Merge pull request #2540 from nf-core/fix-conda

Fix conda environment reference
nf-core · Nov 27, 2023 · 3a3ecbc · 3a3ecbc
2 parents db3c449 + 84f92bc
commit 3a3ecbc
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Showing 3 changed files with 3 additions and 2 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,7 @@
 - Fix writing files to a remote outdir in the NfcoreTemplate helper functions ([#2465](https://github.com/nf-core/tools/pull/2465))
 - Fancier syntax highlighting for example samplesheets in the usage.md template ([#2503](https://github.com/nf-core/tools/pull/2503))
 - Use closure for multiqc ext.args ([#2509](https://github.com/nf-core/tools/pull/2509))
+- Fix how the modules template references the conda environment file ([#2540](https://github.com/nf-core/tools/pull/2540))
 
 ### Linting
 

diff --git a/nf_core/module-template/modules/main.nf b/nf_core/module-template/modules/main.nf
@@ -27,7 +27,7 @@ process {{ component_name_underscore|upper }} {
     //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
     // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     {% endif -%}
-    conda '${modulesDir}/environment.yml'
+    conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         '{{ singularity_container if singularity_container else 'https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE' }}':
         '{{ docker_container if docker_container else 'biocontainers/YOUR-TOOL-HERE' }}' }"

diff --git a/nf_core/modules/lint/environment_yml.py b/nf_core/modules/lint/environment_yml.py
@@ -32,7 +32,7 @@ def environment_yml(module_lint_object: ComponentLint, module: NFCoreComponent)
         # check if the module's main.nf requires a conda environment
         with open(Path(module.component_dir, "main.nf"), "r") as fh:
             main_nf = fh.read()
-            if "conda '${modulesDir}/environment.yml'" in main_nf:
+            if 'conda "${moduleDir}/environment.yml"' in main_nf:
                 module.failed.append(
                     ("environment_yml_exists", "Module's `environment.yml` does not exist", module.environment_yml)
                 )