kkonganti@11: # NextFlow DSL2 Module
kkonganti@11: 
kkonganti@11: ```bash
kkonganti@11: SEQKIT_SEQ
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: ## Description
kkonganti@11: 
kkonganti@11: Run `seqkit seq` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy mentioned using the `ext.args` within the process scope.
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` (`reads`) per sample (`id:`).
kkonganti@11: 
kkonganti@11: Ex:
kkonganti@11: 
kkonganti@11: ```groovy
kkonganti@11: [ 
kkonganti@11:     [ id: 'FAL00870',
kkonganti@11:        strandedness: 'unstranded',
kkonganti@11:        single_end: true,
kkonganti@11:        centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@11:     ],
kkonganti@11:     '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
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:     strandedness: 'unstranded',
kkonganti@11:     single_end: true
kkonganti@11: ]
kkonganti@11: ```
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: #### `reads`
kkonganti@11: 
kkonganti@11: Type: `path`
kkonganti@11: 
kkonganti@11: NextFlow input type of `path` pointing to FASTQ files on which `seqkit seq` should be run.
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: #### `args`
kkonganti@11: 
kkonganti@11: Type: Groovy String
kkonganti@11: 
kkonganti@11: 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@11: 
kkonganti@11: Ex:
kkonganti@11: 
kkonganti@11: ```groovy
kkonganti@11: withName: 'SEQKIT_SEQ' {
kkonganti@11:     ext.args = '--max-len 4000'
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 filtered gzipped FASTQ file.
kkonganti@11: 
kkonganti@11: \
kkonganti@11:  
kkonganti@11: 
kkonganti@11: #### `fastx`
kkonganti@11: 
kkonganti@11: Type: `path`
kkonganti@11: 
kkonganti@11: NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file 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.