launchscript_1.sh

#!/bin/bash
cd /home/ubuntu/
touch pipeline_trace.txt
sleep 5s
node /home/ubuntu/clpush/index.js &
while true;
do
  input_directory=`cat inputpath.txt`
  w=`cat wpath.txt`
  out_directory=`cat outpath.txt`
  sleep 2s

  echo "$input_directory"
  if [ $input_directory ] && [ $w ] && [ $out_directory ]
  then
    sleep 1s
    cd /home/ubuntu
    sudo aws s3 cp $input_directory .

    sleep 3s
    sudo nextflow run https://github.com/OmixPlatform/GWASpipe -c  multidocker_qc.config -r ee3cc42c3888c5e1540266029256e5b7f35b310e --vcf_file ./vcf_samples.csv --pheno SMOKER --covariates AGE,SEX

    sudo nextflow run h3abionet/h3agwas/plink-assoc.nf -c nextflow_gwas.config --pheno SEX --data results/sample.phe --input_pat results --input_dir ./results --assoc 1 --covariate PAT,MAT --freq

    sudo cp /home/ubuntu/results/assoc/SEX.assoc /home/ubuntu/gwas_asscoc.assoc
    # sudo nextflow run h3abionet/h3agwas/qc.nf --input_pat sampleA --input_dir ./sample/
    sleep 2s

    echo "Generating graphs"
    echo "# 1. Convert assoc to csv"
    python3 convert-to-csv.py gwas_asscoc.assoc gwas_assoc.csv
    sleep 1s
    ## 2. Create graphs
    echo "second graph"
    python3 generate-graph-manhatten.py full-gwas_assoc.csv gwas.png
    python3 generate-pca.py cleaned.eigenvec gwas.png
    sleep 1s

    # # Copy result files to s3
    sudo aws s3 cp /home/ubuntu/results $out_directory --recursive

    # # Copy logs to s3
    sudo aws s3 cp pipeline_trace.txt "${out_directory}/pipeline_trace.txt" --recursive

    # # Copy nextlfow log s3
    sudo aws s3 cp qc_pipeline_trace.csv "${out_directory}/qc_pipeline_trace.csv" --recursive

    # # Copy .nextflow.log
    sudo aws s3 cp .nextflow.log "${out_directory}/nextflow.log" --recursive

    # Move graphs
    sudo aws s3 cp . $out_directory --recursive --exclude "*" --exclude "clpush/*" --include "*.png"

    echo "files uploaded succesfully"
    break

  fi
done

sleep 6s
sudo poweroff