src/toil_lib/tools/preprocessing.py
def picard_mark_duplicates(job, bam, bai, validation_stringency='LENIENT'):
    """
    Runs Picard MarkDuplicates on a BAM file. Requires that the BAM file be coordinate sorted.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str bam: FileStoreID for BAM file
    :param str bai: FileStoreID for BAM index file
    :param str validation_stringency: BAM file validation stringency, default is LENIENT
    :return: FileStoreIDs for BAM and BAI files
    :rtype: tuple
    """
    work_dir = job.fileStore.getLocalTempDir()

    # Retrieve file path
    job.fileStore.readGlobalFile(bam, os.path.join(work_dir, 'sorted.bam'))
    job.fileStore.readGlobalFile(bai, os.path.join(work_dir, 'sorted.bai'))

    # Call: picardtools
    command = ['MarkDuplicates',
               'INPUT=sorted.bam',
               'OUTPUT=mkdups.bam',
               'METRICS_FILE=metrics.txt',
               'ASSUME_SORTED=true',
               'CREATE_INDEX=true',
               'VALIDATION_STRINGENCY=%s' % validation_stringency.upper()]

    # picard-tools container doesn't have JAVA_OPTS variable
    # Set TMPDIR to /data to prevent writing temporary files to /tmp
    docker_parameters = ['--rm',
                         '--log-driver', 'none',
                         '-e', 'JAVA_OPTIONS=-Djava.io.tmpdir=/data/ -Xmx{}'.format(job.memory),
                         '-v', '{}:/data'.format(work_dir)]

    start_time = time.time()
    dockerCall(job=job, workDir=work_dir,
               parameters=command,
               tool='quay.io/ucsc_cgl/picardtools:1.95--dd5ac549b95eb3e5d166a5e310417ef13651994e',
               dockerParameters=docker_parameters)
    end_time = time.time()
    _log_runtime(job, start_time, end_time, "Picard MarkDuplicates")

    bam = job.fileStore.writeGlobalFile(os.path.join(work_dir, 'mkdups.bam'))
    bai = job.fileStore.writeGlobalFile(os.path.join(work_dir, 'mkdups.bai'))
    return bam, bai
def picard_mark_duplicates(job, bam, bai, validation_stringency='LENIENT'):
    work_dir = job.fileStore.getLocalTempDir()

    # Retrieve file path
    job.fileStore.readGlobalFile(bam, os.path.join(work_dir, 'sorted.bam'))
    job.fileStore.readGlobalFile(bai, os.path.join(work_dir, 'sorted.bai'))

    # Call: picardtools
    command = ['MarkDuplicates',
               'INPUT=sorted.bam',
               'OUTPUT=mkdups.bam',
               'METRICS_FILE=metrics.txt',
               'ASSUME_SORTED=true',
               'CREATE_INDEX=true',
               'VALIDATION_STRINGENCY=%s' % validation_stringency.upper()]

    # picard-tools container doesn't have JAVA_OPTS variable
    # Set TMPDIR to /data to prevent writing temporary files to /tmp
    docker_parameters = ['--rm',
                         '--log-driver', 'none',
                         '-e', 'JAVA_OPTIONS=-Djava.io.tmpdir=/data/ -Xmx{}'.format(job.memory),
                         '-v', '{}:/data'.format(work_dir)]

    start_time = time.time()
    dockerCall(job=job, workDir=work_dir,
               parameters=command,
               tool='quay.io/ucsc_cgl/picardtools:1.95--dd5ac549b95eb3e5d166a5e310417ef13651994e',
               dockerParameters=docker_parameters)
    end_time = time.time()
    _log_runtime(job, start_time, end_time, "Picard MarkDuplicates")

    bam = job.fileStore.writeGlobalFile(os.path.join(work_dir, 'mkdups.bam'))
    bai = job.fileStore.writeGlobalFile(os.path.join(work_dir, 'mkdups.bai'))
    return bam, bai
def picard_mark_duplicates ( job , bam , bai , validation_stringency = 'LENIENT' ) : work_dir = job . fileStore . getLocalTempDir ( ) # Retrieve file path job . fileStore . readGlobalFile ( bam , os . path . join ( work_dir , 'sorted.bam' ) ) job . fileStore . readGlobalFile ( bai , os . path . join ( work_dir , 'sorted.bai' ) ) # Call: picardtools command = [ 'MarkDuplicates' , 'INPUT=sorted.bam' , 'OUTPUT=mkdups.bam' , 'METRICS_FILE=metrics.txt' , 'ASSUME_SORTED=true' , 'CREATE_INDEX=true' , 'VALIDATION_STRINGENCY=%s' % validation_stringency . upper ( ) ] # picard-tools container doesn't have JAVA_OPTS variable # Set TMPDIR to /data to prevent writing temporary files to /tmp docker_parameters = [ '--rm' , '--log-driver' , 'none' , '-e' , 'JAVA_OPTIONS=-Djava.io.tmpdir=/data/ -Xmx{}' . format ( job . memory ) , '-v' , '{}:/data' . format ( work_dir ) ] start_time = time . time ( ) dockerCall ( job = job , workDir = work_dir , parameters = command , tool = 'quay.io/ucsc_cgl/picardtools:1.95--dd5ac549b95eb3e5d166a5e310417ef13651994e' , dockerParameters = docker_parameters ) end_time = time . time ( ) _log_runtime ( job , start_time , end_time , "Picard MarkDuplicates" ) bam = job . fileStore . writeGlobalFile ( os . path . join ( work_dir , 'mkdups.bam' ) ) bai = job . fileStore . writeGlobalFile ( os . path . join ( work_dir , 'mkdups.bai' ) ) return bam , bai
Runs Picard MarkDuplicates on a BAM file. Requires that the BAM file be coordinate sorted.

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str bam: FileStoreID for BAM file
    :param str bai: FileStoreID for BAM index file
    :param str validation_stringency: BAM file validation stringency, default is LENIENT
    :return: FileStoreIDs for BAM and BAI files
    :rtype: tuple
Runs Picard MarkDuplicates on a BAM file . Requires that the BAM file be coordinate sorted .