kkonganti@105: # NextFlow DSL2 Module
kkonganti@105: 
kkonganti@105: ```bash
kkonganti@105: SEQKIT_RMDUP
kkonganti@105: ```
kkonganti@105: 
kkonganti@105: ## Description
kkonganti@105: 
kkonganti@105: Run `seqkit rmdup` command on reads in FASTQ format. Produces a filtered FASTQ file without duplicate sequences as per the strategy set using `ext.args` within the process scope.
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: ### `input:`
kkonganti@105: 
kkonganti@105: ___
kkonganti@105: 
kkonganti@105: Type: `tuple`
kkonganti@105: 
kkonganti@105: Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
kkonganti@105: 
kkonganti@105: Ex:
kkonganti@105: 
kkonganti@105: ```groovy
kkonganti@105: [
kkonganti@105:     [ id: 'FAL00870',
kkonganti@105:        strandedness: 'unstranded',
kkonganti@105:        single_end: true,
kkonganti@105:        centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
kkonganti@105:     ],
kkonganti@105:     '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
kkonganti@105: ]
kkonganti@105: ```
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `meta`
kkonganti@105: 
kkonganti@105: Type: Groovy Map
kkonganti@105: 
kkonganti@105: A Groovy Map containing the metadata about the FASTQ file.
kkonganti@105: 
kkonganti@105: Ex:
kkonganti@105: 
kkonganti@105: ```groovy
kkonganti@105: [
kkonganti@105:     id: 'FAL00870',
kkonganti@105:     strandedness: 'unstranded',
kkonganti@105:     single_end: true
kkonganti@105: ]
kkonganti@105: ```
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `reads`
kkonganti@105: 
kkonganti@105: Type: `path`
kkonganti@105: 
kkonganti@105: NextFlow input type of `path` pointing to FASTQ files on which `seqkit rmdup` should be run.
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `args`
kkonganti@105: 
kkonganti@105: Type: Groovy String
kkonganti@105: 
kkonganti@105: 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@105: 
kkonganti@105: Ex:
kkonganti@105: 
kkonganti@105: ```groovy
kkonganti@105: withName: 'SEQKIT_DUP' {
kkonganti@105:     ext.args = '-t dna'
kkonganti@105: }
kkonganti@105: ```
kkonganti@105: 
kkonganti@105: ### `output:`
kkonganti@105: 
kkonganti@105: ___
kkonganti@105: 
kkonganti@105: Type: `tuple`
kkonganti@105: 
kkonganti@105: Outputs a tuple of metadata (`meta` from `input:`) and filtered gzipped FASTQ file.
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `fastx`
kkonganti@105: 
kkonganti@105: Type: `path`
kkonganti@105: 
kkonganti@105: NextFlow output type of `path` pointing to the FASTQ format filtered gzipped file per sample (`id:`).
kkonganti@105: 
kkonganti@105: \
kkonganti@105:  
kkonganti@105: 
kkonganti@105: #### `versions`
kkonganti@105: 
kkonganti@105: Type: `path`
kkonganti@105: 
kkonganti@105: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.