atac-post-process-pass-wrapper.sh

#!/bin/bash
set -Eeuxo pipefail
#Usage: bash atac-post-process_wrapper.sh
# On gcp , make sure that the bucket containing the inputs is mounted before running the script
##############################################
#Change the paths to USER DEFINED VARIABLES IN THIS SECTION ONLY BEFORE RUNNING THE SCRIPT
download_dir=gs://rna-seq_araja/PASS/atac-seq/stanford/batch8_20210113/Output/final
croo_output_path=gs://rna-seq_araja/PASS/atac-seq/stanford/batch8_20210113/Output
qc2tsv_report_name=atac_qc.tsv
indir=~/test_mnt/PASS/atac-seq/stanford
in_mnt_dir=~/test_mnt/PASS/atac-seq/stanford/batch8_20210113/Output/final
in_bam_dir=~/test_mnt/PASS/atac-seq/stanford/batch8_20210113/Output #path to raw unfiltered bam files
gcp_project=motrpac-portal
sample_metadata=sample_metadata_20200928.csv
batch_wfids=/home/araja7/atac-pp/stanford/batch8/
batch_filelist=/home/araja7/atac-pp/stanford/batch_list.txt
final_results_dir=batch8_20210113/Output/final
mode=0
batch_count=1
num_cores=12
##############################################
#get replicates to sample mapping file

python3 src/encode_rep_names_from_croo.py ${croo_output_path} ${download_dir}/ ${batch_wfids} ~/mnt/rna-seq_araja/atac-seq/wfids/${batch_wfids} ${gcp_project}

#bash src/extract_rep_names_from_encode.sh ${pipeline_output_path}/ ${download_dir}/
echo "Success! Done creation of sample mapping file"

#get qc tsv report

bash src/qc2tsv.sh ${croo_output_path} ${qc2tsv_report_name}

echo "Success! Done creation of qc2tsv report"

# reorganize croo outputs for quantification

bash src/extract_atac_from_gcp_pass.sh ${num_cores} ${croo_output_path} ${download_dir}

echo "Success! Done copying files for quantification"

# run samtools to generate genome alignment stats
bash src/align_stats.sh ${num_cores} ${in_mnt_dir} ${in_bam_dir}

echo "Success! Done generating alignment stats"

# Create final qc report merging the metadata and workflow qc scores
Rscript src/merge_atac_qc.R -w ~/${in_mnt_dir}/${sample_metadata} -q ~/${in_mnt_dir}/qc/${qc2tsv_report_name} -m ${in_mnt_dir}/rep_to_sample_map.csv -a ${in_mnt_dir}/merged_chr_info.csv -o ${in_mnt_dir}/

echo "Success! Done generating merged qc reports"

#generate counts matrix per batch
if [[ "$batch_count" == "1" ]]; then
    bash src/encode_to_count_matrix.sh ${indir} src ${batch_filelist} ${num_cores} ${final_results_dir} ${mode}
else
    echo "Skipping this step as the batch count is greater than 1, this step has to be run outside of wrapper"
    exit
fi

echo "Success! Finished"