Pipeline install bundle (docker-free)

An experimental .tar.gz bundle to install the Rhapsody Sequence Analysis pipeline, without the use of a docker image.
This contains cwl-runner and all the major required dependencies. Simply download, extract, and run.

Latest Version Download Link

Linux only. Currently tested Linux versions:

  • Ubuntu 16.04 / 20.04 / 22.04
  • Red Hat 7
  • CentOS 7 / 9

Instructions

Extract the tar.gz bundle and enter that folder:

tar -xvzf rhapsodyPipeline-[version].tar.gz
cd rhapsodyPipeline-[version]

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 additional instructions: Extra Utilities

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:

./rhapsody annotateCellLabelUmi inputs.yml

To create a new Reference Archive for use as an input to the Rhapsody Sequence Analysis Pipeline:

./rhapsody makeRhapReference inputs.yml

Example inputs YML:

Genome_fasta:
 - class: File
   location: "./GRCh38.primary_assembly.genome.fa.gz"

Gtf:
 - class: File
   location: "./gencode.v45.primary_assembly.annotation.gtf.gz"

Extra_sequences:
 - class: File
   location: "./gfp.fasta"

WTA_Only: True

To determine the amount of phiX contamination for a fastq file:

./rhapsody phiXContamination inputs.yml

Feedback welcome!