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comparison 0.6.1/modules/multiqc/README.md @ 11:749faef1caa9

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author kkonganti
date Tue, 05 Sep 2023 11:51:40 -0400
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10:1b9de878b04a 11:749faef1caa9
1 # NextFlow DSL2 Module
2
3 ```bash
4 MULTIQC
5 ```
6
7 ## Description
8
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.
10
11 \
12  
13
14 ### `input:`
15
16 ___
17
18 Type: `path`
19
20 Takes in NextFlow input type of `path` which points to many log files that **MultiQC** should parse.
21
22 Ex:
23
24 ```groovy
25 [ '/data/sample1/centrifuge/cent_output.txt', '/data/sample1/kraken/kraken_output.txt'] ]
26 ```
27
28 \
29  
30
31 ### `output:`
32
33 ___
34
35 #### `report`
36
37 Type: `path`
38
39 Outputs a NextFlow output type of `path` pointing to the location of **MultiQC** final HTML report.
40
41 \
42  
43
44 #### `data`
45
46 Type: `path`
47
48 NextFlow output type of `path` pointing to the data files folder generated by **MultiQC** which were used to generate plots and HTML report.
49
50 \
51  
52
53 #### `plots`
54
55 Type: `path`
56 Optional: `true`
57
58 NextFlow output type of `path` pointing to the plots folder generated by **MultiQC**.
59
60 \
61  
62
63 #### `versions`
64
65 Type: `path`
66
67 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.