--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/centrifuge/extract/README.md	Thu Jun 27 14:17:26 2024 -0400
@@ -0,0 +1,113 @@
+# NextFlow DSL2 Module
+
+```bash
+CENTRIFUGE_EXTRACT
+```
+
+## Description
+
+Extract FASTQ reads given a FASTQ file originally used with `centrifuge` tool and a taxa of interest. This specific module uses only GNU Coreutils to create a list of FASTQ read ids that need to be extract. See also `CENTRIFUGE_PROCESS` module which uses a `python` script to generate the FASTQ read ids.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following 2 tuples:
+
+- A tuple of metadata (`meta`) and of type `path` (`centrifuge_output`) per sample (`id:`).
+
+- A tuple of metadata (`meta`) and of type `path` (`centrifuge_report`) 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.cent_out.output.txt'
+]
+
+[ 
+    [ id: 'FAL00870',
+       strandedness: 'unstranded',
+       single_end: true,
+       centrifuge_x: '/hpc/db/centrifuge/2022-04-12/ab'
+    ],
+    '/hpc/scratch/test/FAL000870/f1.merged.cent_out.report.txt'
+]
+```
+
+\
+ 
+
+#### `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'
+]
+```
+
+\
+ 
+
+#### `centrifuge_report`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to `centrifuge` report file generated using `--report-file` option of `centrifuge` tool.
+
+\
+ 
+
+#### `centrifuge_output`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to `centrifuge` output file generated using `-S` option of `centrifuge` tool.
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and list of extracted FASTQ read ids.
+
+\
+ 
+
+#### `extracted`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the extracted FASTQ read ids belonging to a particular taxa (`*.extract-centrifuge-bug-ids.txt`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.