kkonganti@0: # NextFlow DSL2 Module
kkonganti@0: 
kkonganti@0: ```bash
kkonganti@0: CENTRIFUGE_CLASSIFY
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: ## Description
kkonganti@0: 
kkonganti@0: Run `centrifuge` tool on reads in FASTQ format. Produces 3 output files in ASCII text format and optional output files.
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:     centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
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 `centrifuge` classification should be run.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `args`
kkonganti@0: 
kkonganti@0: Type: Groovy String
kkonganti@0: 
kkonganti@0: String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file.
kkonganti@0: 
kkonganti@0: Ex:
kkonganti@0: 
kkonganti@0: ```groovy
kkonganti@0: withName: 'CENTRIFUGE_CLASSIFY' {
kkonganti@0:     ext.args = '--met 3'
kkonganti@0: }
kkonganti@0: ```
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 `centrifuge` result files.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `report`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `centrifuge` report table file (`.report.txt`) per sample (`id:`).
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `output`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `centrifuge` output table file (`.output.txt`) per sample (`id:`).
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `kreport`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `centrifuge` **Kraken** style report table file (`.kreport.txt`) per sample (`id:`).
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `sam`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: \
kkonganti@0: Optional: `true`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `centrifuge` alignment results in SAM (`.sam`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_out_fmt_sam` command-line option when the NextFlow pipeline is called.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `fastq_mapped`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: \
kkonganti@0: Optional: `true`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `centrifuge` alignment results in FASTQ (`.fastq.gz`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_aligned` command-line option when the NextFlow pipeline is called.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `fastq_unmapped`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: \
kkonganti@0: Optional: `true`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `centrifuge` FASTQ (`.fastq.gz`) files of unaligned reads per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_unaligned` command-line option when the NextFlow pipeline is called.
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.