src/toil_lib/tools/preprocessing.py
def run_samblaster(job, sam):
    """
    Marks reads as PCR duplicates using SAMBLASTER

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str sam: FileStoreID for SAM file
    :return: FileStoreID for deduped SAM file
    :rtype: str
    """
    work_dir = job.fileStore.getLocalTempDir()
    job.fileStore.readGlobalFile(sam, os.path.join(work_dir, 'input.sam'))
    command = ['/usr/local/bin/samblaster',
               '-i', '/data/input.sam',
               '-o', '/data/output.sam',
               '--ignoreUnmated']

    start_time = time.time()
    dockerCall(job=job, workDir=work_dir,
               parameters=command,
               tool='quay.io/biocontainers/samblaster:0.1.24--0')
    end_time = time.time()
    _log_runtime(job, start_time, end_time, "SAMBLASTER")
    return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'output.sam'))
def run_samblaster(job, sam):
    work_dir = job.fileStore.getLocalTempDir()
    job.fileStore.readGlobalFile(sam, os.path.join(work_dir, 'input.sam'))
    command = ['/usr/local/bin/samblaster',
               '-i', '/data/input.sam',
               '-o', '/data/output.sam',
               '--ignoreUnmated']

    start_time = time.time()
    dockerCall(job=job, workDir=work_dir,
               parameters=command,
               tool='quay.io/biocontainers/samblaster:0.1.24--0')
    end_time = time.time()
    _log_runtime(job, start_time, end_time, "SAMBLASTER")
    return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'output.sam'))
def run_samblaster ( job , sam ) : work_dir = job . fileStore . getLocalTempDir ( ) job . fileStore . readGlobalFile ( sam , os . path . join ( work_dir , 'input.sam' ) ) command = [ '/usr/local/bin/samblaster' , '-i' , '/data/input.sam' , '-o' , '/data/output.sam' , '--ignoreUnmated' ] start_time = time . time ( ) dockerCall ( job = job , workDir = work_dir , parameters = command , tool = 'quay.io/biocontainers/samblaster:0.1.24--0' ) end_time = time . time ( ) _log_runtime ( job , start_time , end_time , "SAMBLASTER" ) return job . fileStore . writeGlobalFile ( os . path . join ( work_dir , 'output.sam' ) )
Marks reads as PCR duplicates using SAMBLASTER

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str sam: FileStoreID for SAM file
    :return: FileStoreID for deduped SAM file
    :rtype: str
Marks reads as PCR duplicates using SAMBLASTER