kkonganti@11: # NextFlow DSL2 Module
kkonganti@11: 
kkonganti@11: ```bash
kkonganti@11: MASH_SCREEN
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: ## Description
kkonganti@11: 
kkonganti@11: Run `mash screen` on the input FASTQ file.
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: ### `input:`
kkonganti@11: 
kkonganti@11: ___
kkonganti@11: 
kkonganti@11: Type: `tuple`
kkonganti@11: 
kkonganti@11: Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`query`) per sample (`id:`).
kkonganti@11: 
kkonganti@11: Ex:
kkonganti@11: 
kkonganti@11: ```groovy
kkonganti@11: [ 
kkonganti@11:     [ 
kkonganti@11:         id: 'FAL00870'
kkonganti@11:     ],
kkonganti@11:     [
kkonganti@11:         '/hpc/scratch/test/f1.fq.gz'
kkonganti@11:     ]
kkonganti@11: ]
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: #### `meta`
kkonganti@11: 
kkonganti@11: Type: Groovy Map
kkonganti@11: 
kkonganti@11: A Groovy Map containing the metadata about the FASTQ file.
kkonganti@11: 
kkonganti@11: Ex:
kkonganti@11: 
kkonganti@11: ```groovy
kkonganti@11: [ 
kkonganti@11:     id: 'FAL00870'
kkonganti@11: ]
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: #### `query`
kkonganti@11: 
kkonganti@11: Type: `path`
kkonganti@11: 
kkonganti@11: NextFlow input type of `path` pointing to FASTQ file to be screened.
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: ### `output:`
kkonganti@11: 
kkonganti@11: ___
kkonganti@11: 
kkonganti@11: Type: `tuple`
kkonganti@11: 
kkonganti@11: Outputs a tuple of metadata (`meta` from `input:`) and `mash screen` result file ending with suffix `.screened`.
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: #### `screened`
kkonganti@11: 
kkonganti@11: Type: `path`
kkonganti@11: 
kkonganti@11: NextFlow output type of `path` pointing to the result (`*.screened`) of the `mash screen` command per sample (`id:`).
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.