just commit (97b1789a) · Commits · github_fork / ZUMIs

listPrefix.sh

+5 −4

Original line number	Diff line number	Diff line
		@@ -8,6 +8,10 @@ zumisdir=$1
		tmpMerge=$2
		f=$3
		project=$4
		yaml=$5
		samtoolsexc=$6
		Rexc=$7
		pigzexc=$8

		if [[ $f =~ \.gz$ ]]; then
		pref=`basename $f .gz`
		@@ -17,8 +21,5 @@ else
		ls $tmpMerge$pref* \| sed "s\|$tmpMerge$pref\|\|" > $tmpMerge/$project.listPrefix.txt
		fi

		$zumisdir $tmpMerge $f $project $yaml $samtoolsexc $Rexc $pigzexc $zumisdir


		for x in `cat $tmpMerge/$project.listPrefix.txt`; do bash $zumisdir/fqfilter_v2.pl $yaml $samtoolsexc $Rexc $pigzexc $zumisdir $x & done
		for x in `cat $tmpMerge/$project.listPrefix.txt`; do perl $zumisdir/fqfilter_v2.pl $yaml $samtoolsexc $Rexc $pigzexc $zumisdir $x & done
		wait

zUMIs-master.sh

+7 −7

Original line number	Diff line number	Diff line
		@@ -144,14 +144,14 @@ then

		if [[ $f =~ \.gz$ ]]; then
		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
		for i in $fqfiles;do sbatch --cpus-per-task=1 --job-name=splitfq --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 $tmpMerge splitfq $project $f" > $outdir/$project.splitfq.slurmjobid.txt;done
		for i in $fqfiles;do sbatch --cpus-per-task=1 --job-name=splitfq --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' '`

		sbatch --cpus-per-task=1 --dependency=afterok:'$j' --mem=1M --wrap="bash $zumisdir/listPrefix.sh $zumisdir $tmpMerge $f $project $yaml $samtoolsexc $Rexc $pigzexc $zumisdir" > $outdir/$project.listPrefix.slurmjobid.txt
		sbatch --cpus-per-task=1 --job-name=listPrefix --dependency=afterok:'$j' --mem=1M --wrap="bash $zumisdir/listPrefix.sh $zumisdir $tmpMerge $f $project $yaml $samtoolsexc $Rexc $pigzexc" > $outdir/$project.listPrefix.slurmjobid.txt

		j=`cat $outdir/$project.listPrefix.slurmjobid.txt \| cut -f4 -d' '`

		@@ -159,7 +159,7 @@ then

		# j=`cat $outdir/$project.fqfilter_v2.slurmjobid.txt \| cut -f4 -d' '`

		sbatch --cpus-per-task=1 --dependency=afterok:'$j' --mem=1M --wrap="bash $zumisdir/mergeBAM.sh $zumisdir $tmpMerge $num_threads $project $outdir $yaml" > $outdir/$project.mergeBAM.slurmjobid.txt
		sbatch --cpus-per-task=1 --job-name=splitfq=mergeBAM --dependency=afterok:'$j' --mem=1M --wrap="bash $zumisdir/mergeBAM.sh $zumisdir $tmpMerge $num_threads $project $outdir $yaml" > $outdir/$project.mergeBAM.slurmjobid.txt

		j=`cat $outdir/$project.mergeBAM.slurmjobid.txt \| cut -f4 -d' '`

		@@ -189,7 +189,7 @@ then
		if [[ "$isslurm" == "yes" ]]; then
		memory=`du -sh $genomedir \| cut -f1` #STAR genome index size
		j=`cat $outdir/$project.mergeBAM.slurmjobid.txt \| cut -f4 -d' '`
		sbatch --dependency=afterok:'$j' --mem=$memory --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-mapping.R $yaml" > $outdir/$project.mapping.slurmjobid.txt
		sbatch --dependency=afterok:'$j' --job-name=mapping --mem=$memory --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-mapping.R $yaml" > $outdir/$project.mapping.slurmjobid.txt
		else
		$Rexc $zumisdir/zUMIs-mapping.R $yaml
		fi
		@@ -209,7 +209,7 @@ then
		mem_limit=`expr $mem_limit \* 1000`
		fi
		j=`cat $outdir/$project.mapping.slurmjobid.txt \| cut -f4 -d' '`
		sbatch --dependency=afterok:'$j' --mem=$mem_limit --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-dge2.R $yamlnew" > $outdir/$project.dge.slurmjobid.txt
		sbatch --dependency=afterok:'$j' --mem=$mem_limit --job-name=dge --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-dge2.R $yamlnew" > $outdir/$project.dge.slurmjobid.txt
		else
		$Rexc $zumisdir/zUMIs-dge2.R $yamlnew
		fi
		@@ -226,7 +226,7 @@ then
		echo "Starting descriptive statistics..."
		if [[ "$isslurm" == "yes" ]]; then
		j=`cat $outdir/$project.dge.slurmjobid.txt \| cut -f4 -d' '`
		sbatch --dependency=afterok:'$j' --mem=5000 --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-stats2.R $yamlnew" > $outdir/$project.stats.slurmjobid.txt
		sbatch --dependency=afterok:'$j' --mem=5000 --job-name=stats --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-stats2.R $yamlnew" > $outdir/$project.stats.slurmjobid.txt
		else
		$Rexc $zumisdir/zUMIs-stats2.R $yamlnew
		fi

Admin message