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+++ b/0.7.0/modules/cat/fastq/README.md	Mon Jul 15 10:42:02 2024 -0400
@@ -0,0 +1,96 @@
+# NextFlow DSL2 Module
+
+```bash
+CAT_FASTQ
+```
+
+## Description
+
+Concatenates a list of FASTQ files. Produces 2 files per sample (`id:`) if `single_end` is `false` as mentioned in the metadata Groovy Map.
+
+\
+ 
+
+### `input:`
+
+___
+
+Type: `tuple`
+
+Takes in the following tuple of metadata (`meta`) and a list of FASTQ files of input type `path` (`reads`) to be concatenated.
+
+Ex:
+
+```groovy
+[ [id: 'sample1', single_end: true], ['/data/sample1/f_L001.fq', '/data/sample1/f_L002.fq'] ]
+```
+
+\
+ 
+
+#### `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 list of FASTQ files.
+
+\
+ 
+
+#### `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: 'CAT_FASTQ' {
+    ext.args = '--genome_size 5.5m'
+}
+```
+
+\
+ 
+
+### `output:`
+
+___
+
+Type: `tuple`
+
+Outputs a tuple of metadata (`meta` from `input:`) and list of concatenated FASTQ files (`catted_reads`).
+
+\
+ 
+
+#### `catted_reads`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the concatenated FASTQ files per sample (`id:`).
+
+\
+ 
+
+#### `versions`
+
+Type: `path`
+
+NextFlow output type of `path` pointing to the `.yml` file storing software versions for this process.