fixed a bug in slurm splitfq (05f3409a) · Commits · github_fork / ZUMIs

splitfq.sh

+8 −0

Original line number	Diff line number	Diff line
		@@ -49,4 +49,12 @@ nlines=$4
		tmpMerge=$5
		fun=$6
		project=$7
		f=$8

		if [[ $f =~ \.gz$ ]]; then
		nlines=`pigz -p $num_threads -d -c $f \| wc -l`
		else
		nlines=`wc -l $f \| awk '{print $1}'`
		fi

		$fun "$i" "$pigzexc" "$num_threads" "$nlines" "$tmpMerge" "$project"

zUMIs-master.sh

+4 −12

Original line number	Diff line number	Diff line
		@@ -135,10 +135,6 @@ if
		[[ "$whichStage" == "Filtering" ]]
		then
		echo "Starting Filtering..."
		#echo "samtools_exec: $samtoolsexc" >> $yaml
		#echo "pigz_exec: $pigzexc" >> $yaml
		#echo "STAR_exec: $starexc" >> $yaml
		#echo "zUMIs_directory: $zumisdir" >> $yaml

		f=`cut -d' ' -f1 <(echo $fqfiles)` # the first fastq file to determine gzip status

		@@ -147,11 +143,9 @@ then
		if [[ "$isslurm" == "yes" ]]; then

		if [[ $f =~ \.gz$ ]]; then
		nlines=`pigz -p $num_threads -d -c $f \| wc -l`
		for i in $fqfiles;do sbatch --cpus-per-task=1 --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfqgz $project" > $outdir/$project.splitfq.slurmjobid.txt;done
		for i in $fqfiles;do sbatch --cpus-per-task=1 --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfqgz $project $f" > $outdir/$project.splitfq.slurmjobid.txt;done
		else
		nlines=`wc -l $f \| awk '{print $1}'`
		for i in $fqfiles;do sbatch --cpus-per-task=1 --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfq $project" > $outdir/$project.splitfq.slurmjobid.txt;done
		for i in $fqfiles;do sbatch --cpus-per-task=1 --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfq $project $f" > $outdir/$project.splitfq.slurmjobid.txt;done
		fi

		j=`cat $outdir/$project.splitfq.slurmjobid.txt \| cut -f4 -d' '`
		@@ -171,13 +165,11 @@ then
		else

		if [[ $f =~ \.gz$ ]]; then
		nlines=`pigz -p $num_threads -d -c $f \| wc -l`
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfqgz $project;done
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfqgz $project $f;done
		pref=`basename $f .gz`
		l=`ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|" \| sed 's/.gz//'`
		else
		nlines=`wc -l $f \| awk '{print $1}'`
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfq $project;done
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfq $project $f;done
		pref=`basename $f`
		l=`ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|"`
		fi

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