MultiQC (DNAnexus Platform App)

Uses the MultiQC tool developed and maintained by Phil Ewels: ewels/MultiQC

Docker images are available from here

What does this app do?

This app downloads the quality metric files as specified by the location and filename extension in the "dx_sp" field in the config.yaml. Then runs the MultiQC tool to generate a run-wide quality report. Modules and columns to be displayed are specified in the config file, the full list of supported modules can be found here.

It is essential to use a config file that has a "dx_sp" section with "primary" for file extenstions in app/outputs of the primary workflow and "secondary" for file extenstions in app/outputs of the secondary workflow.

What inputs are required to run this app?

• multiqc_docker: Docker image of the MultiQC tool (can be found in 001_Reference:/assets/MultiQC)
• multiqc_config_file: A config.yaml file specifying which modules to run and the search patterns to recognise QC files for each module
• input data, which may come from different sources depending on the use-case

Option 1 - for production run on workflow output folders:

• project_for_multiqc - the name of the project to be used, eg 002_211008_A01303_0030_AHKTMYDRXY_TWE
  • This project must have an 'output' folder in its root directory (project:/output/).
• primary_workflow_output - the exact name of the output directory of the primary workflow, eg. dias_single_v1.2.3-TWE_v1.0.5-211011-1)
  • This folder must have subfolders for each app, like project:/output/primary_workflow/app_output)
• OPTIONAL secondary_workflow_output - The exact name of the output directory of the secondary workflow, eg. dias_multi_v1.2.3-TWE_v1.0.5-211011-1)
  • This folder must have subfolders for each app, like project:/output/primary_workflow/secondary_workflow/app_output)

Option 2 - for testing and development:

• set single_folder to TRUE and provide
• project_for_multiqc - the project name and
• primary_workflow_output - the absolute path to a specific folder in the project with all QC files For example, if you want files from project:/folder/subfolder/data_files, you need to input '/folder/subfolder' into the field This will download all files from only this folder and will break if there are further subfolders inside!

OPTIONAL: to calculate target bases coverage at custom depths set calc_custom_coverage to TRUE and provide depths as a list of comma separated integer values --> config.yaml should be changed accordingly to recognise and display the custom coverage columns

What does this app output?

The following outputs are placed in the DNAnexus project in the specified output folder:

• a HTML QC report (with the name of the runfolder-workflow)
• a folder containing the qc metrics data in text format. (The folder is named after project-workflow-multiqc_data)
• original config_file.yaml that was used to generate the report

How does this app work?

1. The app downloads files within the $project_for_multiQC:/output/$primary_workflow_output/QCapp directories of the project, where 'QCapp' and filename extensions are specified in the config file.
2. The app runs the dockerised MultiQC tool with the config file provided.
3. MultiQC parses all recognised files and displays them in the html report.
4. The MultiQC outputs are uploaded to DNAnexus.

How to run this app from command line?

dx run multiqc-applet_ID \
-imultiqc_docker='{}' \
-imultiqc_config_file='{}' \
-iproject_for_multiqc='{}' \
-iprimary_workflow_output='{}' \
-isecondary_workflow_output='{}' \
--destination='{}'

This app was made by EMEE GLH