--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/kraken2/classify/README.md	Thu Jun 27 14:17:26 2024 -0400
@@ -0,0 +1,121 @@
+# NextFlow DSL2 Module
+
+```bash
+KRAKEN2_CLASSIFY
+```
+
+## Description
+
+Run `kraken2` tool on reads in FASTQ format. Produces 4 output files per sample (`id:`) in ASCII text format.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of reads or FASTA assembly of type `path` (`reads`) per sample (`id:`).
+
+Ex:
+
+```groovy
+[ 
+    [ id: 'FAL00870',
+       strandedness: 'unstranded',
+       single_end: true,
+       is_assembly: false,
+       centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
+       kraken2_db: '/hpc/db/kraken2/standard-210914',
+    ],
+    '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
+]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the FASTQ / FASTA file.
+
+Ex:
+
+```groovy
+[ 
+    id: 'FAL00870',
+    strandedness: 'unstranded',
+    single_end: true,
+    is_assembly: false,
+    kraken2_db: '/hpc/db/kraken2/standard-210914'
+]
+```
+
+\
+ 
+
+#### `reads`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to FASTQ files on which `kraken2` classification should be run.
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and list of `kraken2` result files.
+
+\
+ 
+
+#### `kraken_report`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `kraken2` report table file (`.report.txt`) per sample (`id:`).
+
+\
+ 
+
+#### `kraken_output`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `kraken2` output table file (`.output.txt`) per sample (`id:`).
+
+\
+ 
+
+#### `classified`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that have been classified (`*classified.fastq`) per sample (`id:`).
+
+\
+ 
+
+#### `unclassified`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `kraken2` processed gzipped FASTQ files containing only reads that are unclassified (`*unclassified.fastq`) per sample (`id:`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.