kkonganti@1: # NextFlow DSL2 Module
kkonganti@1: 
kkonganti@1: ```bash
kkonganti@1: MULTIQC
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: ## Description
kkonganti@1: 
kkonganti@1: Generate an aggregated [**MultiQC**](https://multiqc.info/) report. This particular module **will only work** within the framework of `cpipes` as in, it uses many `cpipes` related UNIX absolute paths to store and retrieve **MultiQC** related configration files and `cpipes` context aware metadata. It also uses a custom logo with filename `FDa-Logo-Blue---medium-01.png` which should be located inside an `assets` folder from where the NextFlow script including this module will be executed.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: ### `input:`
kkonganti@1: 
kkonganti@1: ___
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: Takes in NextFlow input type of `path` which points to many log files that **MultiQC** should parse.
kkonganti@1: 
kkonganti@1: Ex:
kkonganti@1: 
kkonganti@1: ```groovy
kkonganti@1: [ '/data/sample1/centrifuge/cent_output.txt', '/data/sample1/kraken/kraken_output.txt'] ]
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: ### `output:`
kkonganti@1: 
kkonganti@1: ___
kkonganti@1: 
kkonganti@1: #### `report`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: Outputs a NextFlow output type of `path` pointing to the location of **MultiQC** final HTML report.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `data`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the data files folder generated by **MultiQC** which were used to generate plots and HTML report.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `plots`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: Optional: `true`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the plots folder generated by **MultiQC**.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `versions`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.