kkonganti@0: # NextFlow DSL2 Module
kkonganti@0: 
kkonganti@0: ```bash
kkonganti@0: SEQTK_SEQ
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: ## Description
kkonganti@0: 
kkonganti@0: Run `seqtk 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. Please note that `seqtk seq` works only on one FASTQ file per command call. For paired-end reads, please use the `SEQKIT_SEQ` module.
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: ]
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 `seqtk seq` 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: 'SEQTK_SEQ' {
kkonganti@0:     ext.args = '-L 4000'
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 filtered gzipped FASTQ file.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `fastx`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file 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.