kkonganti@0: # NextFlow DSL2 Module
kkonganti@0: 
kkonganti@0: ```bash
kkonganti@0: CENTRIFUGE_PROCESS
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: ## Description
kkonganti@0: 
kkonganti@0: Extract FASTQ reads given a FASTQ file originally used with `centrifuge` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTQ read ids and as such requires a `bin` folder with `process_centrifuge_output.py` to be present where the NextFlow script will be executed from. See also `CENTRIFUGE_EXTRACT` module which uses only GNU Coreutils to create a list of FASTQ read ids that need to be extracted.
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 a tuple in order of metadata (`meta`), a `path` (`centrifuge_report`) type and another `path` (`centrifuge_report`) 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.cent_out.report.txt',
kkonganti@0:     '/hpc/scratch/test/FAL000870/f1.merged.cent_out.output.txt'
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:     centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@0: ]
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `centrifuge_report`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `centrifuge_output`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool.
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 extracted FASTQ read ids.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `extracted`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`).
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.