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"