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Simplify charliecloud profile #867

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merged 3 commits into from
Mar 10, 2021
Merged

Simplify charliecloud profile #867

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7261ebd
simplify charliecloud config
phue Mar 5, 2021
e38bac3
Revert "nf-core bump-version: add charliecloud.config"
phue Mar 5, 2021
f1a9600
Update nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextfl…
ewels Mar 10, 2021
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12 changes: 0 additions & 12 deletions nf_core/bump_version.py
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Original file line number Diff line number Diff line change
Expand Up @@ -108,18 +108,6 @@ def bump_pipeline_version(pipeline_obj, new_version):
],
)

# conf/charliecloud.config - environment path
update_file_version(
"conf/charliecloud.config",
pipeline_obj,
[
(
r"nf-core-{}-{}".format(pipeline_obj.pipeline_name.lower(), current_version.replace(".", r"\.")),
"nf-core-{}-{}".format(pipeline_obj.pipeline_name.lower(), new_version),
)
],
)


def bump_nextflow_version(pipeline_obj, new_version):
"""Bumps the required Nextflow version number of a pipeline.
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22 changes: 0 additions & 22 deletions nf_core/pipeline-template/{{cookiecutter.name_noslash}}/conf/charliecloud.config
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4 changes: 3 additions & 1 deletion nf_core/pipeline-template/{{cookiecutter.name_noslash}}/nextflow.config
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Original file line number Diff line number Diff line change
Expand Up @@ -78,7 +78,9 @@ profiles {
shifter {
shifter.enabled = true
}
charliecloud { includeConfig 'conf/charliecloud.config' }
charliecloud {
charliecloud.enabled = true
}
test { includeConfig 'conf/test.config' }
test_full { includeConfig 'conf/test_full.config' }
}
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5 changes: 0 additions & 5 deletions tests/test_bump_version.py
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Expand Up @@ -47,11 +47,6 @@ def test_bump_pipeline_version(datafiles):
assert "ENV PATH /opt/conda/envs/nf-core-testpipeline-1.1/bin:$PATH" in dockerfile
assert "RUN conda env export --name nf-core-testpipeline-1.1 > nf-core-testpipeline-1.1.yml" in dockerfile

# Check charliecloud.config
with open(new_pipeline_obj._fp("conf/charliecloud.config")) as fh:
charliecloud_config = fh.read().splitlines()
assert ' PATH = "/opt/conda/bin:/opt/conda/envs/nf-core-testpipeline-1.1/bin:$PATH"' in charliecloud_config


def test_dev_bump_pipeline_version(datafiles):
""" Test that making a release works with a dev name and a leading v """
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