kkonganti@17: # NextFlow DSL2 Module
kkonganti@17: 
kkonganti@17: ```bash
kkonganti@17: FASTQC
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: ## Description
kkonganti@17: 
kkonganti@17: Run `fastqc` tool on reads in FASTQ format. Produces a HTML report file and a `.zip` file containing plots and data used to produce the plots.
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: ### `input:`
kkonganti@17: 
kkonganti@17: ___
kkonganti@17: 
kkonganti@17: Type: `tuple`
kkonganti@17: 
kkonganti@17: Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: [ 
kkonganti@17:     [ id: 'FAL00870',
kkonganti@17:        strandedness: 'unstranded',
kkonganti@17:        single_end: true,
kkonganti@17:        centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@17:     ],
kkonganti@17:     '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@17: ]
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `meta`
kkonganti@17: 
kkonganti@17: Type: Groovy Map
kkonganti@17: 
kkonganti@17: A Groovy Map containing the metadata about the FASTQ file.
kkonganti@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: [ 
kkonganti@17:     id: 'FAL00870',
kkonganti@17:     strandedness: 'unstranded',
kkonganti@17:     single_end: true
kkonganti@17: ]
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `reads`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow input type of `path` pointing to FASTQ files on which `fastqc` classification should be run.
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `args`
kkonganti@17: 
kkonganti@17: Type: Groovy String
kkonganti@17: 
kkonganti@17: 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@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: withName: 'FASTQC' {
kkonganti@17:     ext.args = '--nano'
kkonganti@17: }
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: ### `output:`
kkonganti@17: 
kkonganti@17: ___
kkonganti@17: 
kkonganti@17: Type: `tuple`
kkonganti@17: 
kkonganti@17: Outputs a tuple of metadata (`meta` from `input:`) and list of `fastqc` result files.
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `html`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output type of `path` pointing to the `fastqc` report file in HTML format per sample (`id:`).
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `zip`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output type of `path` pointing to the zipped `fastqc` results per sample (`id:`).
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `versions`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.