kkonganti@1: # NextFlow DSL2 Module
kkonganti@1: 
kkonganti@1: ```bash
kkonganti@1: KMA_ALIGN
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: ## Description
kkonganti@1: 
kkonganti@1: Run `kma` alinger on input FASTQ files with a pre-formatted `kma` index.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: ### `input:`
kkonganti@1: 
kkonganti@1: ___
kkonganti@1: 
kkonganti@1: Type: `tuple`
kkonganti@1: 
kkonganti@1: Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) and a correspondonding `kma` pre-formatted index folder per sample (`id:`).
kkonganti@1: 
kkonganti@1: Ex:
kkonganti@1: 
kkonganti@1: ```groovy
kkonganti@1: [ 
kkonganti@1:     [ 
kkonganti@1:         id: 'FAL00870',
kkonganti@1:         strandedness: 'unstranded',
kkonganti@1:         single_end: false
kkonganti@1:     ],
kkonganti@1:     [
kkonganti@1:         '/hpc/scratch/test/f1.R1.fq.gz',
kkonganti@1:         '/hpc/scratch/test/f1.R2.fq.gz'
kkonganti@1:     ],
kkonganti@1:     '/path/to/kma/index/folder'
kkonganti@1: ]
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `meta`
kkonganti@1: 
kkonganti@1: Type: Groovy Map
kkonganti@1: 
kkonganti@1: A Groovy Map containing the metadata about the FASTQ file.
kkonganti@1: 
kkonganti@1: Ex:
kkonganti@1: 
kkonganti@1: ```groovy
kkonganti@1: [ 
kkonganti@1:     id: 'FAL00870',
kkonganti@1:     strandedness: 'unstranded',
kkonganti@1:     single_end: true
kkonganti@1: ]
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `reads`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow input type of `path` pointing to paired-end FASTQ files on which `bbmerge.sh` should be run.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `index`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow input type of `path` pointing to folder containing `kma` index files.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `args`
kkonganti@1: 
kkonganti@1: Type: Groovy String
kkonganti@1: 
kkonganti@1: 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@1: 
kkonganti@1: Ex:
kkonganti@1: 
kkonganti@1: ```groovy
kkonganti@1: withName: 'KMA_ALIGN' {
kkonganti@1:     ext.args = '-mint2'
kkonganti@1: }
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: ### `output:`
kkonganti@1: 
kkonganti@1: ___
kkonganti@1: 
kkonganti@1: Type: `tuple`
kkonganti@1: 
kkonganti@1: Outputs a tuple of metadata (`meta` from `input:`) and `kma` result files.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `res`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the `.res` file from `kma` per sample (`id:`).
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `mapstat`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the `.map` file from `kma` per sample (`id:`). Optional: `true`
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `hits`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to a `*_template_hits.txt` file containing only hit IDs. Optional: `true`
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `versions`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.