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2311 interpret docker.registry automatically #2318

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merged 8 commits into from
Jun 15, 2023
+28 −9
Merged

2311 interpret docker.registry automatically #2318

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6a2adc1
feat (2311): Infer docker.registry value from nextflow.config
adamrtalbot Jun 13, 2023
5d16c04
Update test
adamrtalbot Jun 13, 2023
ed184c2
Merge branch 'dev' into 2311-interpret-docker.registry-automatically
adamrtalbot Jun 13, 2023
1d796dc
Update test to remove single quotes
adamrtalbot Jun 14, 2023
56d0c36
better language around help text
adamrtalbot Jun 14, 2023
c91aaa6
Merge branch 'dev' into 2311-interpret-docker.registry-automatically
adamrtalbot Jun 15, 2023
0ed7210
Remove unused functioN
adamrtalbot Jun 15, 2023
10f1807
Merge branch 'dev' into 2311-interpret-docker.registry-automatically
adamrtalbot Jun 15, 2023
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Update test
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adamrtalbot committed Jun 13, 2023

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KyleFromNVIDIA Kyle Edwards
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commit 5d16c043202082d33ac779e2a55f365501c1ea9b
7 changes: 4 additions & 3 deletions tests/modules/lint.py
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Original file line number Diff line number Diff line change
@@ -85,12 +85,13 @@ def test_modules_lint_multiple_remotes(self):
def test_modules_lint_registry(self):
"""Test linting the samtools module and alternative registry"""
self.mods_install.install("samtools")
module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
module_lint.lint(print_results=False, registry="public.ecr.aws", module="samtools")
module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir, registry="public.ecr.aws")
module_lint.lint(print_results=False, module="samtools")
assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
assert len(module_lint.passed) > 0
assert len(module_lint.warned) >= 0
module_lint.lint(print_results=False, registry="quay.io", module="samtools")
module_lint = nf_core.modules.ModuleLint(dir=self.pipeline_dir)
module_lint.lint(print_results=False, module="samtools")
assert len(module_lint.failed) == 0, f"Linting failed with {[x.__dict__ for x in module_lint.failed]}"
assert len(module_lint.passed) > 0
assert len(module_lint.warned) >= 0