workflows/ingestion/bd_rhapsody

Description

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).

If mode is "targeted", then either the --reference or --abseq_reference parameters must be defined.
If mode is "wta", then --reference and --transcriptome_annotation must be defined, --abseq_reference and --supplemental_reference is optional.

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:

Type

nextflow_script

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
id: "run"  
sample_prefix: [ "sample" ]  
output_raw: "$id.$key.output_raw.output_dir"  
output_h5mu: "$id.$key.output_h5mu.h5mu"  
parallel: [ true ]  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision 1.0.4 \  
  -main-script target/nextflow/workflows/ingestion/bd_rhapsody/main.nf \  
  -params-file params.yaml

Inputs

Name	Type & Properties	Description
--mode	string required	Whether to run a whole transcriptome analysis (WTA) or a targeted analysis.
--id	string required	ID of the sample.
--input -i	file required multiple	Path to your read files in the FASTQ.GZ format. You may specify as many R1/R2 read pairs as you want.
--reference -r --reference_genome	file required multiple	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
--transcriptome_annotation -t	file	Path to GTF annotation file (only for `--mode wta`).
--abseq_reference -a	file multiple	Path to the AbSeq reference file in FASTA format. Only needed if BD AbSeq Ab-Oligos are used.
--supplemental_reference -s	file multiple	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`).
--sample_prefix	string	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.

Name

Type & Properties

--mode

string

required

--id

string

required

--input

-i

file

required

multiple

--reference

-r

--reference_genome

file

required

multiple

--transcriptome_annotation

-t

file

--abseq_reference

-a

file

multiple

--supplemental_reference

-s

file

multiple

--sample_prefix

string

Outputs

Name	Type & Properties	Description
--output_raw	file required output	The BD Rhapsody output folder as it comes out of the BD Rhapsody pipeline
--output_h5mu	file required output	The converted h5mu file.

Name

Type & Properties

--output_raw

file

required

output

--output_h5mu

file

required

output

Putative cell calling settings

Name	Type & Properties	Description
--putative_cell_call	string	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.
--exact_cell_count	integer	Exact cell count - Set a specific number (>=1) of cells as putative, based on those with the highest error-corrected read count
--disable_putative_calling	boolean_true	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.

Name

Type & Properties

--putative_cell_call

string

--exact_cell_count

integer

--disable_putative_calling

boolean_true

Subsample arguments

Name	Type & Properties	Description
--subsample	double	A number >1 or fraction (0 < n < 1) to indicate the number or percentage of reads to subsample.
--subsample_seed	integer	A seed for replicating a previous subsampled run.

Name

Type & Properties

--subsample

double

--subsample_seed

integer

Multiplex arguments

Name	Type & Properties	Description
--sample_tags_version	string	Specify if multiplexed run.
--tag_names	string multiple	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: &, (), [], {}, <>, ?, \|

Name

Type & Properties

--sample_tags_version

string

--tag_names

string

multiple

VDJ arguments

Name	Type & Properties	Description
--vdj_version	string	Specify if VDJ run.

Name

Type & Properties

--vdj_version

string

CWL-runner arguments

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

Name

Type & Properties

--parallel

boolean

--timestamps

boolean_true

--dryrun

boolean_true