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@github-actions github-actions released this 27 Jun 23:39
· 139 commits to main since this release
umccrise-pipeline/2.3.1--1__20240627233816
27c8ef9

Overview

MD5Sum: f7897225b40d67a91ef65b765ae2cff8

Documentation

Documentation for umccrise-pipeline v2.3.1--1

Dockstore

Dockstore Version Link

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

Click to expand!

umccrise-pipeline

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

Assets 10
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