kkonganti@1: # NextFlow DSL2 Module
kkonganti@1: 
kkonganti@1: ```bash
kkonganti@1: BBTOOLS_BBMERGE
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: ## Description
kkonganti@1: 
kkonganti@1: Run `bbmerge.sh` from `BBTools` which will merge paired-end reads to produce single-end reads by overlap detection.
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`) 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: ]
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: #### `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: 'BBTOOLS_BBMERGE' {
kkonganti@1:     ext.args = 'minprog=0.5'
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 merged gzipped FASTQ file.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `fastq`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the FASTQ format merged gzipped file per sample (`id:`).
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `log`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to log file from `bbmerge.sh` run per sample (`id:`).
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.