kkonganti@1: # NextFlow DSL2 Module
kkonganti@1: 
kkonganti@1: ```bash
kkonganti@1: SALMON_INDEX
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: ## Description
kkonganti@1: 
kkonganti@1: Run `salmon index` command on input FASTA file.
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 FASTA file of type `path` (`genome_fasta`) per sample (`id:`).
kkonganti@1: 
kkonganti@1: Ex:
kkonganti@1: 
kkonganti@1: ```groovy
kkonganti@1: [ 
kkonganti@1:     [ 
kkonganti@1:         id: 'FAL00870'
kkonganti@1:     ],
kkonganti@1:     [
kkonganti@1:         '/hpc/scratch/test/FAL00870_contigs.fasta',
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 genome FASTA file.
kkonganti@1: 
kkonganti@1: Ex:
kkonganti@1: 
kkonganti@1: ```groovy
kkonganti@1: [ 
kkonganti@1:     id: 'FAL00870'
kkonganti@1: ]
kkonganti@1: ```
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `genome_fasta`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow input type of `path` pointing to the FASTA file (gzipped or unzipped) on which `salmon index` should be run.
kkonganti@1: 
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 index` result files.
kkonganti@1: 
kkonganti@1: \
kkonganti@1:  
kkonganti@1: 
kkonganti@1: #### `idx`
kkonganti@1: 
kkonganti@1: Type: `path`
kkonganti@1: 
kkonganti@1: NextFlow output type of `path` pointing to the `salmon index` 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.