harmonization_combat2stats
Format the CSV stats files (coming from combat) into a TSV format that can be easily consumed by MultiQC or other downstream tools. The combat module currently output a CSV file with the following columns: “sid,site,bundle,metric,mean,age,sex,handedness,disease”. And a separate CSV file PER metric.
This module reformats these CSV files into TSV files with the following columns: “sid,roi,<covariates>,metric1,metric2,…” and aggregates all metrics from the same sites into a single TSV file per site.
Keywords : harmonization, combat, stats, format, tsv, csv, qc
Inputs
Section titled “Inputs”Input 1
Section titled “Input 1”Format : path(harmonized_stats)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| harmonized_stats | file | CSV stats files to be reformatted after harmonization. This CSV should have the following columns: “sid,site,bundle,metric,mean,<covariates>”. These input CSV stats files come from the output of the harmonization modules. | True | *.csv |
Outputs
Section titled “Outputs”stats_for_mqc
Section titled “stats_for_mqc”Format : path(*.tsv)
| Type | Description | Mandatory | Pattern | |
|---|---|---|---|---|
| *.tsv | file | Harmonized stats files in TSV format (MultiQC ready format). | True | *.tsv |
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 | |
|---|---|---|---|---|
| covariates | list | List of columns that are not considered metrics in the input tabular files. These columns will be kept unchanged (except for renaming the columns) while the other columns (i.e. the metrics and their values) will be pivotted or unpivotted. | ['sample', 'roi', 'site', 'age', 'sex', 'handedness', 'disease'] | |
| value_col_name | string | Name of the column containing the metric values in the CSV files. | mean | |
| metric_col_name | string | Name of the column containing the metric names in the CSV files. | metric | |
| suffix | string | Suffix to use for the output files based on the operation performed. The output files will be named as “site.<suffix>.tsv”. | harmonized |
| Description | DOI | |
|---|---|---|
| pandas | Python package used to manipulate the input and output tabular data for this module. |
Authors
Section titled “Authors”Last updated : 2026-02-12