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Important! Template update for nf-core/tools v3.3.1#172

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muffato merged 10 commits into
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nf-core-template-merge-3.3.1
Jul 4, 2025
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Important! Template update for nf-core/tools v3.3.1#172
muffato merged 10 commits into
devfrom
nf-core-template-merge-3.3.1

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@sanger-tolsoft

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Version 3.3.1 of nf-core/tools has just been released with updates to the nf-core template. This automated pull-request attempts to apply the relevant updates to this pipeline.

Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the nf-core-template-merge-3.3.1 branch (or your own fork, if you prefer). Once complete, make a new minor release of your pipeline.

For instructions on how to merge this PR, please see https://nf-co.re/docs/contributing/sync/.

For more information about this release of nf-core/tools, please see the v3.3.1 release page.

@sainsachiko sainsachiko requested a review from muffato June 23, 2025 14:04
@sainsachiko

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Could you please review this @muffato? Thank you!
Please note that more comprehensive nf-test cases and assertions will follow in another PR once the output structure is stable after fixing other issues. Currently, assertions on output contents are disabled due to differing MD5 sums, likely caused by inconsistent reference genome paths in CRAM headers between each runs.

Comment thread tests/default.nf.test Outdated
@sainsachiko sainsachiko reopened this Jun 26, 2025
@sanger-tol sanger-tol deleted a comment from sanger-tolsoft Jun 26, 2025
@muffato muffato force-pushed the nf-core-template-merge-3.3.1 branch from 681d488 to a7dce1a Compare July 2, 2025 23:13
@muffato muffato merged commit 0290662 into dev Jul 4, 2025
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@muffato muffato deleted the nf-core-template-merge-3.3.1 branch July 4, 2025 10:42
@muffato muffato added this to the v1.4.0 milestone Feb 19, 2026
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3 participants