Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.7.0/modules/multiqc/README.md @ 19:4b304d77bbfb
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| author | kkonganti |
|---|---|
| date | Mon, 15 Jul 2024 11:20:22 -0400 |
| parents | 0e7a0053e4a6 |
| children |
| rev | line source |
|---|---|
| kkonganti@17 | 1 # NextFlow DSL2 Module |
| kkonganti@17 | 2 |
| kkonganti@17 | 3 ```bash |
| kkonganti@17 | 4 MULTIQC |
| kkonganti@17 | 5 ``` |
| kkonganti@17 | 6 |
| kkonganti@17 | 7 ## Description |
| kkonganti@17 | 8 |
| kkonganti@17 | 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@17 | 10 |
| kkonganti@17 | 11 \ |
| kkonganti@17 | 12 |
| kkonganti@17 | 13 |
| kkonganti@17 | 14 ### `input:` |
| kkonganti@17 | 15 |
| kkonganti@17 | 16 ___ |
| kkonganti@17 | 17 |
| kkonganti@17 | 18 Type: `path` |
| kkonganti@17 | 19 |
| kkonganti@17 | 20 Takes in NextFlow input type of `path` which points to many log files that **MultiQC** should parse. |
| kkonganti@17 | 21 |
| kkonganti@17 | 22 Ex: |
| kkonganti@17 | 23 |
| kkonganti@17 | 24 ```groovy |
| kkonganti@17 | 25 [ '/data/sample1/centrifuge/cent_output.txt', '/data/sample1/kraken/kraken_output.txt'] ] |
| kkonganti@17 | 26 ``` |
| kkonganti@17 | 27 |
| kkonganti@17 | 28 \ |
| kkonganti@17 | 29 |
| kkonganti@17 | 30 |
| kkonganti@17 | 31 ### `output:` |
| kkonganti@17 | 32 |
| kkonganti@17 | 33 ___ |
| kkonganti@17 | 34 |
| kkonganti@17 | 35 #### `report` |
| kkonganti@17 | 36 |
| kkonganti@17 | 37 Type: `path` |
| kkonganti@17 | 38 |
| kkonganti@17 | 39 Outputs a NextFlow output type of `path` pointing to the location of **MultiQC** final HTML report. |
| kkonganti@17 | 40 |
| kkonganti@17 | 41 \ |
| kkonganti@17 | 42 |
| kkonganti@17 | 43 |
| kkonganti@17 | 44 #### `data` |
| kkonganti@17 | 45 |
| kkonganti@17 | 46 Type: `path` |
| kkonganti@17 | 47 |
| kkonganti@17 | 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@17 | 49 |
| kkonganti@17 | 50 \ |
| kkonganti@17 | 51 |
| kkonganti@17 | 52 |
| kkonganti@17 | 53 #### `plots` |
| kkonganti@17 | 54 |
| kkonganti@17 | 55 Type: `path` |
| kkonganti@17 | 56 Optional: `true` |
| kkonganti@17 | 57 |
| kkonganti@17 | 58 NextFlow output type of `path` pointing to the plots folder generated by **MultiQC**. |
| kkonganti@17 | 59 |
| kkonganti@17 | 60 \ |
| kkonganti@17 | 61 |
| kkonganti@17 | 62 |
| kkonganti@17 | 63 #### `versions` |
| kkonganti@17 | 64 |
| kkonganti@17 | 65 Type: `path` |
| kkonganti@17 | 66 |
| kkonganti@17 | 67 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |