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Merge pull request #3029 from ewels/module-conda-env-remove-defaults
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Linting: Remove 'defaults' from conda environment.yml file.
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mirpedrol authored Aug 23, 2024
2 parents 6c1ec7a + 113fa42 commit 557fe91
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Showing 9 changed files with 6 additions and 8 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -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))

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1 change: 0 additions & 1 deletion nf_core/module-template/environment.yml
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Expand Up @@ -4,6 +4,5 @@ name: "{{ component_name_underscore }}"
channels:
- conda-forge
- bioconda
- defaults
dependencies:
- "{{ bioconda if bioconda else 'YOUR-TOOL-HERE' }}"
2 changes: 1 addition & 1 deletion nf_core/pipeline-template/modules.json
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Expand Up @@ -22,7 +22,7 @@
"nf-core": {
"utils_nextflow_pipeline": {
"branch": "master",
"git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa",
"git_sha": "20c03aede5a80ff520a905cea1f8ca121b5bb661",
"installed_by": ["subworkflows"]
},
"utils_nfcore_pipeline": {
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2 changes: 1 addition & 1 deletion nf_core/pipeline-template/nextflow.config
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Expand Up @@ -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 {
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2 changes: 1 addition & 1 deletion nf_core/utils.py
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Expand Up @@ -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:
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2 changes: 1 addition & 1 deletion tests/test_utils.py
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Expand Up @@ -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`"""
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