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Remove nfcore_external_java_deps.jar from lib directory in pipeline template #2675

Merged
merged 11 commits into from
Jan 26, 2024
Merged

Remove nfcore_external_java_deps.jar from lib directory in pipeline template #2675

merged 11 commits into from
Jan 26, 2024

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drpatelh
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This is no longer required as it should have been replaced by the nf-validation plugin.

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@drpatelh drpatelh changed the base branch from master to dev January 20, 2024 13:51
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Tests are failing due to:

╭─ [✗] 2 Pipeline Tests Failed ────────────────────────────────────────────────╮
│                                                                              │
│ files_exist: File not found: lib/nfcore_external_java_deps.jar               │
│ files_unchanged: File does not exist: lib/nfcore_external_java_deps.jar      │
│                                                                              │
╰──────────────────────────────────────────────────────────────────────────────╯

Do we generate a lint error in the future if this file is found in the template or we keep it there for those to remove if they are using nf-validation?

@mirpedrol mirpedrol added this to the 2.12 milestone Jan 24, 2024
@mashehu mashehu self-assigned this Jan 25, 2024
mirpedrol
mirpedrol reviewed Jan 26, 2024
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mirpedrol
mirpedrol approved these changes Jan 26, 2024
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LGTM!

@mashehu mashehu merged commit 5e4147c into dev Jan 26, 2024
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@mashehu mashehu deleted the rm_nfcore_external_java_deps branch January 26, 2024 11:37
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