--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/0.4.2/modules/seqsero2/README.md	Wed Jul 03 15:16:39 2024 -0400
@@ -0,0 +1,96 @@
+# NextFlow DSL2 Module
+
+```bash
+SEQSERO2
+```
+
+## Description
+
+Run `seqsero2` tool on a list of assembled *Salmonella* contigs in FASTA format or sequencing reads in FASTQ format.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of assemled contig FASTA files or list of sequencing reads in FASTQ format of input type `path` (`reads_or_asm`).
+
+Ex:
+
+```groovy
+[ [id: 'sample1', single_end: true], '/data/sample1/f_assembly.fa' ]
+```
+
+\
+ 
+
+#### `meta`
+
+Type: Groovy Map
+
+A Groovy Map containing the metadata about the FASTQ files or assembly FASTA files.
+
+Ex:
+
+```groovy
+[ id: 'FAL00870', strandedness: 'unstranded', single_end: true ]
+```
+
+\
+ 
+
+#### `reads_or_asm`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to assembled contig file in FASTA format or sequencing reads in FASTQ format.
+
+\
+ 
+
+#### `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: 'SEQSERO2' {
+    ext.args = '-b mem'
+}
+```
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and list of `seqsero2` result files (`serotyped`).
+
+\
+ 
+
+#### `serotyped`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `seqsero2` results table file per sample (`id:`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.