workflows/ingestion/bd_rhapsody

Description

BD Rhapsody Sequence Analysis CWL pipeline v2.2.1

This pipeline performs analysis of single-cell multiomic sequence read (FASTQ) data. The supported
sequencing libraries are those generated by the BD Rhapsody assay kits, including: Whole Transcriptome
mRNA, Targeted mRNA, AbSeq Antibody-Oligonucleotides, Single-Cell Multiplexing, TCR/BCR, and
ATAC-Seq

The CWL pipeline file is obtained by cloning 'https://bitbucket.org/CRSwDev/cwl' and removing all objects with class 'DockerRequirement' from the YAML.

Inputs

Name	Type & Properties	Description
--reads	file multiple	Reads (optional) - Path to your FASTQ.GZ formatted read files from libraries that may include: - WTA mRNA - Targeted mRNA - AbSeq - Sample Multiplexing - VDJ You may specify as many R1/R2 read pairs as you want.
--reads_atac	file multiple	Path to your FASTQ.GZ formatted read files from ATAC-Seq libraries. You may specify as many R1/R2/I2 files as you want.

Name

Type & Properties

--reads

file

multiple

--reads_atac

file

multiple

References

Name	Type & Properties	Description
--reference_archive	file	Path to Rhapsody WTA Reference in the tar.gz format. Structure of the reference archive: - `BD_Rhapsody_Reference_Files/`: top level folder - `star_index/`: sub-folder containing STAR index, that is files created with `STAR --runMode genomeGenerate` - GTF for gene-transcript-annotation e.g. "gencode.v43.primary_assembly.annotation.gtf"
--targeted_reference	file multiple	Path to the targeted reference file in FASTA format.
--abseq_reference	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 to be aligned against in a WTA assay experiment.

Name

Type & Properties

--reference_archive

file

--targeted_reference

file

multiple

--abseq_reference

file

multiple

--supplemental_reference

-s

file

multiple

Outputs

Name	Type & Properties	Description
--output	file required output	The processed output file in h5mu format.
--output_raw -o	file required output	The unprocessed output directory containing all the outputs from the pipeline.

Name

Type & Properties

--output

file

required

output

--output_raw

-o

file

required

output

Putative Cell Calling Settings

Name	Type & Properties	Description
--cell_calling_data	string	Specify the dataset to be used for putative cell calling: mRNA, AbSeq, ATAC, mRNA_and_ATAC For putative cell calling using an AbSeq dataset, please provide an AbSeq_Reference fasta file above. For putative cell calling using an ATAC dataset, please provide a WTA+ATAC-Seq Reference_Archive file above. The default data for putative cell calling, will be determined the following way: - If mRNA Reads and ATAC Reads exist: mRNA_and_ATAC - If only ATAC Reads exist: ATAC - Otherwise: mRNA
--cell_calling_bioproduct_algorithm	string	Specify the bioproduct algorithm to be used for putative cell calling: Basic or Refined By default, the Basic algorithm will be used for putative cell calling.
--cell_calling_atac_algorithm	string	Specify the ATAC-seq algorithm to be used for putative cell calling: Basic or Refined By default, the Basic algorithm will be used for putative cell calling.
--exact_cell_count	integer	Set a specific number of cells as putative, based on those with the highest error-corrected read count
--expected_cell_count	integer	Guide the basic putative cell calling algorithm by providing an estimate of the number of cells expected. Usually this can be the number of cells loaded into the Rhapsody cartridge. If there are multiple inflection points on the second derivative cumulative curve, this will ensure the one selected is near the expected.

Name

Type & Properties

--cell_calling_data

string

--cell_calling_bioproduct_algorithm

string

--cell_calling_atac_algorithm

string

--exact_cell_count

integer

--expected_cell_count

integer

Intronic Reads Settings

Name	Type & Properties	Description
--exclude_intronic_reads	boolean	By default, the flag is false, and reads aligned to exons and introns are considered and represented in molecule counts. When the flag is set to true, intronic reads will be excluded. The value can be true or false.

Name

Type & Properties

--exclude_intronic_reads

boolean

Multiplex Settings

Name	Type & Properties	Description
--sample_tags_version	string	Specify the version of the Sample Tags used in the run: * If Sample Tag Multiplexing was done, specify the appropriate version: human, mouse, flex, nuclei_includes_mrna, nuclei_atac_only * If this is an SMK + Nuclei mRNA run or an SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq) run (and not an SMK + ATAC-Seq only run), choose the "nuclei_includes_mrna" option. * If this is an SMK + ATAC-Seq only run (and not SMK + Multiomic ATAC-Seq (WTA+ATAC-Seq)), choose the "nuclei_atac_only" option.
--tag_names	string multiple	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	If VDJ was done, specify the appropriate option: human, mouse, humanBCR, humanTCR, mouseBCR, mouseTCR

Name

Type & Properties

--vdj_version

string

ATAC options

Name	Type & Properties	Description
--predefined_atac_peaks	file	An optional BED file containing pre-established chromatin accessibility peak regions for generating the ATAC cell-by-peak matrix.

Name

Type & Properties

--predefined_atac_peaks

file

Additional options

Name	Type & Properties	Description
--run_name	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.
--generate_bam	boolean	Specify whether to create the BAM file output
--long_reads	boolean	Use STARlong (default: undefined - i.e. autodetects based on read lengths) - Specify if the STARlong aligner should be used instead of STAR. Set to true if the reads are longer than 650bp.

Name

Type & Properties

--run_name

string

--generate_bam

boolean

--long_reads

boolean

Advanced options

Name	Type & Properties	Description
--custom_star_params	string	Modify STAR alignment parameters - Set this parameter to fully override default STAR mapping parameters used in the pipeline. For reference this is the default that is used: Short Reads: `--outFilterScoreMinOverLread 0 --outFilterMatchNminOverLread 0 --outFilterMultimapScoreRange 0 --clip3pAdapterSeq AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA --seedSearchStartLmax 50 --outFilterMatchNmin 25 --limitOutSJcollapsed 2000000` Long Reads: Same as Short Reads + `--seedPerReadNmax 10000` This applies to fastqs provided in the Reads user input Do NOT set any non-mapping related params like `--genomeDir`, `--outSAMtype`, `--outSAMunmapped`, `--readFilesIn`, `--runThreadN`, etc. We use STAR version 2.7.10b
--custom_bwa_mem2_params	string	Modify bwa-mem2 alignment parameters - Set this parameter to fully override bwa-mem2 mapping parameters used in the pipeline The pipeline does not specify any custom mapping params to bwa-mem2 so program default values are used This applies to fastqs provided in the Reads_ATAC user input Do NOT set any non-mapping related params like `-C`, `-t`, etc. We use bwa-mem2 version 2.2.1

Name

Type & Properties

--custom_star_params

string

--custom_bwa_mem2_params

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.

Name

Type & Properties

--parallel

boolean

--timestamps

boolean_true

Undocumented arguments

Name	Type & Properties	Description
--abseq_umi	integer
--target_analysis	boolean
--vdj_jgene_evalue	double	e-value threshold for J gene. The e-value threshold for J gene call by IgBlast/PyIR, default is set as 0.001
--vdj_vgene_evalue	double	e-value threshold for V gene. The e-value threshold for V gene call by IgBlast/PyIR, default is set as 0.001
--write_filtered_reads	boolean

Name

Type & Properties

--abseq_umi

integer

--target_analysis

boolean

--vdj_jgene_evalue

double

--vdj_vgene_evalue

double

--write_filtered_reads

boolean

Run this component

Run the following command to execute this component with Nextflow:

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

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.2.0 \  
  -main-script target/nextflow/workflows/ingestion/bd_rhapsody/main.nf \  
  -params-file params.yaml

workflows/ingestion/bd_rhapsody

Inputs

References

Outputs

Putative Cell Calling Settings

Intronic Reads Settings

Multiplex Settings

VDJ arguments

ATAC options

Additional options

Advanced options

CWL-runner arguments

Undocumented arguments

Run this component

Relationships

Used by

Uses