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+++ b/0.4.2/modules/flye/assemble/README.md	Fri May 29 13:27:47 2026 +0000
@@ -0,0 +1,96 @@
+# NextFlow DSL2 Module
+
+```bash
+FLYE_ASSEMBLE
+```
+
+## Description
+
+Run `flye` assembler tool on a list of read files in FASTQ format.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of FASTQ files of input type `path` (`reads`).
+
+Ex:
+
+```groovy
+[ [id: 'sample1', single_end: true], '/data/sample1/f_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 ]
+```
+
+\
+ 
+
+#### `reads`
+
+Type: `path`
+
+NextFlow input type of `path` pointing to read files in FASTQ format that need to be *de novo* assembled.
+
+\
+ 
+
+#### `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: 'FLYE_ASSEMBLE' {
+    ext.args = '--casava'
+}
+```
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and `flye` assembled contig file in FASTA format.
+
+\
+ 
+
+#### `assembly`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `flye` assembler results file per sample (`id:`) i.e., the final assembled contig file in FASTA format.
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.