umccrise-pipeline/2.3.1--1__20240627233816
Overview
MD5Sum: f7897225b40d67a91ef65b765ae2cff8
Documentation
Documentation for umccrise-pipeline v2.3.1--1
Dockstore
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: umccrise_prod__2_3_1__20240627233816 / Bundle Version v9_r3__20240627233816
Description
This bundle has been generated by the release of workflows/umccrise-pipeline/2.3.1--1/umccrise-pipeline__2.3.1--1.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/umccrise-pipeline/2.3.1--1__20240627233816.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is v9_r3
Bundle ID: 4b06a809-6d05-4cb4-b17d-a9641de834a8
- Bundle Link
Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
Pipeline Project Name: pipelines
Pipeline ID: e51d4372-4567-4ff8-ac72-f7d754a75af7
Pipeline Code: umccrise-pipeline__2_3_1--1__20240627233816
Projects
- development
- staging
- production
Datasets
- umccrise_202303
Visual Overview
Inputs Template
Yaml
Click to expand!
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/umccrise-pipeline%2F2.3.1--1__20240627233816/umccrise-pipeline__2.3.1--1__20240627233816.schema.json
# debug (Optional)
# Docs: Copy workspace to output directory if workflow fails
debug: false
# dragen germline directory (Required)
# Docs: The dragen germline directory
dragen_germline_directory:
class: Directory
location: icav2://project_id/path/to/dir/
# dragen normal id (Optional)
# Docs: The name of the dragen normal sample
dragen_normal_id: string
# dragen somatic directory (Required)
# Docs: The dragen somatic directory
dragen_somatic_directory:
class: Directory
location: icav2://project_id/path/to/dir/
# dragen tumor id (Optional)
# Docs: The name of the dragen tumor sample
dragen_tumor_id: string
# dry run (Optional)
# Docs: Prints rules and commands to be run without actually executing them
dry_run: false
# genomes tar (Required)
# Docs: The reference umccrise tarball
genomes_tar:
class: File
location: icav2://project_id/path/to/file
# include stage (Optional)
# Docs: Optionally, specify stage(s) to run
include_stage:
- string
# output directory name (Required)
# Docs: The name of the output directory
output_directory_name: string
# skip stage (Optional)
# Docs: Runs all default stage(s) excluding the one selected
skip_stage:
- string
# subject identifier (Required)
# Docs: The subject ID (used to name output files)
subject_identifier: string
# threads (Optional)
# Docs: Number of threads to use
threads: string
Json
Click to expand!
{
"debug": false,
"dragen_germline_directory": {
"class": "Directory",
"location": "icav2://project_id/path/to/dir/"
},
"dragen_normal_id": "string",
"dragen_somatic_directory": {
"class": "Directory",
"location": "icav2://project_id/path/to/dir/"
},
"dragen_tumor_id": "string",
"dry_run": false,
"genomes_tar": {
"class": "File",
"location": "icav2://project_id/path/to/file"
},
"include_stage": [
"string"
],
"output_directory_name": "string",
"skip_stage": [
"string"
],
"subject_identifier": "string",
"threads": "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#umccrise-pipeline--2.3.1--1/run_umccrise_step"
]
Packed workflow
Click to expand!
[
"#main/run_umccrise_step"
]
Inputs
Click to expand!
debug
ID: debug
Optional: True
Type: boolean
Docs:
Copy workspace to output directory if workflow fails
dragen germline directory
ID: dragen_germline_directory
Optional: False
Type: Directory
Docs:
The dragen germline directory
dragen normal id
ID: dragen_normal_id
Optional: True
Type: string
Docs:
The name of the dragen normal sample
dragen somatic directory
ID: dragen_somatic_directory
Optional: False
Type: Directory
Docs:
The dragen somatic directory
dragen tumor id
ID: dragen_tumor_id
Optional: True
Type: string
Docs:
The name of the dragen tumor sample
dry run
ID: dry_run
Optional: True
Type: boolean
Docs:
Prints rules and commands to be run without actually executing them
genomes tar
ID: genomes_tar
Optional: False
Type: File
Docs:
The reference umccrise tarball
include stage
ID: include_stage
Optional: True
Type: .[]
Docs:
Optionally, specify stage(s) to run
output directory name
ID: output_directory_name
Optional: False
Type: string
Docs:
The name of the output directory
skip stage
ID: skip_stage
Optional: True
Type: .[]
Docs:
Runs all default stage(s) excluding the one selected
subject identifier
ID: subject_identifier
Optional: False
Type: string
Docs:
The subject ID (used to name output files)
threads
ID: threads
Optional: True
Type: int
Docs:
Number of threads to use
Steps
Click to expand!
run umccrise step
ID: umccrise-pipeline--2.3.1--1/run_umccrise_step
Step Type: tool
Docs:
Run the UMCCRise pipeline
Outputs
Click to expand!
output directory
ID: umccrise-pipeline--2.3.1--1/output_directory
Optional: False
Output Type: Directory
Docs:
The output directory containing the results of the umccrise pipeline