diff --git a/.nf-core.yml b/.nf-core.yml
index f14a790..8e80851 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -8,12 +8,14 @@ lint:
     - .github/workflows/awstest.yml
     - .github/workflows/awsfulltest.yml
     - conf/igenomes.config
+    - .github/workflows/linting_comment.yml
   files_unchanged:
     - CODE_OF_CONDUCT.md
     - assets/nf-core-accurascoperna_logo_light.png
     - docs/images/nf-core-accurascoperna_logo_light.png
     - docs/images/nf-core-accurascoperna_logo_dark.png
     - .github/ISSUE_TEMPLATE/bug_report.yml
+    - .github/workflows/linting.yml
   multiqc_config:
     - report_comment
   nextflow_config:
diff --git a/docs/parameters.md b/docs/parameters.md
index d5ac4c5..dd5bcb9 100644
--- a/docs/parameters.md
+++ b/docs/parameters.md
@@ -75,7 +75,7 @@ Less common options for the pipeline, typically set in a config file.
 |-----------|-----------|-----------|-----------|-----------|-----------|
 | `help` | Display help text. | `boolean` |  |  | True |
 | `version` | Display version and exit. | `boolean` |  |  | True |
-| `publish_dir_mode` | Method used to save pipeline results to output directory. <details><summary>Help</summary><small>The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.</small></details>| `string` | copy |  | True |
+| `publish_dir_mode` | Method used to save pipeline results to output directory. <details><summary>Help</summary><small>The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.</small></details>| `string` | symlink |  | True |
 | `email_on_fail` | Email address for completion summary, only when pipeline fails. <details><summary>Help</summary><small>An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.</small></details>| `string` |  |  | True |
 | `plaintext_email` | Send plain-text email instead of HTML. | `boolean` |  |  | True |
 | `max_multiqc_email_size` | File size limit when attaching MultiQC reports to summary emails. | `string` | 25.MB |  | True |
diff --git a/nextflow_schema.json b/nextflow_schema.json
index 03ea42c..8a98053 100644
--- a/nextflow_schema.json
+++ b/nextflow_schema.json
@@ -222,7 +222,7 @@
                 },
                 "publish_dir_mode": {
                     "type": "string",
-                    "default": "copy",
+                    "default": "symlink",
                     "description": "Method used to save pipeline results to output directory.",
                     "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.",
                     "fa_icon": "fas fa-copy",