kkonganti@1: # NextFlow DSL2 Module
kkonganti@1: 
kkonganti@1: ```bash
kkonganti@1: SALMON_QUANT
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: ## Description
kkonganti@1: 
kkonganti@1: Run `salmon quant` in `reads` or `alignments` mode. The inputs can be either the alignment (Ex: `.bam`) files or read (Ex: `.fastq.gz`) files.
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 either an alignment file or reads file and a `salmon index` or a transcript FASTA file 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: true
kkonganti@1:     ],
kkonganti@1:     [
kkonganti@1:         '/hpc/scratch/test/FAL00870_R1.fastq.gz'
kkonganti@1:     ],
kkonganti@1:     [
kkonganti@1:         '/hpc/scratch/test/salmon_idx_for_FAL00870'
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 input setup for `salmon quant`.
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_or_bam`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow input type of `path` pointing to either an alignment file (Ex: `.bam`) or a reads file (Ex: `.fastq.gz`) on which `salmon quant` should be run.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `index_or_tr_fasta`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow input type of `path` pointing to either a folder containing `salmon index` files or a trasnscript FASTA file.
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: 'SALMON_QUANT' {
kkonganti@1:     ext.args = '--vbPrior 0.02'
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 a folder containing `salmon quant` result files.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `results`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the `salmon quant` result files 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.