Skip to content

bclconvert-interop-qc/1.3.1--1.25.2__20241120234352
Compare
Choose a tag to compare
@github-actions github-actions released this 20 Nov 23:45
· 12 commits to main since this release
bclconvert-interop-qc/1.3.1--1.25.2__20241120234352
9e63aba

Overview

MD5Sum: bf3fba24832235c0203ea4f72c2a4d53

Documentation

Documentation for bclconvert-interop-qc v1.3.1--1.25.2
This workflow has been designed for BCLConvert 4.2.7 outputs from the Nextflow autolaunch pipeline.
The InterOp directory is expected to contain the IndexMetricsOut.bin file, otherwise the
index summary will not be generated.
It is assumed that the Reports directory will contain the RunInfo.xml file

Dockstore

Dockstore Version Link

ICAv2

Tenant: umccr-prod

Bundles Generated

Bundle Name: bclconvert_interop_qc_prod__1_3_1__1_25_2__20241120234352 / Bundle Version 1.3.1__1.25.2__20241120234352

Description
This bundle has been generated by the release of workflows/bclconvert-interop-qc/1.3.1--1.25.2/bclconvert-interop-qc__1.3.1--1.25.2.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/bclconvert-interop-qc/1.3.1--1.25.2__20241120234352.

Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is 1.3.1__1.25.2

Bundle ID: cbc8246b-325f-4d2d-b0cd-3a5e1167bc4a

  • Bundle Link
    Pipeline Project ID: 5844391a-69db-4b52-86b5-6a0d55c2386f
    Pipeline Project Name: pipelines
    Pipeline ID: dfbf508b-fa4d-47d5-8de5-da63a20c894b
    Pipeline Code: bclconvert-interop-qc__1_3_1--1_25_2__20241120234352

Projects

  • development
  • staging
  • production

Visual Overview

Click to expand!

bclconvert-interop-qc

Inputs Template

Yaml

Click to expand! 
# yaml-language-server: $schema=https://github.com/umccr/cwl-ica/releases/download/bclconvert-interop-qc%2F1.3.1--1.25.2__20241120234352/bclconvert-interop-qc__1.3.1--1.25.2__20241120234352.schema.json

# BCLConvert Report Directory (Required)
# Docs: The output directory from a BCLConvert run named 'Reports'
bclconvert_report_directory:
  class: Directory
  location: icav2://project_id/path/to/dir/

# Instrument Run ID (Required)
# Docs: The instrument run ID
instrument_run_id: string

# Interop Directory (Required)
# Docs: The interop directory
interop_directory:
  class: Directory
  location: icav2://project_id/path/to/dir/

Json

Click to expand! 
{
    "bclconvert_report_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "instrument_run_id": "string",
    "interop_directory": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Outputs Template

Click to expand! 
{
    "interop_output_dir": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    },
    "multiqc_html_report": {
        "class": "File",
        "location": "icav2://project_id/path/to/file"
    },
    "multiqc_output_dir": {
        "class": "Directory",
        "location": "icav2://project_id/path/to/dir/"
    }
}

Overrides Template

Zipped workflow

Click to expand! 
[
    "workflow.cwl#bclconvert-interop-qc--1.3.1--1.25.2/generate_interop_qc_step",
    "workflow.cwl#bclconvert-interop-qc--1.3.1--1.25.2/run_multiqc_step"
]

Packed workflow

Click to expand! 
[
    "#main/generate_interop_qc_step",
    "#main/run_multiqc_step"
]

Inputs

Click to expand!

BCLConvert Report Directory

ID: bclconvert_report_directory

Optional: False
Type: Directory
Docs:
The output directory from a BCLConvert run named 'Reports'

Instrument Run ID

ID: instrument_run_id

Optional: False
Type: string
Docs:
The instrument run ID

Interop Directory

ID: interop_directory

Optional: False
Type: Directory
Docs:
The interop directory

Steps

Click to expand!

Generate InterOp QC

ID: bclconvert-interop-qc--1.3.1--1.25.2/generate_interop_qc_step

Step Type: tool
Docs:

Generate the interop files by mounting the interop directory underneath a directory named by the run id specified.
along with the run info xml file.

Get RunInfo.xml file from Reports Dir

ID: bclconvert-interop-qc--1.3.1--1.25.2/get_run_info_xml_file_from_reports_dir

Step Type: expression
Docs:

Get the RunInfo.xml file from the Reports Directory

Run Multiqc

ID: bclconvert-interop-qc--1.3.1--1.25.2/run_multiqc_step

Step Type: tool
Docs:

Run MultiQC on the input reports directory along with the generated index summary files

Outputs

Click to expand!

interop out dir

ID: bclconvert-interop-qc--1.3.1--1.25.2/interop_output_dir

Optional: False
Output Type: Directory
Docs:
Directory containing the inteop summary csvs

multiqc html report

ID: bclconvert-interop-qc--1.3.1--1.25.2/multiqc_html_report

Optional: False
Output Type: File
Docs:
The HTML report generated by the multiqc step

multiqc output dir

ID: bclconvert-interop-qc--1.3.1--1.25.2/multiqc_output_dir

Optional: False
Output Type: Directory
Docs:
Directory containing the multiqc data

Assets 10
Loading