Merge pull request #3029 from ewels/module-conda-env-remove-defaults

Linting: Remove 'defaults' from conda environment.yml file.
nf-core · Aug 23, 2024 · 557fe91 · 557fe91
2 parents 6c1ec7a + 113fa42
commit 557fe91
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Showing 9 changed files with 6 additions and 8 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -24,6 +24,7 @@
 
 - Fix linting fail on nfcore_external_java_deps if nf_schema is used ([#2976](https://github.com/nf-core/tools/pull/2976))
 - Conda module linting: Include package name in log file ([#3014](https://github.com/nf-core/tools/pull/3014))
+- Remove defaults from conda `environment.yml` file. ([#3029](https://github.com/nf-core/tools/pull/3029))
 - Restructure pipeline tests and move pipeline linting into subfolder ([#3070](https://github.com/nf-core/tools/pull/3070))
 - Fix module linting warning for process_high_memory ([#3086](https://github.com/nf-core/tools/issues/3086))
 

diff --git a/nf_core/module-template/environment.yml b/nf_core/module-template/environment.yml
@@ -4,6 +4,5 @@ name: "{{ component_name_underscore }}"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
   - "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
diff --git a/nf_core/pipeline-template/modules.json b/nf_core/pipeline-template/modules.json
@@ -22,7 +22,7 @@
                 "nf-core": {
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
+                        "git_sha": "20c03aede5a80ff520a905cea1f8ca121b5bb661",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {

diff --git a/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/fastqc/environment.yml
diff --git a/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml b/nf_core/pipeline-template/modules/nf-core/multiqc/environment.yml
diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config
@@ -102,7 +102,7 @@ profiles {
         podman.enabled          = false
         shifter.enabled         = false
         charliecloud.enabled    = false
-        conda.channels          = ['conda-forge', 'bioconda', 'defaults']
+        conda.channels          = ['conda-forge', 'bioconda']
         apptainer.enabled       = false
     }
     mamba {

diff --git a/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf b/nf_core/pipeline-template/subworkflows/nf-core/utils_nextflow_pipeline/main.nf
diff --git a/nf_core/utils.py b/nf_core/utils.py
@@ -654,7 +654,7 @@ def anaconda_package(dep, dep_channels=None):
     """
 
     if dep_channels is None:
-        dep_channels = ["conda-forge", "bioconda", "defaults"]
+        dep_channels = ["conda-forge", "bioconda"]
 
     # Check if each dependency is the latest available version
     if "=" in dep:

diff --git a/tests/test_utils.py b/tests/test_utils.py
@@ -81,7 +81,7 @@ def testload_pipeline_config(self):
     # def test_load_conda_env(self):
     #     """Load the pipeline Conda environment.yml file"""
     #     self.pipeline_obj._load_conda_environment()
-    #     assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda", "defaults"]
+    #     assert self.pipeline_obj.conda_config["channels"] == ["conda-forge", "bioconda"]
 
     def test_list_files_git(self):
         """Test listing pipeline files using `git ls`"""