Linting: Remove 'defaults' from conda environment.yml file.

See nf-core/modules#5829
ewels · Jun 19, 2024 · 1e47693 · 1e47693
1 parent 4157a20
commit 1e47693
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Showing 6 changed files with 3 additions and 6 deletions.
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/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
@@ -98,7 +98,7 @@ 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/tests/test_utils.py b/tests/test_utils.py
@@ -105,7 +105,7 @@ def test_load_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`"""