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guard against shell pipefails in align_and_count in instances where empty inputs would result in div-by-zero conditions #535

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merged 2 commits into from
Apr 26, 2024
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guard against shell pipefails in align_and_count in instances where empty inputs would result in div-by-zero conditions #535

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96dcd95
guard against shell pipefails in align_and_count in instances where e…
tomkinsc Apr 25, 2024
d9720f4
handle case where only catchall count is reported
tomkinsc Apr 25, 2024
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21 changes: 16 additions & 5 deletions pipes/WDL/tasks/tasks_reports.wdl
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Original file line number Diff line number Diff line change
Expand Up @@ -451,16 +451,27 @@ task align_and_count {

sort -b -r -n -k3 "~{reads_basename}.count.~{ref_basename}.txt.unsorted" > "~{reads_basename}.count.~{ref_basename}.txt"
head -n ~{topNHits} "~{reads_basename}.count.~{ref_basename}.txt" > "~{reads_basename}.count.~{ref_basename}.top_~{topNHits}_hits.txt"
TOP_HIT="$(head -1 '~{reads_basename}.count.~{ref_basename}.txt' | cut -f 1 | tee '~{reads_basename}.count.~{ref_basename}.top.txt')"
TOP_HIT="$(head -1 '~{reads_basename}.count.~{ref_basename}.txt' | cut -f 1 | sed 's/\*/\\*/' | tee '~{reads_basename}.count.~{ref_basename}.top.txt')"

TOTAL_COUNT_OF_TOP_HIT=$(grep -E "^($TOP_HIT)" "~{reads_basename}.count.~{ref_basename}.txt" | cut -f3 | tee TOTAL_COUNT_OF_TOP_HIT)
TOTAL_COUNT_OF_LESSER_HITS=$(grep -vE "^(\*|$TOP_HIT)" "~{reads_basename}.count.~{ref_basename}.txt" | cut -f3 | paste -sd+ - | bc -l | tee TOTAL_COUNT_OF_LESSER_HITS)
PCT_MAPPING_TO_LESSER_HITS=$( echo "scale=3; 100 * $TOTAL_COUNT_OF_LESSER_HITS / ($TOTAL_COUNT_OF_LESSER_HITS + $TOTAL_COUNT_OF_TOP_HIT)" | \
bc -l | awk '{printf "%.3f\n", $0}' | tee '~{reads_basename}.count.~{ref_basename}.pct_lesser_hits_of_mapped.txt' )
TOTAL_COUNT_OF_LESSER_HITS=$((grep -vE "^(\*|$TOP_HIT)" "~{reads_basename}.count.~{ref_basename}.txt" || echo "0" ) | cut -f3 | paste -sd+ - | bc -l | tee TOTAL_COUNT_OF_LESSER_HITS)

if [ $TOTAL_COUNT_OF_LESSER_HITS -ne 0 -o $TOTAL_COUNT_OF_TOP_HIT -ne 0 ]; then
PCT_MAPPING_TO_LESSER_HITS=$( echo "scale=3; 100 * $TOTAL_COUNT_OF_LESSER_HITS / ($TOTAL_COUNT_OF_LESSER_HITS + $TOTAL_COUNT_OF_TOP_HIT)" | \
bc -l | awk '{printf "%.3f\n", $0}' | tee '~{reads_basename}.count.~{ref_basename}.pct_lesser_hits_of_mapped.txt' )
else
echo "PCT_MAPPING_TO_LESSER_HITS cannot be calculated: there were no hits to any sequence"
PCT_MAPPING_TO_LESSER_HITS=$( echo "null" | tee '~{reads_basename}.count.~{ref_basename}.pct_lesser_hits_of_mapped.txt')
fi

TOTAL_READS_IN_INPUT=$(samtools view -c "~{reads_basename}.bam")
PCT_OF_INPUT_READS_MAPPED=$( echo "scale=3; 100 * ($TOTAL_COUNT_OF_LESSER_HITS + $TOTAL_COUNT_OF_TOP_HIT) / $TOTAL_READS_IN_INPUT" | \
if [ $TOTAL_READS_IN_INPUT -eq 0 ]; then
echo "no reads in input bam"
PCT_OF_INPUT_READS_MAPPED=$(echo "0" | tee "~{reads_basename}.count.~{ref_basename}.pct_total_reads_mapped.txt")
else
PCT_OF_INPUT_READS_MAPPED=$( echo "scale=3; 100 * ($TOTAL_COUNT_OF_LESSER_HITS + $TOTAL_COUNT_OF_TOP_HIT) / $TOTAL_READS_IN_INPUT" | \
bc -l | awk '{printf "%.3f\n", $0}' | tee '~{reads_basename}.count.~{ref_basename}.pct_total_reads_mapped.txt' )
fi
>>>

output {
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