kkonganti@0: # NextFlow DSL2 Module kkonganti@0: kkonganti@0: ```bash kkonganti@0: SAMPLESHEET_CHECK kkonganti@0: ``` kkonganti@0: kkonganti@0: ## Description kkonganti@0: kkonganti@0: 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@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: ### `input:` kkonganti@0: kkonganti@0: ___ kkonganti@0: kkonganti@0: Type: `path` kkonganti@0: kkonganti@0: Takes in the absolute UNIX path to the sample sheet in CSV format (`samplesheet`). kkonganti@0: kkonganti@0: Ex: kkonganti@0: kkonganti@0: ```groovy kkonganti@0: '/hpc/scratch/test/reads/output/gen_samplesheet/autogen_samplesheet.csv' kkonganti@0: ``` kkonganti@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: ### `output:` kkonganti@0: kkonganti@0: ___ kkonganti@0: kkonganti@0: Type: `path` kkonganti@0: kkonganti@0: NextFlow output of type `path` pointing to properly formatted CSV sample sheet (`csv`). kkonganti@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: #### `csv` kkonganti@0: kkonganti@0: Type: `path` kkonganti@0: kkonganti@0: 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@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: #### `versions` kkonganti@0: kkonganti@0: Type: `path` kkonganti@0: kkonganti@0: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.