--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/1.0.0/modules/salmon/index/README.md	Thu May 28 20:31:42 2026 +0000
@@ -0,0 +1,88 @@
+# NextFlow DSL2 Module
+
+```bash
+SALMON_INDEX
+```
+
+## Description
+
+Run `salmon index` command on input FASTA file.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a FASTA file of type `path` (`genome_fasta`) per sample (`id:`).
+
+Ex:
+
+```groovy
+[ 
+    [ 
+        id: 'FAL00870'
+    ],
+    [
+        '/hpc/scratch/test/FAL00870_contigs.fasta',
+    ]
+]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the genome FASTA file.
+
+Ex:
+
+```groovy
+[ 
+    id: 'FAL00870'
+]
+```
+
+\
+ 
+
+#### `genome_fasta`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to the FASTA file (gzipped or unzipped) on which `salmon index` should be run.
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and a folder containing `salmon index` result files.
+
+\
+ 
+
+#### `idx`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `salmon index` result files per sample (`id:`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.