kkonganti@11: # NextFlow DSL2 Module
kkonganti@11: 
kkonganti@11: ```bash
kkonganti@11: SAMPLESHEET_CHECK
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: ## Description
kkonganti@11: 
kkonganti@11: 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: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: ### `input:`
kkonganti@11: 
kkonganti@11: ___
kkonganti@11: 
kkonganti@11: Type: `path`
kkonganti@11: 
kkonganti@11: Takes in the absolute UNIX path to the sample sheet in CSV format (`samplesheet`).
kkonganti@11: 
kkonganti@11: Ex:
kkonganti@11: 
kkonganti@11: ```groovy
kkonganti@11: '/hpc/scratch/test/reads/output/gen_samplesheet/autogen_samplesheet.csv'
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: ### `output:`
kkonganti@11: 
kkonganti@11: ___
kkonganti@11: 
kkonganti@11: Type: `path`
kkonganti@11: 
kkonganti@11: NextFlow output of type `path` pointing to properly formatted CSV sample sheet (`csv`).
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: #### `csv`
kkonganti@11: 
kkonganti@11: Type: `path`
kkonganti@11: 
kkonganti@11: 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: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: #### `versions`
kkonganti@11: 
kkonganti@11: Type: `path`
kkonganti@11: 
kkonganti@11: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.