Parallel by Region (sh)

This applet performs a basic SAMtools count on a series of sliced (by canonical chromosome) BAM files in parallel using wait.

View full source code on GitHub

How is the SAMtools dependency provided?

The SAMtools dependency is resolved by declaring an Apt-Get package in the dxapp.json runSpec.execDepends.

  "runSpec": {
    ...
    "execDepends": [
      {"name": "samtools"}
    ]
  }

Debugging

The command set -e -x -o pipefail assists you in debugging this applet:

• -e causes the shell to immediately exit if a command returns a non-zero exit code.

• -x prints commands as they are executed, which is useful for tracking the job's status or pinpointing the exact execution failure.

• -o pipefail makes the return code the first non-zero exit code. (Typically, the return code of pipes is the exit code of the last command, which can create difficult to debug problems.)

  set -e -x -o pipefail
  echo "Value of mappings_sorted_bam: '${mappings_sorted_bam}'"
  echo "Value of mappings_sorted_bai: '${mappings_sorted_bai}'"
  
  mkdir workspace
  cd workspace
  dx download "${mappings_sorted_bam}"
  
  if [ -z "$mappings_sorted_bai" ]; then
    samtools index "$mappings_sorted_bam_name"
  else
    dx download "${mappings_sorted_bai}"
  fi

  The *.bai file was an optional job input. You can check for an empty or unset var using the bash built-in test [[ - z ${var}} ]]. Then, you can download or create a *.bai index as needed.

Parallel Run

Bash's job control system allows for convenient management of multiple processes. In this example, you can run bash commands in the background as you control maximum job executions in the foreground. Place processes in the background using the character & after a command.

chromosomes=$( \
  samtools view -H "${mappings_sorted_bam_name}" \
  | grep "\@SQ" \
  | awk -F '\t' '{print $2}' \
  | awk -F ':' '{if ($2 ~ /^chr[0-9XYM]+$|^[0-9XYM]/) {print $2}}')

for chr in $chromosomes; do
  samtools view -b "${mappings_sorted_bam_name}" "${chr}" -o "bam_${chr}.bam"
  echo "bam_${chr}.bam"
done > bamfiles.txt

busyproc=0
while read -r b_file; do
  echo "${b_file}"
  if [[ "${busyproc}" -ge "$(nproc)" ]]; then
    echo Processes hit max
    while [[ "${busyproc}" -gt  0 ]]; do
      wait -n # p_id
      busyproc=$((busyproc-1))
    done
  fi
  samtools view -c "${b_file}"> "count_${b_file%.bam}" &
  busyproc=$((busyproc+1))
done <bamfiles.txt

while [[ "${busyproc}" -gt  0 ]]; do
  wait -n # p_id
  busyproc=$((busyproc-1))
done

Job Output

Once the input BAM has been sliced, counted, and summed, the output counts_txt is uploaded using the command dx-upload-all-outputs. The following directory structure required for dx-upload-all-outputs is below:

├── $HOME
│   ├── out
│       ├── < output name in dxapp.json >
│           ├── output file

In your applet, upload all outputs by:

outputdir="${HOME}/out/counts_txt"
mkdir -p "${outputdir}"
cat count* \
  | awk '{sum+=$1} END{print "Total reads = ",sum}' \
  > "${outputdir}/${mappings_sorted_bam_prefix}_count.txt"

dx-upload-all-outputs