```bash
cwl-runner src/bd_rhapsody/bd_rhapsody_sequence_analysis/rhapsody_pipeline_2.2.1_nodocker.cwl --help
```

usage: src/bd_rhapsody/bd_rhapsody_sequence_analysis/rhapsody_pipeline_2.2.1_nodocker.cwl
       [-h] [--AbSeq_Reference ABSEQ_REFERENCE] [--AbSeq_UMI ABSEQ_UMI]
       [--Cell_Calling_ATAC_Algorithm CELL_CALLING_ATAC_ALGORITHM]
       [--Cell_Calling_Bioproduct_Algorithm CELL_CALLING_BIOPRODUCT_ALGORITHM]
       [--Cell_Calling_Data CELL_CALLING_DATA]
       [--Custom_STAR_Params CUSTOM_STAR_PARAMS]
       [--Custom_bwa_mem2_Params CUSTOM_BWA_MEM2_PARAMS]
       [--Exact_Cell_Count EXACT_CELL_COUNT] [--Exclude_Intronic_Reads]
       [--Expected_Cell_Count EXPECTED_CELL_COUNT] [--Generate_Bam]
       [--Long_Reads] [--Maximum_Threads MAXIMUM_THREADS]
       [--Predefined_ATAC_Peaks PREDEFINED_ATAC_PEAKS] [--Reads READS]
       [--Reads_ATAC READS_ATAC] [--Reference_Archive REFERENCE_ARCHIVE]
       [--Run_Name RUN_NAME] [--Sample_Tags_Version SAMPLE_TAGS_VERSION]
       [--Supplemental_Reference SUPPLEMENTAL_REFERENCE]
       [--Tag_Names TAG_NAMES] [--Target_analysis]
       [--Targeted_Reference TARGETED_REFERENCE]
       [--VDJ_JGene_Evalue VDJ_JGENE_EVALUE]
       [--VDJ_VGene_Evalue VDJ_VGENE_EVALUE] [--VDJ_Version VDJ_VERSION]
       [--Write_Filtered_Reads]
       [job_order]

The BD Rhapsody™ assays are used to create sequencing libraries from single
cell transcriptomes. After sequencing, the analysis pipeline takes the FASTQ
files and a reference file for gene alignment. The pipeline generates
molecular counts per cell, read counts per cell, metrics, and an alignment
file.

positional arguments:
  job_order             Job input json file

options:
  -h, --help            show this help message and exit
  --AbSeq_Reference ABSEQ_REFERENCE
                        AbSeq Reference
  --AbSeq_UMI ABSEQ_UMI
  --Cell_Calling_ATAC_Algorithm CELL_CALLING_ATAC_ALGORITHM
                        Specify the ATAC algorithm to be used for ATAC
                        putative cell calling. The Basic algorithm is the
                        default.
  --Cell_Calling_Bioproduct_Algorithm CELL_CALLING_BIOPRODUCT_ALGORITHM
                        Specify the bioproduct algorithm to be used for
                        mRNA/AbSeq putative cell calling. The Basic algorithm
                        is the default.
  --Cell_Calling_Data CELL_CALLING_DATA
                        Specify the data to be used for putative cell calling.
                        The default data for putative cell calling will be
                        determined the following way: - If mRNA and ATAC Reads
                        exist, mRNA_and_ATAC is the default. - If only ATAC
                        Reads exist, ATAC is the default. - Otherwise, mRNA is
                        the default.
  --Custom_STAR_Params CUSTOM_STAR_PARAMS
                        Allows you to specify custom STAR aligner mapping
                        parameters. Only the mapping parameters you provide
                        here will be used with STAR, meaning that you must
                        provide the complete list of parameters that you want
                        to take effect. For reference, the parameters used by
                        default in the pipeline are: 1. Short Reads:
                        --outFilterScoreMinOverLread 0
                        --outFilterMatchNminOverLread 0
                        --outFilterMultimapScoreRange 0 --clip3pAdapterSeq
                        AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
                        --seedSearchStartLmax 50 --outFilterMatchNmin 25
                        --limitOutSJcollapsed 2000000 2. Long Reads: Same
                        options as short reads + --seedPerReadNmax 10000
                        Example input: --alignIntronMax 500000
                        --outFilterScoreMinOverLread 0 --limitOutSJcollapsed
                        2000000 Important: 1. This applies to fastqs provided
                        in the Reads user input 2. Please do not specify any
                        non-mapping related params like: --runThreadN,
                        --genomeDir --outSAMtype, etc. 3. Please only use
                        params supported by STAR version 2.7.10b
  --Custom_bwa_mem2_Params CUSTOM_BWA_MEM2_PARAMS
                        Allows you to specify custom bwa-mem2 mapping
                        parameters. Only the mapping parameters you provide
                        here will be used with bwa-mem2, meaning that you must
                        provide the complete list of parameters that you want
                        to take effect. The pipeline uses program default
                        mapping parameters. Example input: -k 15 -w 200 -r 2
                        Important: 1. This applies to fastqs provided in the
                        Reads_ATAC user input 2. Please do not specify any
                        non-mapping related params like: -C, -t, etc. 3.
                        Please only use params supported by bwa-mem2 version
                        2.2.1
  --Exact_Cell_Count EXACT_CELL_COUNT
                        Set a specific number (>=1) of cells as putative,
                        based on those with the highest error-corrected read
                        count
  --Exclude_Intronic_Reads
                        By default, reads aligned to exons and introns are
                        considered and represented in molecule counts.
                        Including intronic reads may increase sensitivity,
                        resulting in an increase in molecule counts and the
                        number of genes per cell for both cellular and nuclei
                        samples. Intronic reads may indicate unspliced mRNAs
                        and are also useful, for example, in the study of
                        nuclei and RNA velocity. When set to true, intronic
                        reads will be excluded.
  --Expected_Cell_Count EXPECTED_CELL_COUNT
                        Optional. Guide the basic putative cell calling
                        algorithm by providing an estimate of the number of
                        cells expected. Usually this can be the number of
                        cells loaded into the Rhapsody cartridge. If there are
                        multiple inflection points on the second derivative
                        cumulative curve, this will ensure the one selected is
                        near the expected.
  --Generate_Bam        Default: false. A Bam read alignment file contains
                        reads from all the input libraries, but creating it
                        can consume a lot of compute and disk resources. By
                        setting this field to true, the Bam file will be
                        created. This option is shared for both Bioproduct and
                        ATAC libraries.
  --Long_Reads          By default, we detect if there are any reads longer
                        than 650bp and then flag QualCLAlign to use STARlong
                        instead of STAR. This flag can be explicitly set if it
                        is known in advance that there are reads longer than
                        650bp.
  --Maximum_Threads MAXIMUM_THREADS
                        The maximum number of threads to use in the pipeline.
                        By default, all available cores are used.
  --Predefined_ATAC_Peaks PREDEFINED_ATAC_PEAKS
                        An optional BED file containing pre-established
                        chromatin accessibility peak regions for generating
                        the ATAC cell-by-peak matrix. Only applies to ATAC
                        assays.
  --Reads READS         FASTQ files from libraries that may include WTA mRNA,
                        Targeted mRNA, AbSeq, Sample Multiplexing, and related
                        technologies
  --Reads_ATAC READS_ATAC
                        FASTQ files from libraries generated using the ATAC
                        assay protocol. Each lane of a library is expected to
                        have 3 FASTQs - R1, R2 and I1/I2, where the index read
                        contains the Cell Barcode and UMI sequence. Only
                        applies to ATAC assays.
  --Reference_Archive REFERENCE_ARCHIVE
                        Reference Files Archive
  --Run_Name RUN_NAME   This is a name for output files, for example
                        Experiment1_Metrics_Summary.csv. Default if left empty
                        is to name run based on a library. Any non-alpha
                        numeric characters will be changed to a hyphen.
  --Sample_Tags_Version SAMPLE_TAGS_VERSION
                        The sample multiplexing kit version. This option
                        should only be set for a multiplexed experiment.
  --Supplemental_Reference SUPPLEMENTAL_REFERENCE
                        Supplemental Reference
  --Tag_Names TAG_NAMES
                        Specify the Sample Tag number followed by - (hyphen)
                        and a sample name to appear in the output files. For
                        example: 4-Ramos. Should be alpha numeric, with + -
                        and _ allowed. Any special characters: &, (), [], {},
                        <>, ?, | will be corrected to underscores.
  --Target_analysis
  --Targeted_Reference TARGETED_REFERENCE
                        Targeted Reference
  --VDJ_JGene_Evalue VDJ_JGENE_EVALUE
                        The e-value threshold for J gene call by IgBlast/PyIR,
                        default is set as 0.001
  --VDJ_VGene_Evalue VDJ_VGENE_EVALUE
                        The e-value threshold for V gene call by IgBlast/PyIR,
                        default is set as 0.001
  --VDJ_Version VDJ_VERSION
                        The VDJ species and chain types. This option should
                        only be set for VDJ experiment.
  --Write_Filtered_Reads
