qc_multiqc
Aggregate results from a neuroimaging pipeline using MultiQC into a single HTML report.
Keywords : QC, neuroimaging, report
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : tuple val(meta), path(qc_images)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information e.g. [ id:'sample1' ] | True | |
| qc_images | file | Subject-specific files that will be used in the MultiQC report. | True | *.{nii.gz,trk} |
Input 2
Section titled “Input 2”Format : path(multiqc_files)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| multiqc_files | file | Global files that contain information on multiple subjects. Will be used in the global MultiQC report. | True | *.{tsv,csv,txt} |
Input 3
Section titled “Input 3”Format : path(multiqc_config)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| multiqc_config | file | Optional config yml for MultiQC | True | *.{yml,yaml} |
Input 4
Section titled “Input 4”Format : path(extra_multiqc_config)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| extra_multiqc_config | file | Second optional config yml for MultiQC. Will override common sections in multiqc_config. | True | *.{yml,yaml} |
Input 5
Section titled “Input 5”Format : path(multiqc_logo)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| multiqc_logo | file | Optional logo file for MultiQC | True | *.{png} |
Input 6
Section titled “Input 6”Format : path(replace_names)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| replace_names | file | Optional two-column sample renaming file. First column a set of patterns, second column a set of corresponding replacements. Passed via MultiQC’s --replace-names option. | True | *.{tsv} |
Input 7
Section titled “Input 7”Format : path(sample_names)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| sample_names | file | Optional TSV file with headers, passed to the MultiQC —sample_names argument. | True | *.{tsv} |
Outputs
Section titled “Outputs”Format : val(meta)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| meta | map | Groovy Map containing sample information, kept for linting purposes. e.g. [ id:'sample1' ] | True |
report
Section titled “report”Format : path(*.html)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| *.html | file | MultiQC report file | True | .html |
Format : path(*_data)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| *_data | directory | MultiQC data dir | True | multiqc_data |
Format : path(*_plots)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| *_plots | file | Plots created by MultiQC | True | *_data |
versions
Section titled “versions”Format : path(versions.yml)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| versions.yml | file | File containing software versions | True | versions.yml |
Arguments (see process.ext)
Section titled “Arguments (see process.ext)”| Type | Description | Default | Choices | |
|---|---|---|---|---|
| single_subject | boolean | If true, generates a subject-specific MultiQC report. If false, generates a global report. This will change which module are run within MultiQC. | False |
| Description | DOI | |
|---|---|---|
| multiqc | MultiQC searches a given directory for analysis logs and compiles a HTML report. It’s a general use tool, perfect for summarising the output from numerous bioinformatics tools. | |
| neuroimaging | Neuroimaging is a python MultiQC plugin containing various tools for generating QC reports for neuroimaging data. |
Authors
Section titled “Authors”Last updated : 2025-12-22