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Remove GNU parallel dependency #33

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merged 3 commits into from
Jan 30, 2023
Merged

Remove GNU parallel dependency #33

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3935b6d
Remove unnecessary GNU parallel dependency
semenko Jan 19, 2023
9b2a5ea
Remove parallel from readme
semenko Jan 19, 2023
d2dcbe0
Merge branch 'master' into master
jamorrison Jan 30, 2023
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1 change: 0 additions & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,6 @@ the user's `PATH` environment variable:
- [samtools](http://www.htslib.org/)
- [bedtools](https://bedtools.readthedocs.io/en/latest/index.html)
- [GNU awk](https://www.gnu.org/software/gawk/manual/gawk.html)
- [GNU parallel](https://www.gnu.org/software/parallel/)

It is also useful to have [samblaster](https://github.com/GregoryFaust/samblaster)
installed for marking duplicate reads during the alignment phase.
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47 changes: 25 additions & 22 deletions scripts/QC.sh
100755 → 100644
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Expand Up @@ -7,7 +7,7 @@
## showing the different BISCUIT QC metrics
##
## Notes:
## 1.) biscuit, samtools, bedtools, awk, and parallel all must be in PATH for
## 1.) biscuit, samtools, bedtools, and awk all must be in PATH for
## script to work
##
## Created by:
Expand Down Expand Up @@ -40,6 +40,7 @@
## - Create qc subcommand and integrate into QC.sh
## Jan 2023 -
## - Fix bug so new versions of GNU parallel work
## - Remove GNU parallel dependency
##
################################################################################

Expand Down Expand Up @@ -77,19 +78,6 @@ function check_path {
exit 1
fi
fi
if [[ `which parallel 2>&1 > /dev/null` ]]; then
>&2 echo "parallel does not exist in PATH"
>&2 echo "Make sure to add GNU parallel to PATH"
exit 1
else
if parallel --version | grep -q GNU; then
>&2 echo "Using GNU parallel found at: `which parallel`"
else
>&2 echo "It doesn't appear you are using GNU parallel."
>&2 echo "Try adding GNU parallel at the front of PATH"
exit 1
fi
fi
}

# Check that certain variables have been set and files exist
Expand All @@ -109,6 +97,18 @@ function check_variables {
done
}

# Wait for jobs, exit if they're unsuccessful
# Via: https://stackoverflow.com/questions/1131484/wait-for-bash-background-jobs-in-script-to-be-finished/
function wait_for_jobs {
while true; do
wait -n || {
code="$?"
([[ $code = "127" ]] && exit 0 || exit "$code")
break
}
done;
}

# Workhorse function for processing BISCUIT QC
function biscuitQC {
# Simple check for necessary command line tools
Expand All @@ -133,16 +133,19 @@ function biscuitQC {

if [[ "${run_cov_qc}" == true ]]; then
# Create genomecov_all, genomecov_q40, genomecov_all_dup, genomecov_q40_dup
samtools view -hb ${in_bam} | parallel -j4 -k --tmpdir ${outdir} --pipe --tee {} ::: \
"bedtools genomecov -bga -split -ibam stdin | LC_ALL=C sort -k1,1 -k2,2n -T ${outdir} > ${outdir}/${sample}_genomecov_all.tmp.bed" \
"samtools view -q 40 -b | bedtools genomecov -bga -split -ibam stdin | LC_ALL=C sort -k1,1 -k2,2n -T ${outdir} > ${outdir}/${sample}_genomecov_q40.tmp.bed" \
"samtools view -f 0x400 -b | bedtools genomecov -bga -split -ibam stdin | LC_ALL=C sort -k1,1 -k2,2n -T ${outdir} > ${outdir}/${sample}_genomecov_all_dup.tmp.bed" \
"samtools view -f 0x400 -q 40 -b | bedtools genomecov -bga -split -ibam stdin | LC_ALL=C sort -k1,1 -k2,2n -T ${outdir} > ${outdir}/${sample}_genomecov_q40_dup.tmp.bed"
# Spawn these to the background
bedtools genomecov -bga -split -ibam ${in_bam} | LC_ALL=C sort -k1,1 -k2,2n -T ${outdir} > ${outdir}/${sample}_genomecov_all.tmp.bed &
samtools view -q 40 -b ${in_bam} | bedtools genomecov -bga -split -ibam stdin | LC_ALL=C sort -k1,1 -k2,2n -T ${outdir} > ${outdir}/${sample}_genomecov_q40.tmp.bed &
samtools view -f 0x400 -b ${in_bam} | bedtools genomecov -bga -split -ibam stdin | LC_ALL=C sort -k1,1 -k2,2n -T ${outdir} > ${outdir}/${sample}_genomecov_all_dup.tmp.bed &
samtools view -f 0x400 -q 40 -b ${in_bam} | bedtools genomecov -bga -split -ibam stdin | LC_ALL=C sort -k1,1 -k2,2n -T ${outdir} > ${outdir}/${sample}_genomecov_q40_dup.tmp.bed &

wait_for_jobs

# Create cpg_all, cpg_q40
cat ${BISCUIT_CPGS} | parallel -j2 -k --tmpdir ${outdir} --pipe --tee {} ::: \
"bedtools intersect -sorted -wo -b ${outdir}/${sample}_genomecov_all.tmp.bed -a stdin | bedtools groupby -g 1-3 -c 7 -o min > ${outdir}/${sample}_cpg_all.tmp.bed" \
"bedtools intersect -sorted -wo -b ${outdir}/${sample}_genomecov_q40.tmp.bed -a stdin | bedtools groupby -g 1-3 -c 7 -o min > ${outdir}/${sample}_cpg_q40.tmp.bed"
bedtools intersect -sorted -wo -b ${outdir}/${sample}_genomecov_all.tmp.bed -a ${BISCUIT_CPGS} | bedtools groupby -g 1-3 -c 7 -o min > ${outdir}/${sample}_cpg_all.tmp.bed &
bedtools intersect -sorted -wo -b ${outdir}/${sample}_genomecov_q40.tmp.bed -a ${BISCUIT_CPGS} | bedtools groupby -g 1-3 -c 7 -o min > ${outdir}/${sample}_cpg_q40.tmp.bed &

wait_for_jobs

# Coverage distributions and uniformity
echo -e "BISCUITqc Uniformity Table" > ${outdir}/${sample}_cv_table.txt
Expand Down