Input Specification File

Procedure

An example input specification file pipeline_inputs_template.yml is found in the CWL folder for the specific pipeline version. It is generally recommended to start with this file and modify it with your specific needs.

Obtain the FASTQ files. See FASTQ files.
Obtain the targeted mRNA reference FASTA file or the WTA or WTA+ATAC-Seq Reference Files Archive file. See Reference Files.
If your experiment contains BD® AbSeq Ab-Oligos, obtain the AbSeq Reference file. See Reference Files.
Specify the file paths in the YML file for Reads and Reference with the exact input field listed in the Pipeline parameters table.
- The required input fields for Targeted assays are: Reads and Targeted_Reference.
- The required input fields for WTA assays are: Reads and Reference_Archive.
- The required input fields for ATAC-Seq assays are: Reads_ATAC and Reference_Archive.
- The required input fields for Multiomic WTA+ATAC-Seq assays are: Reads, Reads_ATAC and Reference_Archive.
- The required input fields for AbSeq-only assays are: Reads and AbSeq_Reference.
Set any other optional parameters applicable to your assay, for instance, Sample Multiplexing, VDJ version, or cell calling parameters. See possible parameters in the pipeline_inputs_template.yml file, or Pipeline parameters.
Save the modified template YML file

Example YML input specification files:

Targeted assay:

#!/usr/bin/env cwl-runner
cwl:tool: rhapsody

Reads:
 - class: File
   location: "path/to/mySample_R1_.fastq.gz"
 - class: File
   location: "path/to/mySample_R2_.fastq.gz"

Targeted_Reference:
 - class: File
   location: "path/to/BD_Rhapsody_Immune_Response_Panel_Hs.fasta"

WTA assay with AbSeq:

#!/usr/bin/env cwl-runner
cwl:tool: rhapsody

Reads:
 - class: File
   location: "path/to/WTALibrary_R1_.fastq.gz"
 - class: File
   location: "path/to/WTALibrary_R2_.fastq.gz"
 - class: File
   location: "path/to/AbSeqLibrary_R1_.fastq.gz"
 - class: File
   location: "path/to/AbSeqLibrary_R2_.fastq.gz"

Reference_Archive:
  class: File
  location: "path/to/RhapRef_Human_WTA_2023-02.tar.gz"

AbSeq_Reference:
 - class: File
   location: "path/to/AbSeq_reference.fasta"

WTA assay with Sample multiplexing and TCR/BCR(VDJ) analysis:

#!/usr/bin/env cwl-runner
cwl:tool: rhapsody

Reads:
 - class: File
   location: "path/to/WTALibrary_R1_.fastq.gz"
 - class: File
   location: "path/to/WTALibrary_R2_.fastq.gz"
 - class: File
   location: "path/to/SampleTagLibrary_R1_.fastq.gz"
 - class: File
   location: "path/to/SampleTagLibrary_R2_.fastq.gz"
 - class: File
   location: "path/to/TCRBCRLibrary_R1_.fastq.gz"
 - class: File
   location: "path/to/TCRBCRLibrary_R2_.fastq.gz"

Reference_Archive:
  class: File
  location: "path/to/RhapRef_Human_WTA_2023-02.tar.gz"

Sample_Tags_Version: flex

VDJ_Version: human

AbSeq only assay:

#!/usr/bin/env cwl-runner
cwl:tool: rhapsody

Reads:
 - class: File
   location: "path/to/AbSeqLibrary_R1_.fastq.gz"
 - class: File
   location: "path/to/AbSeqLibrary_R2_.fastq.gz"

AbSeq_Reference:
 - class: File
   location: "path/to/AbSeq_reference.fasta"

Putative_Cell_Call: AbSeq

ATAC-Seq only assay:

#!/usr/bin/env cwl-runner
cwl:tool: rhapsody

Reads_ATAC:
 - class: File
   location: "path/to/ATACLibrary_S2_L001_R1_001.fastq.gz"
 - class: File
   location: "path/to/ATACLibrary_S2_L001_R2_001.fastq.gz"
 - class: File
   location: "path/to/ATACLibrary_S2_L001_I2_001.fastq.gz"

Reference_Archive:
  class: File
  location: "path/to/RhapRef_Human_WTA-ATAC_2023-08.tar.gz"

Multiomic WTA + ATAC-Seq assay

#!/usr/bin/env cwl-runner
cwl:tool: rhapsody

Reads_ATAC:
 - class: File
   location: "path/to/ATACLibrary_S2_L001_R1_001.fastq.gz"
 - class: File
   location: "path/to/ATACLibrary_S2_L001_R2_001.fastq.gz"
 - class: File
   location: "path/to/ATACLibrary_S2_L001_I2_001.fastq.gz"

Reads:
 - class: File
   location: "path/to/WTALibrary_R1_.fastq.gz"
 - class: File
   location: "path/to/WTALibrary_R2_.fastq.gz"

Reference_Archive:
  class: File
  location: "path/to/RhapRef_Human_WTA-ATAC_2023-08.tar.gz"