/pedigree/${PROJECT_CONFIG}.ped" \
--quac_watch_config "configs/quac_watch/exome_quac_watch_config.yaml" \
--include_prior_qc \
--exome \
--extra_args "--rulegraph -F | dot -Tpng > ${DAG_DIR}/exome_rulegraph.png"