kkonganti@0: # NextFlow DSL2 Module kkonganti@0: kkonganti@0: ```bash kkonganti@0: GEN_SAMPLESHEET kkonganti@0: ``` kkonganti@0: kkonganti@0: ## Description kkonganti@0: kkonganti@0: 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@0: kkonganti@0: \ kkonganti@0:   kkonganti@0: kkonganti@0: ### `input:` kkonganti@0: kkonganti@0: ___ kkonganti@0: kkonganti@0: Type: `val` kkonganti@0: kkonganti@0: Takes in the absolute UNIX path to a folder containing only FASTQ files (`inputdir`). kkonganti@0: kkonganti@0: Ex: kkonganti@0: kkonganti@0: ```groovy kkonganti@0: '/hpc/scratch/test/reads' 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 auto-generated 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.