kkonganti@0: # NextFlow DSL2 Module
kkonganti@0: 
kkonganti@0: ```bash
kkonganti@0: KRAKEN2_CLASSIFY
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: ## Description
kkonganti@0: 
kkonganti@0: Run `kraken2` tool on reads in FASTQ format. Produces 4 output files per sample (`id:`) in ASCII text format.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: ### `input:`
kkonganti@0: 
kkonganti@0: ___
kkonganti@0: 
kkonganti@0: Type: `tuple`
kkonganti@0: 
kkonganti@0: Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@0: 
kkonganti@0: Ex:
kkonganti@0: 
kkonganti@0: ```groovy
kkonganti@0: [ 
kkonganti@0:     [ id: 'FAL00870',
kkonganti@0:        strandedness: 'unstranded',
kkonganti@0:        single_end: true,
kkonganti@0:        centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@0:     ],
kkonganti@0:     '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@0: ]
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `meta`
kkonganti@0: 
kkonganti@0: Type: Groovy Map
kkonganti@0: 
kkonganti@0: A Groovy Map containing the metadata about the FASTQ file.
kkonganti@0: 
kkonganti@0: Ex:
kkonganti@0: 
kkonganti@0: ```groovy
kkonganti@0: [ 
kkonganti@0:     id: 'FAL00870',
kkonganti@0:     strandedness: 'unstranded',
kkonganti@0:     single_end: true,
kkonganti@0:     kraken2_db: '/hpc/db/kraken2/standard-210914'
kkonganti@0: ]
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `reads`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow input type of `path` pointing to FASTQ files on which `kraken2` classification should be run.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: ### `output:`
kkonganti@0: 
kkonganti@0: ___
kkonganti@0: 
kkonganti@0: Type: `tuple`
kkonganti@0: 
kkonganti@0: Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `kraken_report`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`).
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `kraken_output`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`).
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `classified`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that have been classified (`*classified.fastq`) per sample (`id:`).
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `unclassified`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that are unclassified (`*unclassified.fastq`) per sample (`id:`).
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.