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Download: Add apptainer to the list of false positve container strings #2353

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Jun 30, 2023
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Download: Add apptainer to the list of false positve container strings #2353

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d2b8a45
Add apptainer keyword to the list of false positive matches. Bare min…
MatthiasZepper Jun 30, 2023
464f2fb
update changelog
mirpedrol Jun 30, 2023
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -29,6 +29,7 @@
- Refactored the CLI parameters related to container images. Although downloading other images than those of the Singularity/Apptainer container system is not supported for the time being, a generic name for the parameters seemed preferable. So the new parameter `--singularity-cache-index` introduced in [#2247](https://github.com/nf-core/tools/pull/2247) has been renamed to `--container-cache-index` prior to release ([#2336](https://github.com/nf-core/tools/pull/2336)).
- To address issue [#2311](https://github.com/nf-core/tools/issues/2311), a new parameter `--container-library` was created allowing to specify the container library (registry) from which container images in OCI format (Docker) should be pulled ([#2336](https://github.com/nf-core/tools/pull/2336)).
- Container detection in configs was improved. This allows for DSL2-like container definitions inside the container parameter value provided to process scopes [#2346](https://github.com/nf-core/tools/pull/2346).
- Add apptainer to the list of false positve container strings ([#2353](https://github.com/nf-core/tools/pull/2353)).

#### Updated CLI parameters

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5 changes: 2 additions & 3 deletions nf_core/download.py
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Expand Up @@ -733,8 +733,7 @@ def find_container_images(self, workflow_directory):
re.DOTALL is used to account for the string to be spread out across multiple lines.
"""
container_regex = re.compile(
r"container\s+[\s{}=$]*(?P<quote>[\'\"])(?P<param>(?:.(?!\1))*.?)\1[\s}]*",
re.DOTALL,
r"container\s+[\s{}=$]*(?P<quote>[\'\"])(?P<param>(?:.(?!\1))*.?)\1[\s}]*", re.DOTALL
)

local_module_findings = re.findall(container_regex, search_space)
Expand Down Expand Up @@ -850,7 +849,7 @@ def rectify_raw_container_matches(self, raw_findings):

for _, capture in container_value_defs:
# common false positive(s)
if capture in ["singularity"]:
if capture in ["singularity", "apptainer"]:
continue

# Look for a http download URL.
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