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
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!
Inputs Template
Yaml
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# 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
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[
"workflow.cwl#dragen-instrument-run-fastq-to-ora-pipeline--4.2.4/run_dragen_instrument_run_fastq_to_ora_step"
]
Packed workflow
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[
"#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