kkonganti@0: # NextFlow DSL2 Module
kkonganti@0: 
kkonganti@0: ```bash
kkonganti@0: KRAKEN2_EXTRACT
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: ## Description
kkonganti@0: 
kkonganti@0: Extract FASTA reads or contigs given a FASTA file originally used with `kraken2` tool and a taxa of interest. This specific module uses a `python` script to generate the FASTA reads or contigs and as such requires a `bin` folder with `extract_assembled_filtered_contigs.py` script to be present where the NextFlow script will be executed from.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: ### `input:`
kkonganti@0: 
kkonganti@0: ___
kkonganti@0: 
kkonganti@0: Type: `tuple`
kkonganti@0: 
kkonganti@0: Takes in a tuple in order of metadata (`meta`), a `path` (`kraken2_output`) type and another `path` (`assembly`) per sample (`id:`).
kkonganti@0: 
kkonganti@0: Ex:
kkonganti@0: 
kkonganti@0: ```groovy
kkonganti@0: [ 
kkonganti@0:     [ id: 'FAL00870',
kkonganti@0:        strandedness: 'unstranded',
kkonganti@0:        single_end: true,
kkonganti@0:        kraken2_db: '/hpc/db/kraken2/standard-210914'
kkonganti@0:     ],
kkonganti@0:     '/hpc/scratch/test/FAL000870/f1.merged.kraken2.output.txt',
kkonganti@0:     '/hpc/scratch/test/FAL000870/f1.assembly.fasta'
kkonganti@0: ]
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `meta`
kkonganti@0: 
kkonganti@0: Type: Groovy Map
kkonganti@0: 
kkonganti@0: A Groovy Map containing the metadata about the FASTA file.
kkonganti@0: 
kkonganti@0: Ex:
kkonganti@0: 
kkonganti@0: ```groovy
kkonganti@0: [ 
kkonganti@0:     id: 'FAL00870',
kkonganti@0:     strandedness: 'unstranded',
kkonganti@0:     single_end: true,
kkonganti@0:     kraken2_db: '/hpc/db/kraken2/standard-210914'
kkonganti@0: ]
kkonganti@0: ```
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `kraken2_output`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow input type of `path` pointing to `kraken2` output file generated using `--output` option of `kraken2` tool.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `assembly`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow input type of `path` pointing to a FASTA format file, in this case an assembled contig file in FASTA format.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: ### `output:`
kkonganti@0: 
kkonganti@0: ___
kkonganti@0: 
kkonganti@0: Type: `tuple`
kkonganti@0: 
kkonganti@0: Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `asm_filtered_contigs`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the extracted FASTA reads or contigs belonging to a particular taxa.
kkonganti@0: 
kkonganti@0: \
kkonganti@0:  
kkonganti@0: 
kkonganti@0: #### `versions`
kkonganti@0: 
kkonganti@0: Type: `path`
kkonganti@0: 
kkonganti@0: NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.