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Fix duplicate -b short flag in pipelines sync#4311

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ewels merged 1 commit into
nf-core:devfrom
ewels:fix-duplicate-b-flag
May 29, 2026
Merged

Fix duplicate -b short flag in pipelines sync#4311
ewels merged 1 commit into
nf-core:devfrom
ewels:fix-duplicate-b-flag

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@ewels ewels commented May 29, 2026

Summary

Fixes a pre-existing UserWarning: The parameter -b is used more than once emitted on startup.

nf-core pipelines sync assigned the -b short flag to two different options:

  • -b, --from-branch
  • -b, --blog-post

This made -b ambiguous and triggered the warning whenever the CLI was loaded.

Fix

Drop -b from --blog-post (now long-form only), keeping -b for --from-branch. This matches the -b/branch convention used elsewhere in the CLI (for example test-datasets ... --branch).

🤖 Generated with Claude Code

`nf-core pipelines sync` assigned `-b` to both `--from-branch` and
`--blog-post`, which triggered a `UserWarning: The parameter -b is used more
than once` and made the short flag ambiguous. Drop `-b` from `--blog-post`
(now long-form only), keeping `-b` for `--from-branch` to match the `-b`/branch
convention used elsewhere in the CLI.

Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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codecov Bot commented May 29, 2026

Codecov Report

✅ All modified and coverable lines are covered by tests.
✅ Project coverage is 78.34%. Comparing base (b6c5737) to head (f35a62b).
⚠️ Report is 39 commits behind head on dev.

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@ewels ewels requested a review from a team May 29, 2026 08:46
@ewels ewels merged commit 03bcc65 into nf-core:dev May 29, 2026
117 of 118 checks passed
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2 participants