To run the BD Rhapsody Sequence Analysis Pipeline:

First, define the input files and pipeline parameters in a pipeline_inputs.yml file.  See the included 'pipeline_inputs_template.yml' for instructions on formatting the YML file.
Then, start the pipeline with this command:
> ./rhapsody pipeline --outdir results_dir pipeline_inputs.yml

To run a small test of the BD Rhapsody Sequence Analysis Pipeline with built-in demo data:
> ./rhapsody pipeline --outdir test_results test_files/test_smallDemo.yml


By default, the pipeline allows parallel node execution. To turn this off, use the --no-parallel option:
> ./rhapsody pipeline --no-parallel pipeline_inputs.yml


Any cwltool option can be added to the pipeline command. The YML file should always be the last argument.  Examples are --outdir, --tmpdir-prefix, --leave-tmpdir.  
> ./rhapsody pipeline --leave-tmpdir --outdir /path/to/directory pipeline_inputs.yml



Extra Utilities:
See https://bd-rhapsody-bioinfo-docs.genomics.bd.com/resources/extra_utilities.html


Given pairs of R1/R2 FASTQ files from Rhapsody libraries, only annotate the cell label and UMI of R1 and put it in the header of R2. run:
> ./rhapsody annotateCellLabelUmi inputs.yml


To create an archive containing Genome Index and Transcriptome annotation files needed for the BD Rhapsody Sequencing Analysis Pipeline, run:
> ./rhapsody makeRhapReference inputs.yml


To determine the amount of phiX contamination for a fastq file, run:
> ./rhapsody phiXContamination inputs.yml