Overview
MD5Sum: 0b3e09b773f9648f73d7a6339c6b1fbf
Documentation
Documentation for bclconvert-interop-qc v1.3.1--1.21
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
ICAv2
Tenant: umccr-prod
Bundles Generated
Bundle Name: bclconvert-interop-qc__1_3_1__1_21__20240410040204 / Bundle Version 1.3.1__1.21__20240410040204
Description
This bundle has been generated by the release of workflows/bclconvert-interop-qc/1.3.1--1.21/bclconvert-interop-qc__1.3.1--1.21.cwl. The pipeline can be found at https://github.com/umccr/cwl-ica/releases/tag/bclconvert-interop-qc/1.3.1--1.21__20240410040204.
Version Description
Bundle version description is currently redundant while we cannot append versions to bundles. Regardless - the bunch version is 1.3.1__1.21
Bundle ID: 6113ac8a-53b7-4225-ba9a-5d483d95c8c6
- Bundle Link
Pipeline Project ID: 0ad6a751-c854-4b77-833b-705132a22801
Pipeline Project Name: pipelines-trial
Pipeline ID: 213cf8cb-27ab-4078-aa1c-2e97e0061c35
Pipeline Code: bclconvert-interop-qc__1_3_1--1_21__20240410040204
Projects
- trial
Visual Overview
Inputs Template
Click to expand!
{
"bclconvert_report_directory": {
"class": "Directory",
"location": "icav2://project_id/path/to/dir/"
},
"interop_directory": {
"class": "Directory",
"location": "icav2://project_id/path/to/dir/"
},
"run_id": "string"
}
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--1.21/generate_interop_qc_step",
"workflow.cwl#bclconvert-interop-qc--1.3.1--1.21/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'
Interop Directory
ID: interop_directory
Optional: False
Type: Directory
Docs:
The interop directory
Run ID
ID: run_id
Optional: False
Type: string
Docs:
The run ID
Steps
Click to expand!
Generate InterOp QC
ID: bclconvert-interop-qc--1.3.1--1.21/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--1.21/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--1.21/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--1.21/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--1.21/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--1.21/multiqc_output_dir
Optional: False
Output Type: Directory
Docs:
Directory containing the multiqc data