kkonganti@17: # NextFlow DSL2 Module
kkonganti@17: 
kkonganti@17: ```bash
kkonganti@17: SAMPLESHEET_CHECK
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: ## Description
kkonganti@17: 
kkonganti@17: 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@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: ### `input:`
kkonganti@17: 
kkonganti@17: ___
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: Takes in the absolute UNIX path to the sample sheet in CSV format (`samplesheet`).
kkonganti@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: '/hpc/scratch/test/reads/output/gen_samplesheet/autogen_samplesheet.csv'
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: ### `output:`
kkonganti@17: 
kkonganti@17: ___
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output of type `path` pointing to properly formatted CSV sample sheet (`csv`).
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `csv`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: 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@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `versions`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.