def usage()

in src/main/scripts/sc_rna_expression_cellranger_fastq.py [0:0]

• 37 lines of code
• 1 McCabe index (conditional complexity)

def usage():
    print('Usage:\n')
    print('-s <species> (required)          The species (human/mouse).\n')
    print('-t <read_type>                   The read type (paired/single).\n')
    print('-j <job_name>                    The job ID.\n')
    print('-o <dir_out> (required)          The output directory for the analysis.\n')
    print('-b <feature_reference>           A feature reference csv file that declares the set of Feature Barcode '
          'reagents in use in the experiment.\n')
    print('-x <target_panel>                Target panel csv path.\n')
    print('-l <fastq_list> (required)       The path to the input manifest file or fastq folder '
          'or comma-delimited fastq file list for R1.\n')
    print('-q <fastq_list_r2>               The comma-delimited fastq file list for R2.\n')
    print('-L <library_type>                The list of library types of each libraries will enable additional '
          'downstream processing, specifically for CRISPR Guide Capture and Antibody Capture.\n')
    print('-M <master>                      The list of the overall sample names.\n')
    print('-e <expected_cells>              The expected number of recovered cells.\n')
    print('-f <forced_cells>                Force pipeline to use this number of cells, bypassing the cell '
          'detection algorithm.\n')
    print('-c <chemistry> (required)        Assay configuration.\n')
    print('-a <nosecondary>                 Skip secondary analysis of the feature-barcode matrix.\n')
    print('-R <r1_length> (required)        Hard-trim the input R1 sequence to this length.\n')
    print('-r <r2_length> (required)        Hard-trim the input R2 sequence to this length.\n')
    print('-G <genome_build> (required)     Genome build.\n')
    print('-m <transcriptome> (required)    Path to the Cell Ranger compatible transcriptome reference.\n')
    print('-g <vdj_genome> (required)       Path to the Cell Ranger V(D)J compatible reference.\n')
    print('-d <detect_doublet>              If enabled, doubletdetection step will be added to the toolset.\n')
    print('-p <project>                     The project ID.\n')
    print('-u <run>                         The run ID.\n')
    print('-n <toolset>                     A number of tools to run in a specific pipeline.\n')
    print('-k <cores_per_sample>            A number of cores per sample for sge cluster.\n')
    print('--sync                           The flag (true/false) enables or disables "-sync" option '
          '("true" by default).\n')
    print('-i <sample_name_list>            The comma-delimited list of sample names.\n')
    print('-z <toolchain> (required)        A user-defined toolchain.\n')
    print('-F <mem_free>                    Restricts cellranger to use specified amount of memory (in GB).\n')
    print('--master_mode                    The flag enables "-master" option.\n')
    print('-v <verbose>                     The enable debug verbosity output.\n')