BD Rhapsody

A generic pipeline for running BD Rhapsody WTA or Targeted mapping, with support for AbSeq, VDJ and/or SMK.

Info

ID: bd_rhapsody
Namespace: workflows/ingestion

A wrapper for the BD Rhapsody Analysis CWL v1.10.1 pipeline.

This pipeline can be used for a targeted analysis (with --mode targeted) or for a whole transcriptome analysis (with --mode wta).

The reference_genome and transcriptome_annotation files can be generated with the make_reference pipeline. Alternatively, BD also provides standard references which can be downloaded from these locations:

Example commands

You can run the pipeline using nextflow run.

View help

You can use --help as a parameter to get an overview of the possible parameters.

nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -main-script target/nextflow/workflows/ingestion/bd_rhapsody/main.nf \
  --help

Run command

Example of params.yaml 
# Inputs
mode: # please fill in - example: "wta"
id: # please fill in - example: "foo"
input: # please fill in - example: ["input.fastq.gz"]
reference: # please fill in - example: ["reference_genome.tar.gz|reference.fasta"]
# transcriptome_annotation: "transcriptome.gtf"
# abseq_reference: ["abseq_reference.fasta"]
# supplemental_reference: ["supplemental_reference.fasta"]
sample_prefix: "sample"

# Outputs
# output_raw: "$id.$key.output_raw.output_raw"
# output_h5mu: "$id.$key.output_h5mu.h5mu"

# Putative cell calling settings
# putative_cell_call: "mRNA"
# exact_cell_count: 10000
disable_putative_calling: false

# Subsample arguments
# subsample: 0.01
# subsample_seed: 3445

# Multiplex arguments
# sample_tags_version: "human"
# tag_names: ["4-mySample", "9-myOtherSample", "6-alsoThisSample"]

# VDJ arguments
# vdj_version: "human"

# CWL-runner arguments
parallel: true
timestamps: false
dryrun: false

# Nextflow input-output arguments
publish_dir: # please fill in - example: "output/"
# param_list: "my_params.yaml"
nextflow run openpipelines-bio/openpipeline \
  -r 1.0.1 -latest \
  -profile docker \
  -main-script target/nextflow/workflows/ingestion/bd_rhapsody/main.nf \
  -params-file params.yaml
Note

Replace -profile docker with -profile podman or -profile singularity depending on the desired backend.

Argument groups

Inputs

Name Description Attributes
--mode Whether to run a whole transcriptome analysis (WTA) or a targeted analysis. string, required, example: "wta"
--id ID of the sample. string, required, example: "foo"
--input Path to your read files in the FASTQ.GZ format. You may specify as many R1/R2 read pairs as you want. List of file, required, example: "input.fastq.gz", multiple_sep: ";"
--reference Refence to map to. For --mode wta, this is the path to STAR index as a tar.gz file. For --mode targeted, this is the path to mRNA reference file for pre-designed, supplemental, or custom panel, in FASTA format List of file, required, example: "reference_genome.tar.gz|reference.fasta", multiple_sep: ";"
--transcriptome_annotation Path to GTF annotation file (only for --mode wta). file, example: "transcriptome.gtf"
--abseq_reference Path to the AbSeq reference file in FASTA format. Only needed if BD AbSeq Ab-Oligos are used. List of file, example: "abseq_reference.fasta", multiple_sep: ";"
--supplemental_reference Path to the supplemental reference file in FASTA format. Only needed if there are additional transgene sequences used in the experiment (only for --mode wta). List of file, example: "supplemental_reference.fasta", multiple_sep: ";"
--sample_prefix Specify a run name to use as the output file base name. Use only letters, numbers, or hyphens. Do not use special characters or spaces. string, default: "sample"

Outputs

Name Description Attributes
--output_raw The BD Rhapsody output folder as it comes out of the BD Rhapsody pipeline file, required, example: "output_dir"
--output_h5mu The converted h5mu file. file, required, example: "output.h5mu"

Putative cell calling settings

Name Description Attributes
--putative_cell_call Specify the dataset to be used for putative cell calling. For putative cell calling using an AbSeq dataset, please provide an AbSeq_Reference fasta file above. string, example: "mRNA"
--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 integer, example: 10000
--disable_putative_calling Disable Refined Putative Cell Calling - Determine putative cells using only the basic algorithm (minimum second derivative along the cumulative reads curve). The refined algorithm attempts to remove false positives and recover false negatives, but may not be ideal for certain complex mixtures of cell types. Does not apply if Exact Cell Count is set. boolean_true

Subsample arguments

Name Description Attributes
--subsample A number >1 or fraction (0 < n < 1) to indicate the number or percentage of reads to subsample. double, example: 0.01
--subsample_seed A seed for replicating a previous subsampled run. integer, example: 3445

Multiplex arguments

Name Description Attributes
--sample_tags_version Specify if multiplexed run. string, example: "human"
--tag_names Tag_Names (optional) - Specify the tag number followed by ‘-’ and the desired sample name to appear in Sample_Tag_Metrics.csv. Do not use the special characters: &, (), [], {}, <>, ?, | List of string, example: "4-mySample", "9-myOtherSample", "6-alsoThisSample", multiple_sep: ";"

VDJ arguments

Name Description Attributes
--vdj_version Specify if VDJ run. string, example: "human"

CWL-runner arguments

Name Description Attributes
--parallel Run jobs in parallel. boolean, default: TRUE
--timestamps Add timestamps to the errors, warnings, and notifications. boolean_true
--dryrun If true, the output directory will only contain the CWL input files, but the pipeline itself will not be executed. boolean_true

Authors

  • Robrecht Cannoodt (maintainer)

Visualisation

flowchart TB
    v0(Channel.fromList)
    v17(bd_rhapsody_component)
    v38(from_bdrhap_to_h5mu)
    v65(Output)
    v0-->v17
    v17-->v38
    v38-->v65
    style v0 fill:#e3dcea,stroke:#7a4baa;
    style v17 fill:#e3dcea,stroke:#7a4baa;
    style v38 fill:#e3dcea,stroke:#7a4baa;
    style v65 fill:#e3dcea,stroke:#7a4baa;