```bash
cwl-runner src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl --help
```

usage: src/bd_rhapsody/bd_rhapsody_make_reference/make_rhap_reference_2.2.1_nodocker.cwl
       [-h] [--Archive_prefix ARCHIVE_PREFIX]
       [--Extra_STAR_params EXTRA_STAR_PARAMS]
       [--Extra_sequences EXTRA_SEQUENCES] [--Filtering_off] --Genome_fasta
       GENOME_FASTA --Gtf GTF [--Maximum_threads MAXIMUM_THREADS]
       [--Mitochondrial_Contigs MITOCHONDRIAL_CONTIGS] [--WTA_Only]
       [job_order]

The Reference Files Generator creates an archive containing Genome Index and
Transcriptome annotation files needed for the BD Rhapsodyâ„¢ Sequencing
Analysis Pipeline. The app takes as input one or more FASTA and GTF files and
produces a compressed archive in the form of a tar.gz file. The archive
contains:\n - STAR index\n - Filtered GTF file

positional arguments:
  job_order             Job input json file

options:
  -h, --help            show this help message and exit
  --Archive_prefix ARCHIVE_PREFIX
                        A prefix for naming the compressed archive file
                        containing the Reference genome index and annotation
                        files. The default value is constructed based on the
                        input Reference files.
  --Extra_STAR_params EXTRA_STAR_PARAMS
                        Additional parameters to pass to STAR when building
                        the genome index. Specify exactly like how you would
                        on the command line. Example: --limitGenomeGenerateRAM
                        48000 --genomeSAindexNbases 11
  --Extra_sequences EXTRA_SEQUENCES
                        Additional sequences in FASTA format to use when
                        building the STAR index. (E.g. phiX genome)
  --Filtering_off       By default the input Transcript Annotation files are
                        filtered based on the gene_type/gene_biotype
                        attribute. Only features having the following
                        attribute values are are kept: - protein_coding -
                        lncRNA (lincRNA and antisense for Gencode <
                        v31/M22/Ensembl97) - IG_LV_gene - IG_V_gene -
                        IG_V_pseudogene - IG_D_gene - IG_J_gene -
                        IG_J_pseudogene - IG_C_gene - IG_C_pseudogene -
                        TR_V_gene - TR_V_pseudogene - TR_D_gene - TR_J_gene -
                        TR_J_pseudogene - TR_C_gene If you have already pre-
                        filtered the input Annotation files and/or wish to
                        turn-off the filtering, please set this option to
                        True.
  --Genome_fasta GENOME_FASTA
                        Reference genome file in FASTA format. The BD
                        Rhapsodyâ„¢ Sequencing Analysis Pipeline uses GRCh38
                        for Human and GRCm39 for Mouse.
  --Gtf GTF             Transcript annotation files in GTF format. The BD
                        Rhapsodyâ„¢ Sequencing Analysis Pipeline uses Gencode
                        v42 for Human and M31 for Mouse.
  --Maximum_threads MAXIMUM_THREADS
                        The maximum number of threads to use in the pipeline.
                        By default, all available cores are used.
  --Mitochondrial_Contigs MITOCHONDRIAL_CONTIGS
                        Names of the Mitochondrial contigs in the provided
                        Reference Genome. Fragments originating from contigs
                        other than these are identified as 'nuclear fragments'
                        in the ATACseq analysis pipeline.
  --WTA_Only            Build a WTA only index, otherwise builds a WTA + ATAC
                        index.
