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Changing retrieval of file extension from EDAM #3512

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Merged
merged 4 commits into from
Mar 27, 2025
Merged

Changing retrieval of file extension from EDAM #3512

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6db7989
changing retrieval of file extension from EDAM https://github.com/nf-…
toniher Mar 26, 2025
5d510e9
[automated] Update CHANGELOG.md
nf-core-bot Mar 26, 2025
570b628
Update nf_core/modules/modules_utils.py
toniher Mar 27, 2025
ec7a139
[automated] Fix code linting
nf-core-bot Mar 27, 2025
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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 @@ -52,6 +52,7 @@
- Ontology fix comment yaml ([#3502](https://github.com/nf-core/tools/pull/3502))
- Bugfix - add back logo to the README ([#3504](https://github.com/nf-core/tools/pull/3504))
- Update dead link ([#3505](https://github.com/nf-core/tools/pull/3505))
- Changing retrieval of file extension from EDAM ([#3512](https://github.com/nf-core/tools/pull/3512))

## [v3.2.0 - Pewter Pangolin](https://github.com/nf-core/tools/releases/tag/3.2.0) - [2025-01-27]

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8 changes: 6 additions & 2 deletions nf_core/modules/modules_utils.py
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Expand Up @@ -108,6 +108,10 @@ def load_edam():
for line in response.content.splitlines():
fields = line.decode("utf-8").split("\t")
if fields[0].split("/")[-1].startswith("format"):
extension = fields[1].lower().split(" ")[0]
edam_formats[extension] = (fields[0], fields[1]) # URL, name
# We choose an already provided extension
if fields[14]:
extensions = fields[14].split("|")
for extension in extensions:
if extension not in edam_formats:
edam_formats[extension] = (fields[0], fields[1]) # URL, name
return edam_formats
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