Examples with VersionedToolCommand com.hartwig.pipeline.calling.command.VersionedToolCommand used on opensource projects

Example 1 with VersionedToolCommand

use of com.hartwig.pipeline.calling.command.VersionedToolCommand in project pipeline5 by hartwigmedical.

the class RnaStarMapping method execute.

@Override
public VirtualMachineJobDefinition execute(InputBundle inputs, RuntimeBucket bucket, BashStartupScript startupScript, RuntimeFiles executionFlags) {
    InputFileDescriptor descriptor = inputs.get();
    final String batchInputs = descriptor.inputValue();
    final String[] batchItems = batchInputs.split(",");
    // required format: SampleId,RefGenomeVersion (37 by default),FASTA file bucket
    /*
        if(batchItems.length != 2)
        {
            System.out.print(String.format("invalid input arguments(%s) - expected SampleId,RefGenomeVersion,FastqFileBucketDir", batchInputs));
            return null;
        }
        */
    final String sampleId = batchItems[0];
    final RefGenomeVersion refGenomeVersion = batchItems.length >= 2 ? RefGenomeVersion.valueOf(batchItems[1]) : V37;
    final String sampleBucket = batchItems[2];
    /*
        if(batchItems.length >= 3)
        {
            final String fastqFilelist = batchItems[2];

            final List<String> sampleFastqFiles = getSampleFastqFileList(sampleId, fastqFilelist);

            if(sampleFastqFiles.isEmpty()) {
                System.out.print(String.format("sampleId(%s) fastq files not found", sampleId));
                return null;
            }

            // copy down FASTQ files for this sample
            for(final String fastqFile : sampleFastqFiles)
            {
                startupScript.addCommand(() -> format("gsutil -u hmf-crunch cp %s %s", fastqFile, VmDirectories.INPUT));
            }
        }
        else
        {
            // expected location: "gs://cpct02010255tii-rna-reads/1.3/CPCT02010255TII_AHWGLNBGX5_S4_L002_R1_001.fastq.gz
            final String sampleFastqFiles = String.format("gs://%s-rna-reads/1.3/*.fastq.gz", sampleId.toLowerCase());
            startupScript.addCommand(() -> format("gsutil -u hmf-crunch cp %s %s", sampleFastqFiles, VmDirectories.INPUT));
        }
        */
    final String sampleFastqFiles = String.format("%s/*.fastq.gz", sampleBucket);
    startupScript.addCommand(() -> format("gsutil -u hmf-crunch cp %s %s", sampleFastqFiles, VmDirectories.INPUT));
    // locate the FASTQ files for reads 1 and 2
    final String r1Files = format("$(ls %s/*_R1* | tr '\\n' ',')", VmDirectories.INPUT);
    final String r2Files = format("$(ls %s/*_R2* | tr '\\n' ',')", VmDirectories.INPUT);
    // copy reference files for STAR
    final String starGenomeDir = getRnaResourceDirectory(refGenomeVersion, STAR_DIR);
    final String localStarGenomeDir = String.format("%s/%s", VmDirectories.INPUT, STAR_DIR);
    startupScript.addCommand(() -> format("mkdir %s", localStarGenomeDir));
    startupScript.addCommand(() -> format("gsutil -u hmf-crunch cp %s/* %s", starGenomeDir, localStarGenomeDir));
    final String threadCount = Bash.allCpus();
    startupScript.addCommand(() -> format("cd %s", VmDirectories.OUTPUT));
    // run the STAR mapper
    final String[] starArgs = { "--runThreadN", threadCount, "--genomeDir", localStarGenomeDir, "--genomeLoad", "NoSharedMemory", "--readFilesIn", r1Files, r2Files, "--readFilesCommand", "zcat", "--outSAMtype", "BAM", "Unsorted", "--outSAMunmapped", "Within", "--outBAMcompression", "0", "--outSAMattributes", "All", "--outFilterMultimapNmax", "10", "--outFilterMismatchNmax", "3", "limitOutSJcollapsed", "3000000", "--chimSegmentMin", "10", "--chimOutType", "WithinBAM", "SoftClip", "--chimJunctionOverhangMin", "10", "--chimSegmentReadGapMax", "3", "--chimScoreMin", "1", "--chimScoreDropMax", "30", "--chimScoreJunctionNonGTAG", "0", "--chimScoreSeparation", "1", "--outFilterScoreMinOverLread", "0.33", "--outFilterMatchNminOverLread", "0.33", "--outFilterMatchNmin", "35", "--alignSplicedMateMapLminOverLmate", "0.33", "--alignSplicedMateMapLmin", "35", "--alignSJstitchMismatchNmax", "5", "-1", "5", "5" };
    startupScript.addCommand(new VersionedToolCommand("star", "STAR", "2.7.3a", starArgs));
    final String bamFile = "Aligned.out.bam";
    // sort the BAM
    final String sortedBam = sampleId + ".sorted.bam";
    final String[] sortArgs = { "sort", "-@", threadCount, "-m", "2G", "-T", "tmp", "-O", "bam", bamFile, "-o", sortedBam };
    startupScript.addCommand(new VersionedToolCommand("samtools", "samtools", Versions.SAMTOOLS, sortArgs));
    // mark duplicate fragment reads within the BAM
    final String sortedDedupedBam = sampleId + ".sorted.dups.bam";
    final String[] dupArgs = { "markdup", "-t", threadCount, "--overflow-list-size=45000000", sortedBam, sortedDedupedBam };
    startupScript.addCommand(new SambambaCommand(dupArgs));
    final String[] indexArgs = { "index", sortedDedupedBam };
    startupScript.addCommand(new VersionedToolCommand("samtools", "samtools", Versions.SAMTOOLS, indexArgs));
    // clean up intermediary BAMs
    startupScript.addCommand(() -> format("rm -f %s", bamFile));
    startupScript.addCommand(() -> format("rm -f %s", sortedBam));
    final String starStats = "Log.final.out";
    final String statsFile = sampleId + "." + starStats;
    startupScript.addCommand(() -> format("mv %s %s", starStats, statsFile));
    // run QC stats on the fast-Qs as well
    // final String fastqcOutputDir = format("%s/fastqc", VmDirectories.OUTPUT);
    // startupScript.addCommand(() -> format("mkdir %s", fastqcOutputDir));
    // final String allFastQs = format("%s/*gz", VmDirectories.INPUT);
    // final String[] fastqcArgs = {"-o", fastqcOutputDir, allFastQs};
    // TEMP until reimage has taken place
    // startupScript.addCommand(() -> format("chmod a+x /opt/tools/fastqc/0.11.4/fastqc"));
    // startupScript.addCommand(new VersionedToolCommand("fastqc", "fastqc", "0.11.4", fastqcArgs));
    // upload the results
    startupScript.addCommand(new OutputUpload(GoogleStorageLocation.of(bucket.name(), "star"), executionFlags));
    // copy results to crunch
    final String samplesDir = String.format("%s/%s", getRnaCohortDirectory(refGenomeVersion), "samples");
    startupScript.addCommand(() -> format("gsutil -m cp %s/* %s/%s/", VmDirectories.OUTPUT, samplesDir, sampleId));
    return ImmutableVirtualMachineJobDefinition.builder().name("rna-star-mapping").startupCommand(startupScript).namespacedResults(ResultsDirectory.defaultDirectory()).workingDiskSpaceGb(500).performanceProfile(VirtualMachinePerformanceProfile.custom(12, 48)).build();
}

Example 2 with VersionedToolCommand

use of com.hartwig.pipeline.calling.command.VersionedToolCommand in project pipeline5 by hartwigmedical.

the class SageCreatePonData method cramToBam.

private List<BashCommand> cramToBam(String cram) {
    final String output = cram.replace("cram", "bam");
    final BashCommand toBam = new VersionedToolCommand("samtools", "samtools", Versions.SAMTOOLS, "view", "-o", output, "-O", "bam", "-@", Bash.allCpus(), cram);
    final BashCommand index = new VersionedToolCommand("samtools", "samtools", Versions.SAMTOOLS, "index", "-@", Bash.allCpus(), output);
    return Lists.newArrayList(toBam, index);
}

Example 3 with VersionedToolCommand

use of com.hartwig.pipeline.calling.command.VersionedToolCommand in project pipeline5 by hartwigmedical.

the class SageRerunOld method cramToBam.

static List<BashCommand> cramToBam(String cram) {
    final String output = cram.replace("cram", "bam");
    final BashCommand toBam = new VersionedToolCommand("samtools", "samtools", Versions.SAMTOOLS, "view", "-o", output, "-O", "bam", "-@", Bash.allCpus(), cram);
    final BashCommand index = new VersionedToolCommand("samtools", "samtools", Versions.SAMTOOLS, "index", "-@", Bash.allCpus(), output);
    return Lists.newArrayList(toBam, index);
}

Example 4 with VersionedToolCommand

use of com.hartwig.pipeline.calling.command.VersionedToolCommand in project pipeline5 by hartwigmedical.

the class FlagstatGenerator method execute.

@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket bucket, final BashStartupScript startupScript, final RuntimeFiles executionFlags) {
    InputFileDescriptor input = inputs.get();
    InputFileDescriptor existingFlagstat = InputFileDescriptor.from(input).withInputValue(input.inputValue().replaceAll("\\.bam$", ".flagstat"));
    String localCopyOfOriginalFlagstat = format("%s/%s", VmDirectories.OUTPUT, new File(existingFlagstat.inputValue()).getName());
    String outputFile = VmDirectories.outputFile(new File(input.inputValue()).getName().replaceAll("\\.bam$", ".batch.flagstat"));
    String localInput = format("%s/%s", VmDirectories.INPUT, new File(input.inputValue()).getName());
    startupScript.addCommand(() -> input.toCommandForm(localInput));
    startupScript.addCommand(() -> existingFlagstat.toCommandForm(localCopyOfOriginalFlagstat));
    startupScript.addCommand(new PipeCommands(new VersionedToolCommand("sambamba", "sambamba", Versions.SAMBAMBA, "flagstat", "-t", Bash.allCpus(), localInput), () -> "tee " + outputFile));
    startupScript.addCommand(() -> format("diff %s %s", localCopyOfOriginalFlagstat, outputFile));
    startupScript.addCommand(new OutputUpload(GoogleStorageLocation.of(bucket.name(), "flagstat"), executionFlags));
    return VirtualMachineJobDefinition.builder().name("flagstat").startupCommand(startupScript).namespacedResults(ResultsDirectory.defaultDirectory()).performanceProfile(VirtualMachinePerformanceProfile.custom(4, 6)).build();
}

Example 5 with VersionedToolCommand

use of com.hartwig.pipeline.calling.command.VersionedToolCommand in project pipeline5 by hartwigmedical.

the class HlaBamSlicer method execute.

@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript commands, final RuntimeFiles executionFlags) {
    // Inputs: SampleId,ExpectedAlleles
    final InputFileDescriptor runData = inputs.get();
    final String batchInputs = runData.inputValue();
    final String[] batchItems = batchInputs.split(",");
    final String sampleId = batchItems[0];
    // final String bamType = batchItems[1];
    final String sampleBam = String.format("%s.sorted.dups.bam", sampleId);
    final String bamLocation = format("%s/%s/%s", RNA_COHORT_LOCATION_V37, sampleId, sampleBam);
    commands.addCommand(() -> format("gsutil -u hmf-crunch cp %s* %s", bamLocation, VmDirectories.INPUT));
    // get HLA bed for slicing
    commands.addCommand(() -> format("gsutil -u hmf-crunch cp %s/%s/%s %s", BATCH_RESOURCE_BUCKET, LILAC_DIR, HLA_BED_FILE, VmDirectories.INPUT));
    // /opt/tools/sambamba/0.6.8/sambamba view -f bam ./samples/CPCT02020378T/CPCT02020378T.sorted.dups.bam -L /data/lilac/ref/hla.bed
    // > ./samples/CPCT02020378T/CPCT02020378T.rna.hla.bam
    // download pilot Lilac jar
    final String sambamba = "sambamba/0.6.8/sambamba";
    final String slicedBam = String.format("%s.hla.bam", sampleId);
    commands.addCommand(() -> format("%s/%s slice %s/%s -L %s/%s -o %s/%s", VmDirectories.TOOLS, sambamba, VmDirectories.INPUT, sampleBam, VmDirectories.INPUT, HLA_BED_FILE, VmDirectories.OUTPUT, slicedBam));
    // commands.addCommand(() -> format("ls -l %s", VmDirectories.OUTPUT));
    final String slicedSortedBam = String.format("%s.rna.hla.bam", sampleId);
    // samtools sort -@ 8 -m 2G -T tmp -O bam Aligned.out.bam -o Aligned.sorted.bam
    final String[] sortArgs = { "sort", "-@", "8", "-m", "2G", "-T", "tmp", "-O", "bam", String.format("%s/%s", VmDirectories.OUTPUT, slicedBam), "-o", String.format("%s/%s", VmDirectories.OUTPUT, slicedSortedBam) };
    commands.addCommand(new VersionedToolCommand("samtools", "samtools", Versions.SAMTOOLS, sortArgs));
    // create an index
    commands.addCommand(() -> format("%s/%s index %s/%s", VmDirectories.TOOLS, sambamba, VmDirectories.OUTPUT, slicedSortedBam));
    // copy the sliced RNA bam back to the HLA BAM directory
    final String sampleHlaDir = String.format("gs://%s/%s", HLA_BAMS_BUCKET, sampleId);
    commands.addCommand(() -> format("gsutil -m cp %s/%s* %s", VmDirectories.OUTPUT, slicedSortedBam, sampleHlaDir));
    commands.addCommand(new OutputUpload(GoogleStorageLocation.of(runtimeBucket.name(), "lilac"), executionFlags));
    return ImmutableVirtualMachineJobDefinition.builder().name("lilac").startupCommand(commands).namespacedResults(ResultsDirectory.defaultDirectory()).build();
}