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annotate 0.4.2/modules/multiqc/README.md @ 105:52045ea4679d

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author kkonganti
date Thu, 27 Jun 2024 14:17:26 -0400
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kkonganti@105 1 # NextFlow DSL2 Module
kkonganti@105 2
kkonganti@105 3 ```bash
kkonganti@105 4 MULTIQC
kkonganti@105 5 ```
kkonganti@105 6
kkonganti@105 7 ## Description
kkonganti@105 8
kkonganti@105 9 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@105 10
kkonganti@105 11 \
kkonganti@105 12  
kkonganti@105 13
kkonganti@105 14 ### `input:`
kkonganti@105 15
kkonganti@105 16 ___
kkonganti@105 17
kkonganti@105 18 Type: `path`
kkonganti@105 19
kkonganti@105 20 Takes in NextFlow input type of `path` which points to many log files that **MultiQC** should parse.
kkonganti@105 21
kkonganti@105 22 Ex:
kkonganti@105 23
kkonganti@105 24 ```groovy
kkonganti@105 25 [ '/data/sample1/centrifuge/cent_output.txt', '/data/sample1/kraken/kraken_output.txt'] ]
kkonganti@105 26 ```
kkonganti@105 27
kkonganti@105 28 \
kkonganti@105 29  
kkonganti@105 30
kkonganti@105 31 ### `output:`
kkonganti@105 32
kkonganti@105 33 ___
kkonganti@105 34
kkonganti@105 35 #### `report`
kkonganti@105 36
kkonganti@105 37 Type: `path`
kkonganti@105 38
kkonganti@105 39 Outputs a NextFlow output type of `path` pointing to the location of **MultiQC** final HTML report.
kkonganti@105 40
kkonganti@105 41 \
kkonganti@105 42  
kkonganti@105 43
kkonganti@105 44 #### `data`
kkonganti@105 45
kkonganti@105 46 Type: `path`
kkonganti@105 47
kkonganti@105 48 NextFlow output type of `path` pointing to the data files folder generated by **MultiQC** which were used to generate plots and HTML report.
kkonganti@105 49
kkonganti@105 50 \
kkonganti@105 51  
kkonganti@105 52
kkonganti@105 53 #### `plots`
kkonganti@105 54
kkonganti@105 55 Type: `path`
kkonganti@105 56 Optional: `true`
kkonganti@105 57
kkonganti@105 58 NextFlow output type of `path` pointing to the plots folder generated by **MultiQC**.
kkonganti@105 59
kkonganti@105 60 \
kkonganti@105 61  
kkonganti@105 62
kkonganti@105 63 #### `versions`
kkonganti@105 64
kkonganti@105 65 Type: `path`
kkonganti@105 66
kkonganti@105 67 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.