Distributed bash-interpreter apps use bash functions to declare entry points. This app has the following entry points specified as bash functions:
main
count_func
sum_reads
Entry points are executed on a new worker with its own system requirements. The instance type can be set in the dxapp.json file’s runSpec.systemRequirements:
The main function slices the initial *.bam file and generates an index *.bai if needed. The input *.bam is then sliced into smaller *.bam files containing only reads from canonical chromosomes. First, the main function downloads the BAM file and gets the headers.
if [ -z "${mappings_sorted_bai}" ]; then
samtools index "${mappings_sorted_bam_name}"
else
dx download "${mappings_sorted_bai}" -o "${mappings_sorted_bam_name}.bai"
fi
count_jobs=()
for chr in $chromosomes; do
seg_name="${mappings_sorted_bam_prefix}_${chr}.bam"
samtools view -b "${mappings_sorted_bam_name}" "${chr}" > "${seg_name}"
bam_seg_file=$(dx upload "${seg_name}" --brief)
count_jobs+=($(dx-jobutil-new-job \
-isegmentedbam_file="${bam_seg_file}" \
-ichr="${chr}" \
count_func))
done
Outputs from the count_func entry points are referenced as Job Based Object References (JBOR) and used as inputs for the sum_reads entry point.
for job in "${count_jobs[@]}"; do
readfiles+=("-ireadfiles=${job}:counts_txt")
done
sum_reads_job=$(
dx-jobutil-new-job \
"${readfiles[@]}" \
-ifilename="${mappings_sorted_bam_prefix}" \
sum_reads
)
The output of the sum_reads entry point is used as the output of the main entry point via JBOR reference using the command dx-jobutil-add-output.
count_func
This entry point downloads and runs the command samtools view -c on the sliced *.bam. The generated counts_txt output file is uploaded as the entry point’s job output via the command dx-jobutil-add-output.
The main entry point triggers this sub job, providing the output of count_func as an input. This entry point gathers all the files generated by the count_func jobs and sums them.
This function returns read_sum_file as the entry point output.
sum_reads () {
set -e -x -o pipefail
printf "Value of read file array %s" "${readfiles[@]}"
echo "Filename: ${filename}"
echo "Summing values in files and creating output read file"
for read_f in "${readfiles[@]}"; do
echo "${read_f}"
dx download "${read_f}" -o - >> chromosome_result.txt
done
count_file="${filename}_chromosome_count.txt"
total=$(awk '{s+=$2} END {print s}' chromosome_result.txt)
echo "Total reads: ${total}" >> "${count_file}"
readfile_name=$(dx upload "${count_file}" --brief)
dx-jobutil-add-output read_sum_file "${readfile_name}" --class=file
}
Sliced *.bam files are uploaded and their file IDs are passed to the count_func entry point using the command.
