faster zUMIs2.0 is ready (d22c364e) · Commits · github_fork / ZUMIs

zUMIs-master.sh

+8 −12

Original line number	Diff line number	Diff line
		@@ -134,7 +134,7 @@ if grep -q 'samtools_exec:' $yaml
		if
		[[ "$whichStage" == "Filtering" ]]
		then
		echo "Starting Filtering..."
		echo "Filtering..."

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

		@@ -143,21 +143,17 @@ then
		if [[ "$isslurm" == "yes" ]]; then

		if [[ $f =~ \.gz$ ]]; then
		echo "splitfq"

		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.slurmjobid.txt;done
		else
		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.slurmjobid.txt;done
		fi

		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`
		echo $j

		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.slurmjobid.txt
		echo "listPrefix"
		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`
		echo $j
		# for x in `cat $tmpMerge/$project.listPrefix.txt`;do sbatch --cpus-per-task=$num_threads --dependency=afterok:$j --mem=10M --wrap="bash $zumisdir/fqfilter_v2.pl $yaml $samtoolsexc $Rexc $pigzexc $zumisdir $x" > $outdir/$project.slurmjobid.txt;done

		# j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`
		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`

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

		@@ -187,7 +183,7 @@ if
		[[ "$whichStage" == "Filtering" ]] \|\|
		[[ "$whichStage" == "Mapping" ]]
		then
		echo "Starting Mapping..."
		echo "Mapping..."
		if [[ "$isslurm" == "yes" ]]; then
		memory=`du -sh $genomedir \| cut -f1` #STAR genome index size
		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`
		@@ -202,7 +198,7 @@ if
		[[ "$whichStage" == "Mapping" ]] \|\|
		[[ "$whichStage" == "Counting" ]]
		then
		echo "Starting Counting..."
		echo "Counting..."
		yamlnew=$outdir/$project.postmap.yaml #note! mapping creates a temporary new yaml because of custom GTF!
		if [[ "$isslurm" == "yes" ]]; then
		if [[ $mem_limit == "null" ]]; then
		@@ -225,7 +221,7 @@ if
		then
		yamlnew=$outdir/$project.postmap.yaml #note! mapping creates a temporary new yaml because of custom GTF!
		if [[ "$isstats" == "yes" ]]; then
		echo "Starting descriptive statistics..."
		echo "Descriptive statistics..."
		if [[ "$isslurm" == "yes" ]]; then
		j=`cat $outdir/$project.slurmjobid.txt \| cut -f4 -d' ' \| tr '\n' ':' \| sed 's/.$//'`
		sbatch --dependency=afterok:$j --mem=5000 --job-name=stats --cpus-per-task=$num_threads --wrap="$Rexc $zumisdir/zUMIs-stats2.R $yamlnew" >> $outdir/$project.slurmjobid.txt

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