kkonganti@17: # NextFlow DSL2 Module
kkonganti@17: 
kkonganti@17: ```bash
kkonganti@17: SALMON_INDEX
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: ## Description
kkonganti@17: 
kkonganti@17: Run `salmon index` command on input FASTA file.
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: ### `input:`
kkonganti@17: 
kkonganti@17: ___
kkonganti@17: 
kkonganti@17: Type: `tuple`
kkonganti@17: 
kkonganti@17: Takes in the following tuple of metadata (`meta`) and a FASTA file of type `path` (`genome_fasta`) per sample (`id:`).
kkonganti@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: [ 
kkonganti@17:     [ 
kkonganti@17:         id: 'FAL00870'
kkonganti@17:     ],
kkonganti@17:     [
kkonganti@17:         '/hpc/scratch/test/FAL00870_contigs.fasta',
kkonganti@17:     ]
kkonganti@17: ]
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `meta`
kkonganti@17: 
kkonganti@17: Type: Groovy Map
kkonganti@17: 
kkonganti@17: A Groovy Map containing the metadata about the genome FASTA file.
kkonganti@17: 
kkonganti@17: Ex:
kkonganti@17: 
kkonganti@17: ```groovy
kkonganti@17: [ 
kkonganti@17:     id: 'FAL00870'
kkonganti@17: ]
kkonganti@17: ```
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `genome_fasta`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow input type of `path` pointing to the FASTA file (gzipped or unzipped) on which `salmon index` should be run.
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: ### `output:`
kkonganti@17: 
kkonganti@17: ___
kkonganti@17: 
kkonganti@17: Type: `tuple`
kkonganti@17: 
kkonganti@17: Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon index` result files.
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `idx`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output type of `path` pointing to the `salmon index` result files per sample (`id:`).
kkonganti@17: 
kkonganti@17: \
kkonganti@17:  
kkonganti@17: 
kkonganti@17: #### `versions`
kkonganti@17: 
kkonganti@17: Type: `path`
kkonganti@17: 
kkonganti@17: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.