Distributed by Region (sh)

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Entry Points

Distributed bash-interpreter apps use bash functions to declare entry points. Entry points are executed as subjobs on new workers with their own respective system requirements. This app has the following entry points specified as bash functions:

• main

• count_func

• sum_reads

main

The main function takes the initial *.bam, generates an index *.bai if needed, and obtains the list of regions from the *.bam file. Every 10 regions are sent, as input, to the count_func entry point using dx-jobutil-new-job command.

# Extract list of reference regions from BAM header
regions=$(
  samtools view -H "${mappings_sorted_bam_name}" | \
  grep "@SQ" | \
  sed 's/.*SN:\(\S*\)\s.*/\1/'
)

echo "Segmenting into regions"

count_jobs=()
counter=0
temparray=()

# Loop through each region
for r in $(echo "$regions"); do
  if [[ "${counter}" -ge 10 ]]; then
    echo "${temparray[@]}"
    count_jobs+=($(
      dx-jobutil-new-job \
        -ibam_file="${mappings_sorted_bam}" \
        -ibambai_file="${mappings_sorted_bai}" \
        "${temparray[@]}" \
        count_func
    ))
    temparray=()
    counter=0
  fi
  # Add region to temp array of -i<parameter>s
  temparray+=("-iregions=${r}")
  counter=$((counter + 1))
done

# Handle remaining regions (less than 10)
if [[ $counter -gt 0 ]]; then
  echo "${temparray[@]}"
  count_jobs+=($(
    dx-jobutil-new-job \
      -ibam_file="${mappings_sorted_bam}" \
      -ibambai_file="${mappings_sorted_bai}" \
      "${temparray[@]}" \
      count_func
  ))
fi

Job outputs from the count_func entry point are referenced as Job Based Object References JBOR and used as inputs for the sum_reads entry point.

echo "Merge count files, jobs:"
echo "${count_jobs[@]}"
readfiles=()
for count_job in "${count_jobs[@]}"; do
  readfiles+=("-ireadfiles=${count_job}:counts_txt")
done
echo "file name: ${sorted_bamfile_name}"
echo "Set file, readfile variables:"
echo "${readfiles[@]}"
countsfile_job=$(dx-jobutil-new-job -ifilename="${mappings_sorted_bam_prefix}" "${readfiles[@]}" sum_reads)

Job outputs of the sum_reads entry point is used as the output of the main entry point via JBOR reference in the dx-jobutil-add-output command.

echo "Specifying output file"
dx-jobutil-add-output counts_txt "${countsfile_job}:read_sum" --class=jobref

count_func

This entry point performs a SAMtools count of the 10 regions passed as input. This execution runs on a new worker. As a result, variables from other functions are not accessible here. This includes variables from the main() function.

Once the output file with counts is created, it is uploaded to the platform and assigned as the entry point's job output counts_txt via the command dx-jobutil-add-output.

count_func() {

  set -e -x -o pipefail

  echo "Value of bam_file: '${bam_file}'"
  echo "Value of bambai_file: '${bambai_file}'"
  echo "Regions being counted '${regions[@]}'"


  dx-download-all-inputs


  mkdir workspace
  cd workspace || exit
  mv "${bam_file_path}" .
  mv "${bambai_file_path}" .
  outputdir="./out/samtool/count"
  mkdir -p "${outputdir}"
  samtools view -c "${bam_file_name}" "${regions[@]}" >> "${outputdir}/readcounts.txt"


  counts_txt_id=$(dx upload "${outputdir}/readcounts.txt" --brief)
  dx-jobutil-add-output counts_txt "${counts_txt_id}" --class=file
}

sum_reads

The main entry point triggers this subjob, providing the output of count_func as an input JBOR. This entry point gathers all the readcount.txt files generated by the count_func jobs and sums the totals.

This entry point returns read_sum as a JBOR, which is then referenced as job output.

sum_reads() {

  set -e -x -o pipefail
  echo "$filename"

  echo "Value of read file array '${readfiles[@]}'"
  dx-download-all-inputs
  echo "Value of read file path array '${readfiles_path[@]}'"

  echo "Summing values in files"
  readsum=0
  for read_f in "${readfiles_path[@]}"; do
    temp=$(cat "$read_f")
    readsum=$((readsum + temp))
  done

  echo "Total reads: ${readsum}" > "${filename}_counts.txt"

  read_sum_id=$(dx upload "${filename}_counts.txt" --brief)
  dx-jobutil-add-output read_sum "${read_sum_id}" --class=file
}

In the main function, the output is referenced

echo "Specifying output file"
dx-jobutil-add-output counts_txt "${countsfile_job}:read_sum" --class=jobref