kkonganti@92: # NextFlow DSL2 Module
kkonganti@92: 
kkonganti@92: ```bash
kkonganti@92: SEQKIT_GREP
kkonganti@92: ```
kkonganti@92: 
kkonganti@92: ## Description
kkonganti@92: 
kkonganti@92: Run `seqkit grep` command on reads in FASTQ format. Produces a filtered FASTQ file as per the filter strategy in the supplied input file.
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: ### `input:`
kkonganti@92: 
kkonganti@92: ___
kkonganti@92: 
kkonganti@92: Type: `tuple`
kkonganti@92: 
kkonganti@92: Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@92: 
kkonganti@92: Ex:
kkonganti@92: 
kkonganti@92: ```groovy
kkonganti@92: [ 
kkonganti@92:     [ id: 'FAL00870',
kkonganti@92:        strandedness: 'unstranded',
kkonganti@92:        single_end: true,
kkonganti@92:        centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@92:     ],
kkonganti@92:     '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@92: ]
kkonganti@92: ```
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: #### `meta`
kkonganti@92: 
kkonganti@92: Type: Groovy Map
kkonganti@92: 
kkonganti@92: A Groovy Map containing the metadata about the FASTQ file.
kkonganti@92: 
kkonganti@92: Ex:
kkonganti@92: 
kkonganti@92: ```groovy
kkonganti@92: [ 
kkonganti@92:     id: 'FAL00870',
kkonganti@92:     strandedness: 'unstranded',
kkonganti@92:     single_end: true
kkonganti@92: ]
kkonganti@92: ```
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: #### `reads`
kkonganti@92: 
kkonganti@92: Type: `path`
kkonganti@92: 
kkonganti@92: NextFlow input type of `path` pointing to FASTQ files on which `seqkit grep` should be run.
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: #### `pattern_file`
kkonganti@92: 
kkonganti@92: Type: path
kkonganti@92: 
kkonganti@92: NextFlow input type of `path` pointing to the pattern file which has the patterns, one per line, by which FASTQ sequence ids should be searched and whose reads will be extracted.
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: #### `args`
kkonganti@92: 
kkonganti@92: Type: Groovy String
kkonganti@92: 
kkonganti@92: 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@92: 
kkonganti@92: Ex:
kkonganti@92: 
kkonganti@92: ```groovy
kkonganti@92: withName: 'SEQKIT_GREP' {
kkonganti@92:     ext.args = '--only-positive-strand'
kkonganti@92: }
kkonganti@92: ```
kkonganti@92: 
kkonganti@92: ### `output:`
kkonganti@92: 
kkonganti@92: ___
kkonganti@92: 
kkonganti@92: Type: `tuple`
kkonganti@92: 
kkonganti@92: Outputs a tuple of metadata (`meta` from `input:`) and and filtered gzipped FASTQ file.
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: #### `fastx`
kkonganti@92: 
kkonganti@92: Type: `path`
kkonganti@92: 
kkonganti@92: NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`).
kkonganti@92: 
kkonganti@92: \
kkonganti@92:  
kkonganti@92: 
kkonganti@92: #### `versions`
kkonganti@92: 
kkonganti@92: Type: `path`
kkonganti@92: 
kkonganti@92: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.