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Modules restructure #1859

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merged 29 commits into from
Oct 4, 2022
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6cfe78e
change path for testing module structure
mirpedrol Sep 26, 2022
ae958d1
change module folder structure from pipeline template
mirpedrol Sep 26, 2022
1c8e634
change path from pipeline template
mirpedrol Sep 26, 2022
11e5d0d
change path from module_utils
mirpedrol Sep 26, 2022
ac38a14
change paths added to pytest_modules.yml
mirpedrol Sep 26, 2022
5235405
modify modules create command
mirpedrol Sep 26, 2022
05f1cb4
fix create-test-yml
mirpedrol Sep 26, 2022
7a2d46e
add variables to ModuleCommand
mirpedrol Sep 26, 2022
e2ec9a7
fix paths for linting modules
mirpedrol Sep 27, 2022
a7d62a3
fix paths for bump-versions
mirpedrol Sep 27, 2022
3cd1336
try to add any custom folder as nf-core inside modules
mirpedrol Sep 27, 2022
139818f
modules_json.py working (hopefully)
mirpedrol Sep 27, 2022
2d40c7e
lint bug fixed but lint not passing :(
mirpedrol Sep 27, 2022
cb7e95a
pipeline linting passing
mirpedrol Sep 30, 2022
2433fe8
modify modules structure with two levels modules/nf-core or modules/c…
mirpedrol Sep 30, 2022
4cc55e5
fix some pytests
mirpedrol Oct 1, 2022
8366a77
more tests fixed
mirpedrol Oct 2, 2022
f7bdf41
fix sha tests
mirpedrol Oct 3, 2022
58f1491
fix gitlab workflow
mirpedrol Oct 3, 2022
94231c4
fix linting
mirpedrol Oct 3, 2022
3a02093
gitlab force
mirpedrol Oct 3, 2022
e96386e
fix yaml sha
mirpedrol Oct 3, 2022
dd7fb4f
fix isort
mirpedrol Oct 3, 2022
aa0e6c8
Merge branch 'dev' into modules-restructure
mirpedrol Oct 3, 2022
79a48fd
remove branch and url from specific modules command
mirpedrol Oct 4, 2022
9ddc614
update changelog
mirpedrol Oct 4, 2022
683568a
change nf-core/modules branch to master
mirpedrol Oct 4, 2022
cb0ab31
change sha for master branch
mirpedrol Oct 4, 2022
ee8459a
update custom/dumpsoftwareversions to last commit
mirpedrol Oct 4, 2022
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fix paths for linting modules
  • Loading branch information
mirpedrol committed Sep 27, 2022
commit e2ec9a7493474e0f803cb2fe4d8bfe7a1da0dfeb
2 changes: 1 addition & 1 deletion nf_core/modules/lint/__init__.py
Original file line number Diff line number Diff line change
Expand Up @@ -102,7 +102,7 @@ def __init__(
else:
raise LookupError(f"No modules from {self.modules_repo.remote_url} installed in pipeline.")
else:
module_dir = Path(self.dir, "modules")
module_dir = Path(self.dir, self.default_modules_path)
self.all_remote_modules = [
NFCoreModule(m, None, module_dir / m, self.repo_type, Path(self.dir))
for m in self.get_modules_clone_modules()
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2 changes: 1 addition & 1 deletion nf_core/modules/modules_command.py
Original file line number Diff line number Diff line change
Expand Up @@ -40,7 +40,7 @@ def get_modules_clone_modules(self):
"""
Get the modules available in a clone of nf-core/modules
"""
module_base_path = Path(self.dir, "modules")
module_base_path = Path(self.dir, self.default_modules_path)
return [
str(Path(dir).relative_to(module_base_path))
for dir, _, files in os.walk(module_base_path)
Expand Down
2 changes: 1 addition & 1 deletion nf_core/modules/nfcore_module.py
Original file line number Diff line number Diff line change
Expand Up @@ -43,7 +43,7 @@ def __init__(self, module_name, repo_name, module_dir, repo_type, base_dir, nf_c
self.main_nf = self.module_dir / "main.nf"
self.meta_yml = self.module_dir / "meta.yml"

self.test_dir = Path(self.base_dir, "tests", "modules", self.module_name)
self.test_dir = Path(self.base_dir, "tests", self.module_dir)
self.test_yml = self.test_dir / "test.yml"
self.test_main_nf = self.test_dir / "main.nf"

Expand Down