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+# NextFlow DSL2 Module
+
+```bash
+KRAKEN2_EXTRACT
+```
+
+## Description
+
+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.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in a tuple in order of metadata (`meta`), a `path` (`kraken2_output`) type and another `path` (`assembly`) per sample (`id:`).
+
+Ex:
+
+```groovy
+[ 
+    [ id: 'FAL00870',
+       strandedness: 'unstranded',
+       single_end: true,
+       kraken2_db: '/hpc/db/kraken2/standard-210914'
+    ],
+    '/hpc/scratch/test/FAL000870/f1.merged.kraken2.output.txt',
+    '/hpc/scratch/test/FAL000870/f1.assembly.fasta'
+]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the FASTA file.
+
+Ex:
+
+```groovy
+[ 
+    id: 'FAL00870',
+    strandedness: 'unstranded',
+    single_end: true,
+    kraken2_db: '/hpc/db/kraken2/standard-210914'
+]
+```
+
+\
+ 
+
+#### `kraken2_output`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to `kraken2` output file generated using `--output` option of `kraken2` tool.
+
+\
+ 
+
+#### `assembly`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to a FASTA format file, in this case an assembled contig file in FASTA format.
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
+
+\
+ 
+
+#### `asm_filtered_contigs`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the extracted FASTA reads or contigs belonging to a particular taxa.
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.