Fix params.save_merged to properly save merged files

CHANGELOG.md

@@ -14,6 +14,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Fixed`
 
+- [#163](https://github.com/nf-core/bacass/pull/163) Fixed `params.save_merged` to properly save merged files
 - [#160](https://github.com/nf-core/bacass/pull/160) Fixed memory issues in KmerFinder, fixed handling of no species detected, and fixed handling of empty fasta files in the prokka/bakkta channel.
 - [#157](https://github.com/nf-core/bacass/pull/157) Fixed corrupted zenodo URL of Kmerfinder database.
 - [#154](https://github.com/nf-core/bacass/pull/154) Fixed kmerfinder script and increase resources to prevent memory issues.

conf/modules.config

@@ -270,6 +270,12 @@ if (!params.skip_fastp) {
                     mode: params.publish_dir_mode,
                     pattern: "*.fail.fastq.gz",
                     enabled: params.save_trimmed_fail
+                ],
+                [
+                    path: { "${params.outdir}/trimming/shortreads" },
+                    mode: params.publish_dir_mode,
+                    pattern: "*.merged.fastq.gz",
+                    enabled: params.save_merged
                 ]
             ]
         }

nextflow_schema.json

@@ -56,7 +56,7 @@
                 },
                 "save_merged": {
                     "type": "boolean",
-                    "description": "save all merged reads to the a file ending in `*.merged.fastq.gz`"
+                    "description": "save all merged reads to the a file ending in `*.merged.fastq.gz`. This option enables read merging and saves all merged reads to a file ending in `*.merged.fastq.gz`; these reads will be won't be  passed to the assembly process."
                 },
                 "skip_fastqc": {
                     "type": "boolean",