src/toil_lib/tools/preprocessing.py
def run_samtools_faidx(job, ref_id):
    """
    Use SAMtools to create reference index file

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str ref_id: FileStoreID for the reference genome
    :return: FileStoreID for reference index
    :rtype: str
    """
    job.fileStore.logToMaster('Created reference index')
    work_dir = job.fileStore.getLocalTempDir()
    job.fileStore.readGlobalFile(ref_id, os.path.join(work_dir, 'ref.fasta'))
    command = ['faidx', 'ref.fasta']
    dockerCall(job=job, workDir=work_dir, parameters=command,
               tool='quay.io/ucsc_cgl/samtools:0.1.19--dd5ac549b95eb3e5d166a5e310417ef13651994e')
    return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'ref.fasta.fai'))
def run_samtools_faidx(job, ref_id):
    job.fileStore.logToMaster('Created reference index')
    work_dir = job.fileStore.getLocalTempDir()
    job.fileStore.readGlobalFile(ref_id, os.path.join(work_dir, 'ref.fasta'))
    command = ['faidx', 'ref.fasta']
    dockerCall(job=job, workDir=work_dir, parameters=command,
               tool='quay.io/ucsc_cgl/samtools:0.1.19--dd5ac549b95eb3e5d166a5e310417ef13651994e')
    return job.fileStore.writeGlobalFile(os.path.join(work_dir, 'ref.fasta.fai'))
def run_samtools_faidx ( job , ref_id ) : job . fileStore . logToMaster ( 'Created reference index' ) work_dir = job . fileStore . getLocalTempDir ( ) job . fileStore . readGlobalFile ( ref_id , os . path . join ( work_dir , 'ref.fasta' ) ) command = [ 'faidx' , 'ref.fasta' ] dockerCall ( job = job , workDir = work_dir , parameters = command , tool = 'quay.io/ucsc_cgl/samtools:0.1.19--dd5ac549b95eb3e5d166a5e310417ef13651994e' ) return job . fileStore . writeGlobalFile ( os . path . join ( work_dir , 'ref.fasta.fai' ) )
Use SAMtools to create reference index file

    :param JobFunctionWrappingJob job: passed automatically by Toil
    :param str ref_id: FileStoreID for the reference genome
    :return: FileStoreID for reference index
    :rtype: str
Use SAMtools to create reference index file