2nd stab at creating a pipeline [not quite finished yet].
Modularized the system to emulate what it will look like in firehose. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1605 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
794bd26b20
commit
84c8374e68
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#!/usr/bin/perl -w
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use strict;
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use Getopt::Long;
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sub usage {
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print "Usage: perl runCleaningPipeline.pl\n\t-i <input bam>\n\t-odir <output directory>\n\t-obam <output bam name>\n\t[-sting Sting dir]\n\t[-inject]\n\t[-q farm queue; default:gsa]\n\t[-wait farm wait id]\n\t[-job final farm job name]\n\t[-dry]\n";
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exit(1);
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}
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my $inputBam = undef;
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my $outputDir = undef;
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my $outputBam = undef;
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my $jobName = undef;
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my $wait = undef;
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my $dry;
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my $inject;
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my $queue = "gsa";
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my $sting = "/humgen/gsa-scr1/ebanks/Sting";
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GetOptions( "i=s" => \$inputBam,
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"odir=s" => \$outputDir,
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"obam=s" => \$outputBam,
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"q:s" => \$queue,
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"dry!" => \$dry,
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"inject!" => \$inject,
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"job:s" => \$jobName,
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"wait:s" => \$wait,
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"sting:s" => \$sting );
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usage() if ( !$inputBam || !$outputDir || !$outputBam );
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my $indelIntervals = "$outputDir/$outputBam.indels.intervals";
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my $command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $indelIntervals -oarg o -j $outputDir/$outputBam.intervals -q $queue";
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if ($dry) {
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$command .= " -dry";
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}
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if ($wait) {
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$command .= " -wait $wait";
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}
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system($command);
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my $mismatchIntervals = "$outputDir/$outputBam.mismatches.intervals";
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$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam\" -o $mismatchIntervals -oarg o -j $outputDir/$outputBam.intervals -q $queue";
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if ($dry) {
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$command .= " -dry";
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}
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if ($wait) {
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$command .= " -wait $wait";
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}
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system($command);
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my $mergedIntervals = "$outputDir/$outputBam.merged.intervals";
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$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -intervals $indelIntervals -intervals $mismatchIntervals\" -o $mergedIntervals -oarg o -wait $outputDir/$outputBam.intervals -j $outputDir/$outputBam.merged -q $queue";
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if ($dry) {
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$command .= " -dry";
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}
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system($command);
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my $cleanedBam;
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if ($inject) {
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$cleanedBam = "$outputDir/$outputBam.cleaned.bam";
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} else {
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$cleanedBam = "$outputDir/$outputBam";
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}
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$command = "perl $sting/perl/splitAndEnqueueGATKjobs.pl -cmd \"java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -compress 1";
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if ($inject) {
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$command .= " -cleanedOnly\" -j $outputDir/$outputBam.cleaned";
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} else {
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$command .= "\" -j $jobName";
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}
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$command .= "\" -o $cleanedBam -oarg O -wait $outputDir/$outputBam.merged -q $queue -bam -i $mergedIntervals -n 50";
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if ($dry) {
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$command .= " -dry";
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}
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system($command);
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if ($inject) {
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my $bam = "$outputDir/$outputBam";
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$command = "bsub -q $queue -o $bam.sdout";
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if ($jobName) {
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$command .= " -J $jobName";
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}
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$command .= " -w \"ended($outputDir/$outputBam.cleaned)\" java -Xmx4096m -jar $sting/dist/GenomeAnalysisTK.jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam --output_bam $bam --cleaned_reads $cleanedBam -compress 1";
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if ($dry) {
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print "$command\n";
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} else {
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system($command);
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}
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}
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#!/usr/bin/perl -w
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use strict;
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use Getopt::Long;
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sub usage {
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print "Usage: perl runPilot1Pipeline.pl\n\t-i <input dir>\n\t-o <output directory>\n\t[-sting Sting dir]\n\t[-q farm queue; default:gsa]\n\t[-dry]\n";
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exit(1);
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}
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my $inputDir = undef;
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my $outputDir = undef;
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my $dry;
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my $queue = "gsa";
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my $sting = "/humgen/gsa-scr1/ebanks/Sting";
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GetOptions( "i=s" => \$inputDir,
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"odir=s" => \$outputDir,
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"q:s" => \$queue,
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"dry!" => \$dry,
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"sting:s" => \$sting );
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usage() if ( !$inputDir || !$outputDir );
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my @samples = ("ceu","yri","chb_jpt");
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foreach my $sample (@samples) {
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$inputBam = "$inputDir/low_coverage_$sample.bam";
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$outputHead = "$outputDir/$sample";
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clean($inputBam, $outputDir, "$outputHead.bam", $queue, $sting, $dry);
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# call($outputBam, $outputHead, $queue, $sting, $dry);
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}
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sub clean {
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my $inputBam = $_[0];
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my $outputDir = $_[1];
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my $outputBam = $_[2];
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my $queue = $_[3];
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my $sting = $_[4];
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my $dry = $_[5];
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my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -odir $outputDir -obam $outputBam -q $queue -j $outputBam.cleaningpipeline -sting $sting";
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if ($dry) {
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$cmd .= " -dry";
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}
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system($cmd);
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}
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sub call {
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my $inputBam = $_[0];
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my $outputHead = $_[1];
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my $queue = $_[2];
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my $sting = $_[3];
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my $dry = $_[4];
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$cmd = "perl $sting/perl/1kgScripts/runCallingPipeline.pl -i $inputBam -o $outputHead -q $queue -wait $inputBam.cleaningpipeline -sting $sting";
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if ($dry) {
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$cmd .= " -dry";
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}
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system($cmd);
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}
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#!/usr/bin/perl -w
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use strict;
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use Getopt::Long;
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sub usage {
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print "Usage: perl runPilot2Pipeline.pl\n\t-i <input dir>\n\t-o <output directory>\n\t[-sting Sting dir]\n\t[-q farm queue; default:gsa]\n\t[-dry]\n";
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exit(1);
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}
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my $inputDir = undef;
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my $outputDir = undef;
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my $dry;
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my $queue = "gsa";
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my $sting = "/humgen/gsa-scr1/ebanks/Sting";
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GetOptions( "i=s" => \$inputDir,
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"odir=s" => \$outputDir,
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"q:s" => \$queue,
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"dry!" => \$dry,
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"sting:s" => \$sting );
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usage() if ( !$inputDir || !$outputDir );
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my @samples = ("NA19238","NA19239","NA19240","NA12878","NA12891","NA12892");
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foreach my $sample (@samples) {
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my $inputBamSLX = "$inputDir/$sample.pilot2.SLX.bam";
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my $outputHead = "$outputDir/$sample.SLX";
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clean($inputBamSLX, $outputDir, "$outputHead.bam", $queue, $sting, $dry);
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# call($outputBam, $outputHead, $queue, $sting, $dry);
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if ($sample eq "NA12878" || $sample eq "NA19240") {
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my $inputBamSOLID = "$inputDir/$sample.pilot2.SOLID.bam";
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$outputHead = "$outputDir/$sample.SOLID";
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clean($inputBamSOLID, $outputDir, "$outputHead.bam", $queue, $sting, $dry);
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# call($outputBam, $outputHead, $queue, $sting, $dry);
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my $inputBam454 = "$inputDir/$sample.pilot2.454.bam";
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$outputHead = "$outputDir/$sample.454";
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# call($inputBam454, $outputHead, $queue, $sting, $dry);
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my @inputBams = ($inputBamSOLID, $inputBam454);
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$outputHead = "$outputDir/$sample.SOLID_454";
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# multicall($inputBams, $outputHead, $queue, $sting, $dry);
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@inputBams = ($inputBamSLX, $inputBamSOLID, $inputBam454);
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$outputHead = "$outputDir/$sample.allTechs";
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# multicall($inputBams, $outputHead, $queue, $sting, $dry);
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}
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}
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sub clean {
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my $inputBam = $_[0];
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my $outputDir = $_[1];
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my $outputBam = $_[2];
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my $queue = $_[3];
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my $sting = $_[4];
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my $dry = $_[5];
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my $cmd = "perl $sting/perl/1kgScripts/runCleaningPipeline.pl -i $inputBam -odir $outputDir -obam $outputBam -q $queue -inject -j $outputBam.cleaningpipeline -sting $sting";
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if ($dry) {
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$cmd .= " -dry";
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}
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system($cmd);
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}
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sub call {
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my $inputBam = $_[0];
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my $outputHead = $_[1];
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my $queue = $_[2];
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my $sting = $_[3];
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my $dry = $_[4];
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my $cmd = "perl $sting/perl/1kgScripts/runCallingPipeline.pl -i $inputBam -o $outputHead -q $queue -snps -wait $inputBam.cleaningpipeline -sting $sting";
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if ($dry) {
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$cmd .= " -dry";
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}
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system($cmd);
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}
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#perl /humgen/gsa-scr1/ebanks/Sting/perl/1kgScripts/runPilot1Pipeline.pl -i /humgen/gsa-hphome1/projects/1kg_pilot1/mergedBamsByPopulation -o /broad/hptmp/ebanks/1kg_pilot1/cleaned -dry
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perl /humgen/gsa-scr1/ebanks/Sting/perl/1kgScripts/runPilot2Pipeline.pl -i /broad/1KG/DCC_merged/freeze5.2 -o /broad/hptmp/ebanks/1kg_pilot2/cleaned -dry
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@ -1,111 +0,0 @@
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#!/usr/bin/perl -w
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use strict;
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use Getopt::Long;
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my $walker = undef;
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my $pilot = "pilot2";
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my $queue = "gsa";
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my $tech = "SLX";
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my $jar = "/humgen/gsa-scr1/ebanks/Sting/dist/GenomeAnalysisTK.jar";
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GetOptions( "T=s" => \$walker,
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"p:s" => \$pilot,
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"q:s" => \$queue,
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"tech:s" => \$tech,
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"j:s" => \$jar );
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exit(1) if ( !$walker );
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my @samples;
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if ($pilot eq "pilot1") {
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@samples = ("CEU","YRI","CHB-JPT");
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} elsif ($pilot eq "pilot2") {
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@samples = ("NA19238","NA19239","NA19240","NA12878","NA12891","NA12892");
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}
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foreach my $sample (@samples) {
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my $num = 1;
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while ($num < 23) {
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enqueue($sample, $num, $pilot, $queue, $jar, $walker, $tech);
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$num++;
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}
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enqueue($sample, "X", $pilot, $queue, $jar, $walker, $tech);
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enqueue($sample, "Y", $pilot, $queue, $jar, $walker, $tech);
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}
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sub enqueue {
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my $sample = $_[0];
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my $chr = $_[1];
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my $pilot = $_[2];
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my $queue = $_[3];
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my $jar = $_[4];
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my $walker = $_[5];
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my $tech = $_[6];
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my $inputBam;
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if ($pilot eq "pilot2") {
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$inputBam = "/broad/1KG/DCC/ftp/pilot_data/$sample/alignment/$sample.chrom$chr.$tech.SRP000032.2009_07.bam";
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} else {
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$inputBam = "/broad/hptmp/ebanks/1kg_pilot1/".$sample."_BAMS.list";
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}
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my $outputDir;
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if ($pilot eq "pilot1") {
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$outputDir = "/broad/hptmp/ebanks/1kg_pilot1/cleaned";
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} else {
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$outputDir = "/broad/hptmp/ebanks/1kg_pilot2/cleaned";
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}
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my $cmd;
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my $outputFile;
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SWITCH: {
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$walker eq "IndelIntervals" && do {
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$outputFile = "$outputDir/intervals/$sample.chr$chr.$tech.indels.intervals";
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$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IndelIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr";
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last SWITCH;
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};
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$walker eq "MismatchIntervals" && do {
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$outputFile = "$outputDir/intervals/$sample.chr$chr.$tech.mismatches.intervals";
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$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T MismatchIntervals -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr";
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last SWITCH;
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};
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$walker eq "SNPClusters" && do {
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$outputFile = "$outputDir/intervals/$sample.chr$chr.$tech.clusters.intervals";
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$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T SNPClusters -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr";
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last SWITCH;
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};
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$walker eq "IntervalMerger" && do {
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$outputFile = "$outputDir/intervals/$sample.chr$chr.$tech.merged.intervals";
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$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IntervalMerger -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr -intervals $outputDir/intervals/$sample.chr$chr.$tech.indels.intervals -intervals $outputDir/intervals/$sample.chr$chr.$tech.mismatches.intervals";
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last SWITCH;
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};
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$walker eq "IntervalCleaner" && do {
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if ($pilot eq "pilot2") {
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$outputFile = "$outputDir/cleaner/$sample.chr$chr.$tech.bam";
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} else {
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$outputFile = "$outputDir/bams/$sample.chr$chr.$tech.bam";
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}
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$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T IntervalCleaner -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -O $outputFile -L $chr -intervals $outputDir/intervals/$sample.chr$chr.$tech.merged.intervals -compress 1";
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if ($pilot eq "pilot2") {
|
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$cmd .= " -cleanedOnly";
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}
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last SWITCH;
|
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};
|
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$walker eq "CleanedReadInjector" && do {
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$outputFile = "$outputDir/bams/$sample.chr$chr.$tech.bam";
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$cmd = "bsub -q $queue -o $outputFile.sdout java -Xmx4096m -jar $jar -S SILENT -T CleanedReadInjector -R /broad/1KG/reference/human_b36_both.fasta -I $inputBam -o $outputFile -L $chr";
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last SWITCH;
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||||
};
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||||
|
||||
print "$walker is not a supported class\n";
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||||
exit(1);
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||||
}
|
||||
|
||||
# print "$cmd\n";
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system($cmd);
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||||
}
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@ -0,0 +1,151 @@
|
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#!/usr/bin/perl -w
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|
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# Runs a given GATK walker genome-wide, but splits up the jobs
|
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# and then merges the results together. One should really use
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# scatter-gather here, but I wanted to test against that framework
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# (to ensure consistency) so I wrote this temporary script.
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# Also, it allowed me to add in farm commands for wait ids
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# (which is currently unavailable in scatter-gather).
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# If intervals file is left blank, it splits by chromosome.
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use strict;
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||||
use Getopt::Long;
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||||
|
||||
sub usage {
|
||||
print "Usage: perl enqueueGATKjobsByChromosome.pl\n\t-cmd <GATK command without output or -L args>\n\t-o <output file>\n\t[-oarg GATK output argument; default:o]\n\t[-i intervals file]\n\t[-n number of splits to make]\n\t[-q farm queue; default:gsa]\n\t[-wait farm wait id]\n\t[-job farm job name]\n\t[-dry]\n\t[-bam is output format bam?; default:no]\n";
|
||||
exit(1);
|
||||
}
|
||||
|
||||
my $cmd = undef;
|
||||
my $output = undef;
|
||||
my $outputArg = "o";
|
||||
my $jobName = undef;
|
||||
my $wait = undef;
|
||||
my $queue = "gsa";
|
||||
my $breaks = 24;
|
||||
my $intervalsFile = undef;
|
||||
my $dry;
|
||||
my $isBam;
|
||||
|
||||
GetOptions( "cmd=s" => \$cmd,
|
||||
"o=s" => \$output,
|
||||
"oarg:s" => \$outputArg,
|
||||
"job:s" => \$jobName,
|
||||
"wait:s" => \$wait,
|
||||
"n:i" => \$breaks,
|
||||
"i:s" => \$intervalsFile,
|
||||
"dry!" => \$dry,
|
||||
"bam!" => \$isBam,
|
||||
"q:s" => \$queue);
|
||||
|
||||
usage() if ( !$cmd || !$output );
|
||||
|
||||
my @intervals;
|
||||
if (!$intervalsFile) {
|
||||
my $num = 1;
|
||||
while ($num < 23) {
|
||||
push(@intervals, $num);
|
||||
$num++;
|
||||
}
|
||||
push(@intervals, "X");
|
||||
push(@intervals, "Y");
|
||||
} else {
|
||||
open(FILE, "< $intervalsFile") or die "can't open $intervalsFile: $!";
|
||||
my @lines = <FILE>;
|
||||
chomp(@lines);
|
||||
my $linecount = scalar(@lines);
|
||||
if ($linecount < $breaks) {
|
||||
$breaks = $linecount;
|
||||
}
|
||||
|
||||
my $linesPerJob = $linecount / $breaks;
|
||||
my $index = 0;
|
||||
for (my $i = 1; $i < $breaks; $i++) {
|
||||
my $interval = "";
|
||||
for (my $j = 0; $j < $linesPerJob; $j++) {
|
||||
$interval .= "$lines[$index];";
|
||||
$index++;
|
||||
}
|
||||
push(@intervals, $interval);
|
||||
}
|
||||
my $interval = "";
|
||||
while ($index < $linecount) {
|
||||
$interval .= "$lines[$index];";
|
||||
$index++;
|
||||
}
|
||||
push(@intervals, $interval);
|
||||
}
|
||||
|
||||
my $intervalcount = scalar(@intervals);
|
||||
for (my $i = 0; $i < $intervalcount; $i++) {
|
||||
enqueue($intervals[$i], $cmd, $output, $outputArg, $wait, $queue, $dry, $isBam, ($i+1));
|
||||
}
|
||||
|
||||
mergeResults($output, $queue, $dry, $isBam, $jobName, $intervalcount);
|
||||
|
||||
sub enqueue {
|
||||
|
||||
my $interval = $_[0];
|
||||
my $cmd = $_[1];
|
||||
my $outArg = $_[3];
|
||||
my $waitid = $_[4];
|
||||
my $queue = $_[5];
|
||||
my $dry = $_[6];
|
||||
my $bam = $_[7];
|
||||
my $index = $_[8];
|
||||
|
||||
my $output = "$_[2].$index";
|
||||
if ($bam) {
|
||||
$output .= ".bam";
|
||||
}
|
||||
|
||||
my $bsub = "bsub -q $queue -o $output.sdout -J $_[2]";
|
||||
if ($waitid) {
|
||||
$bsub .= " -w \"ended($waitid)\"";
|
||||
}
|
||||
|
||||
my $command = "$bsub $cmd -$outputArg $output -L $interval";
|
||||
execute($command, $dry);
|
||||
}
|
||||
|
||||
sub mergeResults {
|
||||
|
||||
my $output = $_[0];
|
||||
my $queue = $_[1];
|
||||
my $dry = $_[2];
|
||||
my $bam = $_[3];
|
||||
my $jobName = $_[4];
|
||||
my $intervalcount = $_[5];
|
||||
|
||||
my $cmd = "bsub -q $queue -o $output.sdout -w \"ended($output)\"";
|
||||
if ($jobName) {
|
||||
$cmd .= " -J $jobName";
|
||||
}
|
||||
|
||||
if ($bam) {
|
||||
$cmd .= " samtools merge $output ";
|
||||
for (my $i = 1; $i <= $intervalcount; $i++) {
|
||||
$cmd .= "$output.$i.bam ";
|
||||
}
|
||||
} else {
|
||||
$cmd .= " cat ";
|
||||
for (my $i = 1; $i <= $intervalcount; $i++) {
|
||||
$cmd .= "$output.$i ";
|
||||
}
|
||||
$cmd .= "> $output";
|
||||
}
|
||||
|
||||
execute($cmd, $dry);
|
||||
}
|
||||
|
||||
sub execute {
|
||||
|
||||
my $cmd = $_[0];
|
||||
my $dry = $_[1];
|
||||
|
||||
if ($dry) {
|
||||
print "$cmd\n";
|
||||
} else {
|
||||
system($cmd);
|
||||
}
|
||||
}
|
||||
Loading…
Reference in New Issue