fixed a bug in slurm (194933c2) · Commits · github_fork / ZUMIs

splitfq.sh

+5 −5

Original line number	Diff line number	Diff line
		@@ -45,11 +45,11 @@ function splitfqgz() {
		i=$1
		pigzexc=$2
		num_threads=$3
		nlines=$4
		tmpMerge=$5
		fun=$6
		project=$7
		f=$8
		tmpMerge=$4
		fun=$5
		project=$6
		f=$7


		if [[ $f =~ \.gz$ ]]; then
		nlines=`pigz -p $num_threads -d -c $f \| wc -l`

zUMIs-master.sh

+5 −4

Original line number	Diff line number	Diff line
		@@ -143,9 +143,10 @@ then
		if [[ "$isslurm" == "yes" ]]; then

		if [[ $f =~ \.gz$ ]]; then
		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
		echo "splitfq"
		for i in $fqfiles;do sbatch --cpus-per-task=1 --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $f" > $outdir/$project.splitfq.slurmjobid.txt;done
		else
		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
		for i in $fqfiles;do sbatch --cpus-per-task=1 --mem=10M --wrap="bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfq $project $f" > $outdir/$project.splitfq.slurmjobid.txt;done
		fi

		j=`cat $outdir/$project.splitfq.slurmjobid.txt \| cut -f4 -d' '`
		@@ -165,11 +166,11 @@ then
		else

		if [[ $f =~ \.gz$ ]]; then
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfqgz $project $f;done
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfqgz $project $f;done
		pref=`basename $f .gz`
		l=`ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|" \| sed 's/.gz//'`
		else
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $nlines $tmpMerge splitfq $project $f;done
		for i in $fqfiles;do bash $zumisdir/splitfq.sh $i $pigzexc $num_threads $tmpMerge splitfq $project $f;done
		pref=`basename $f`
		l=`ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|"`
		fi

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