Mercurial > repos > kkonganti > cfsan_bettercallsal
annotate 0.6.1/modules/samplesheet_check/README.md @ 11:749faef1caa9
"planemo upload"
| author | kkonganti |
|---|---|
| date | Tue, 05 Sep 2023 11:51:40 -0400 |
| parents | |
| children |
| rev | line source |
|---|---|
| kkonganti@11 | 1 # NextFlow DSL2 Module |
| kkonganti@11 | 2 |
| kkonganti@11 | 3 ```bash |
| kkonganti@11 | 4 SAMPLESHEET_CHECK |
| kkonganti@11 | 5 ``` |
| kkonganti@11 | 6 |
| kkonganti@11 | 7 ## Description |
| kkonganti@11 | 8 |
| kkonganti@11 | 9 Checks the validity of the sample sheet in CSV format to make sure there are required mandatory fields. This module generally succeeds `GEN_SAMPLESHEET` module as part of the `cpipes` pipelines to make sure that all fields of the columns are properly formatted to be used as Groovy Map for `meta` which is of input type `val`. This module requires the `check_samplesheet.py` script to be present in the `bin` folder from where the NextFlow script including this module will be executed |
| kkonganti@11 | 10 |
| kkonganti@11 | 11 \ |
| kkonganti@11 | 12 |
| kkonganti@11 | 13 |
| kkonganti@11 | 14 ### `input:` |
| kkonganti@11 | 15 |
| kkonganti@11 | 16 ___ |
| kkonganti@11 | 17 |
| kkonganti@11 | 18 Type: `path` |
| kkonganti@11 | 19 |
| kkonganti@11 | 20 Takes in the absolute UNIX path to the sample sheet in CSV format (`samplesheet`). |
| kkonganti@11 | 21 |
| kkonganti@11 | 22 Ex: |
| kkonganti@11 | 23 |
| kkonganti@11 | 24 ```groovy |
| kkonganti@11 | 25 '/hpc/scratch/test/reads/output/gen_samplesheet/autogen_samplesheet.csv' |
| kkonganti@11 | 26 ``` |
| kkonganti@11 | 27 |
| kkonganti@11 | 28 \ |
| kkonganti@11 | 29 |
| kkonganti@11 | 30 |
| kkonganti@11 | 31 ### `output:` |
| kkonganti@11 | 32 |
| kkonganti@11 | 33 ___ |
| kkonganti@11 | 34 |
| kkonganti@11 | 35 Type: `path` |
| kkonganti@11 | 36 |
| kkonganti@11 | 37 NextFlow output of type `path` pointing to properly formatted CSV sample sheet (`csv`). |
| kkonganti@11 | 38 |
| kkonganti@11 | 39 \ |
| kkonganti@11 | 40 |
| kkonganti@11 | 41 |
| kkonganti@11 | 42 #### `csv` |
| kkonganti@11 | 43 |
| kkonganti@11 | 44 Type: `path` |
| kkonganti@11 | 45 |
| kkonganti@11 | 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@11 | 47 |
| kkonganti@11 | 48 \ |
| kkonganti@11 | 49 |
| kkonganti@11 | 50 |
| kkonganti@11 | 51 #### `versions` |
| kkonganti@11 | 52 |
| kkonganti@11 | 53 Type: `path` |
| kkonganti@11 | 54 |
| kkonganti@11 | 55 NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process. |