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+++ b/0.2.1/modules/centrifuge/classify/README.md	Mon Jun 27 15:55:37 2022 -0400
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+# NextFlow DSL2 Module
+
+```bash
+CENTRIFUGE_CLASSIFY
+```
+
+## Description
+
+Run `centrifuge` tool on reads in FASTQ format. Produces 3 output files in ASCII text format and optional output files.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of reads of type `path` (`reads`) per sample (`id:`).
+
+Ex:
+
+```groovy
+[ 
+    [ id: 'FAL00870',
+       strandedness: 'unstranded',
+       single_end: true,
+       centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
+    ],
+    '/hpc/scratch/test/FAL000870/f1.merged.fq.gz'
+]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the FASTQ file.
+
+Ex:
+
+```groovy
+[ 
+    id: 'FAL00870',
+    strandedness: 'unstranded',
+    single_end: true,
+    centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
+]
+```
+
+\
+ 
+
+#### `reads`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to FASTQ files on which `centrifuge` classification should be run.
+
+\
+ 
+
+#### `args`
+
+Type: Groovy String
+
+String of optional command-line arguments to be passed to the tool. This can be mentioned in `process` scope within `withName:process_name` block using `ext.args` option within your `nextflow.config` file.
+
+Ex:
+
+```groovy
+withName: 'CENTRIFUGE_CLASSIFY' {
+    ext.args = '--met 3'
+}
+```
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and list of `centrifuge` result files.
+
+\
+ 
+
+#### `report`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `centrifuge` report table file (`.report.txt`) per sample (`id:`).
+
+\
+ 
+
+#### `output`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `centrifuge` output table file (`.output.txt`) per sample (`id:`).
+
+\
+ 
+
+#### `kreport`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `centrifuge` **Kraken** style report table file (`.kreport.txt`) per sample (`id:`).
+
+\
+ 
+
+#### `sam`
+
+Type: `path`
+\
+Optional: `true`
+
+NextFlow output type of `path` pointing to the `centrifuge` alignment results in SAM (`.sam`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_out_fmt_sam` command-line option when the NextFlow pipeline is called.
+
+\
+ 
+
+#### `fastq_mapped`
+
+Type: `path`
+\
+Optional: `true`
+
+NextFlow output type of `path` pointing to the `centrifuge` alignment results in FASTQ (`.fastq.gz`) format per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_aligned` command-line option when the NextFlow pipeline is called.
+
+\
+ 
+
+#### `fastq_unmapped`
+
+Type: `path`
+\
+Optional: `true`
+
+NextFlow output type of `path` pointing to the `centrifuge` FASTQ (`.fastq.gz`) files of unaligned reads per sample (`id:`). Obtaining this output will depend on the mention of `--centrifuge_save_unaligned` command-line option when the NextFlow pipeline is called.
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.