Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.5.0/modules/gen_samplesheet/README.md @ 2:4678c2cd1c9e
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 06 Jun 2023 09:46:25 -0400 |
| parents | 365849f031fd |
| children |
| rev | line source |
|---|---|
| kkonganti@1 | 1 # NextFlow DSL2 Module |
| kkonganti@1 | 2 |
| kkonganti@1 | 3 ```bash |
| kkonganti@1 | 4 GEN_SAMPLESHEET |
| kkonganti@1 | 5 ``` |
| kkonganti@1 | 6 |
| kkonganti@1 | 7 ## Description |
| kkonganti@1 | 8 |
| kkonganti@1 | 9 Generates a sample sheet in CSV format that contains required fields to be used to construct a Groovy Map of metadata. It requires as input, an absolute UNIX path to a folder containing only FASTQ files. This module requires the `fastq_dir_to_samplesheet.py` script to be present in the `bin` folder from where the NextFlow script including this module will be executed. |
| kkonganti@1 | 10 |
| kkonganti@1 | 11 \ |
| kkonganti@1 | 12 |
| kkonganti@1 | 13 |
| kkonganti@1 | 14 ### `input:` |
| kkonganti@1 | 15 |
| kkonganti@1 | 16 ___ |
| kkonganti@1 | 17 |
| kkonganti@1 | 18 Type: `val` |
| kkonganti@1 | 19 |
| kkonganti@1 | 20 Takes in the absolute UNIX path to a folder containing only FASTQ files (`inputdir`). |
| kkonganti@1 | 21 |
| kkonganti@1 | 22 Ex: |
| kkonganti@1 | 23 |
| kkonganti@1 | 24 ```groovy |
| kkonganti@1 | 25 '/hpc/scratch/test/reads' |
| kkonganti@1 | 26 ``` |
| kkonganti@1 | 27 |
| kkonganti@1 | 28 \ |
| kkonganti@1 | 29 |
| kkonganti@1 | 30 |
| kkonganti@1 | 31 ### `output:` |
| kkonganti@1 | 32 |
| kkonganti@1 | 33 ___ |
| kkonganti@1 | 34 |
| kkonganti@1 | 35 Type: `path` |
| kkonganti@1 | 36 |
| kkonganti@1 | 37 NextFlow output of type `path` pointing to auto-generated CSV sample sheet (`csv`). |
| kkonganti@1 | 38 |
| kkonganti@1 | 39 \ |
| kkonganti@1 | 40 |
| kkonganti@1 | 41 |
| kkonganti@1 | 42 #### `csv` |
| kkonganti@1 | 43 |
| kkonganti@1 | 44 Type: `path` |
| kkonganti@1 | 45 |
| kkonganti@1 | 46 NextFlow output type of `path` pointing to auto-generated CSV sample sheet for all FASTQ files present in the folder given by NextFlow input type of `val` (`inputdir`). |
| kkonganti@1 | 47 |
| kkonganti@1 | 48 \ |
| kkonganti@1 | 49 |
| kkonganti@1 | 50 |
| kkonganti@1 | 51 #### `versions` |
| kkonganti@1 | 52 |
| kkonganti@1 | 53 Type: `path` |
| kkonganti@1 | 54 |
| kkonganti@1 | 55 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |