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@github-actions github-actions released this 22 Nov 07:07
· 8 commits to main since this release
dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241122070556
c2f2d1a

Overview

MD5Sum: 597d249e2e4c99a0d3846b27bcd7fea5

Documentation

This tool can be used for archiving purposes by first compressing fastqs prior to transfer to a long-term storage location.

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: ora_instrument_run_compression_pipeline_with_reference__4_2_4__20241122070556 / Bundle Version v2__20241122070556

Description
This bundle has been generated by the release of workflows/dragen-instrument-run-fastq-to-ora-pipeline/4.2.4/dragen-instrument-run-fastq-to-ora-pipeline__4.2.4.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/dragen-instrument-run-fastq-to-ora-pipeline/4.2.4__20241122070556.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v2

Bundle ID: 43ad35e4-6017-44e6-b7cf-4a9f059d0ae6

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: 0540fca4-cc40-45ac-88e2-d32df69c6954
    Pipeline Code: dragen-instrument-run-fastq-to-ora-pipeline__4_2_4__20241122070556

Projects

  • development
  • staging
  • production

Datasets

  • ora_reference_v2

Visual Overview

Click to expand!

dragen-instrument-run-fastq-to-ora-pipeline

Inputs Template

Yaml

Click to expand! 
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/dragen-instrument-run-fastq-to-ora-pipeline%2F4.2.4__20241122070556/dragen-instrument-run-fastq-to-ora-pipeline__4.2.4__20241122070556.schema.json

# instrument run directory (Required)
# Docs: The directory containing the instrument run. Expected to be in the BCLConvert 4.2.7 output format, with the following structure:
#   Reports/
#   InterOp/
#   Logs/
#   Samples/
#   Samples/Lane_1/
#   Samples/Lane_1/Sample_ID/
#   Samples/Lane_1/Sample_ID/Sample_ID_S1_L001_R1_001.fastq.gz
#   Samples/Lane_1/Sample_ID/Sample_ID_S1_L001_R2_001.fastq.gz
#   etc...
instrument_run_directory:
  class: Directory
  location: icav2://project_id/path/to/dir/

# ora check file integrity (Optional)
# Default value: False
# Docs: Set to true to perform and output result of FASTQ file and decompressed FASTQ.ORA integrity check. The default value is false.
ora_check_file_integrity: false

# ora parallel files (Optional)
# Default value: 2
# Docs: The number of files to compress in parallel. If using an FPGA medium instance in the 
# run_dragen_instrument_run_fastq_to_ora_step this should be set to 16 / ora_threads_per_file.
ora_parallel_files: 2

# ora print file info (Optional)
# Default value: False
# Docs: Prints file information summary of ORA compressed files.
ora_print_file_info: false

# ora reference (Required)
# Docs: The reference tar to use for the ORA compression
ora_reference:
  class: File
  location: icav2://project_id/path/to/file

# ora threads per file (Optional)
# Default value: 8
# Docs: The number of threads to use per file. If using an FPGA medium instance in the 
# run_dragen_instrument_run_fastq_to_ora_step this should be set to 4 since there are only 16 cores available
ora_threads_per_file: 8

# sample id list (Optional)
# Docs: Optional list of samples to process.  
# Samples NOT in this list are NOT compressed AND NOT transferred to the final output directory!
sample_id_list:
- string

Json

Click to expand! 
{
    "instrument_run_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "ora_check_file_integrity": false,
    "ora_parallel_files": 2,
    "ora_print_file_info": false,
    "ora_reference": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "ora_threads_per_file": 8,
    "sample_id_list": [
        "string"
    ]
}

Outputs Template

Click to expand! 
{
    "output_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Overrides Template

Zipped workflow

Click to expand! 
[
    "workflow.cwl#dragen-instrument-run-fastq-to-ora-pipeline--4.2.4/run_dragen_instrument_run_fastq_to_ora_step"
]

Packed workflow

Click to expand! 
[
    "#main/run_dragen_instrument_run_fastq_to_ora_step"
]

Inputs

Click to expand!

instrument run directory

ID: instrument_run_directory

Optional: False
Type: Directory
Docs:
The directory containing the instrument run. Expected to be in the BCLConvert 4.2.7 output format, with the following structure:
Reports/
InterOp/
Logs/
Samples/
Samples/Lane_1/
Samples/Lane_1/Sample_ID/
Samples/Lane_1/Sample_ID/Sample_ID_S1_L001_R1_001.fastq.gz
Samples/Lane_1/Sample_ID/Sample_ID_S1_L001_R2_001.fastq.gz
etc...

ora check file integrity

ID: ora_check_file_integrity

Optional: False
Type: boolean
Docs:
Set to true to perform and output result of FASTQ file and decompressed FASTQ.ORA integrity check. The default value is false.

ora parallel files

ID: ora_parallel_files

Optional: True
Type: int
Docs:
The number of files to compress in parallel. If using an FPGA medium instance in the
run_dragen_instrument_run_fastq_to_ora_step this should be set to 16 / ora_threads_per_file.

ora print file info

ID: ora_print_file_info

Optional: False
Type: boolean
Docs:
Prints file information summary of ORA compressed files.

ora reference

ID: ora_reference

Optional: False
Type: File
Docs:
The reference tar to use for the ORA compression

ora threads per file

ID: ora_threads_per_file

Optional: True
Type: int
Docs:
The number of threads to use per file. If using an FPGA medium instance in the
run_dragen_instrument_run_fastq_to_ora_step this should be set to 4 since there are only 16 cores available

sample id list

ID: sample_id_list

Optional: True
Type: .[]
Docs:
Optional list of samples to process.
Samples NOT in this list are NOT compressed AND NOT transferred to the final output directory!

Steps

Click to expand!

Run Dragen Instrument Run Fastq to ORA

ID: dragen-instrument-run-fastq-to-ora-pipeline--4.2.4/run_dragen_instrument_run_fastq_to_ora_step

Step Type: tool
Docs:

Run the dragen instrument run fastq to ora tool

Outputs

Click to expand!

output directory

ID: dragen-instrument-run-fastq-to-ora-pipeline--4.2.4/output_directory

Optional: False
Output Type: Directory
Docs:
The output directory of the instrument run with fastqs converted to oras

Assets 10
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