Important! Template update for nf-core/tools v3.5.1#66
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Warning Newer version of the nf-core template is available. Your pipeline is using an old version of the nf-core template: 3.5.1. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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The 'Should run with both bed and bam input' snapshot stored a stale file count of 407, causing the CI run to fail with a snapshot mismatch. Regenerated with current pipeline output.
Two issues prevented 'nextflow run . --help' from working with the v2 syntax parser: 1. utils_nfschema_plugin: With v2, params.help is the string "true" (not a boolean) when --help is passed without a value. Guard against this by also checking != "true" before using it as a section filter in paramsHelp(). 2. utils_nfcore_tfactivity_pipeline: samplesheetToList() was called unconditionally, crashing when params.input/input_bam/counts_design are not real file paths (e.g. when --help is passed). Guard each call with an instanceof String check so channels are only created from valid file paths.
Upstream nf-core updates: - utils_nfcore_pipeline: removed imNotification() function - utils_nfschema_plugin tests: bumped nf-schema to 2.6.1 - utils_nfcore_pipeline tests: renamed test file from main.workflow.nf.test to main.nf.test Remove the imNotification include and call from utils_nfcore_tfactivity_pipeline since the function no longer exists in the upstream subworkflow.
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3.5.1of nf-core/tools has just been released with updates to the nf-core template. For more details, check out the blog post: https://nf-co.re/blog/2025/tools-3_5_0Please make sure to merge this pull-request as soon as possible, resolving any merge conflicts in the
nf-core-template-merge-3.5.1branch (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
v3.5.1release page.Note
Since nf-core/tools 3.5.0, older template update PRs will not be automatically closed, but will remain open in your pipeline repository. Older template PRs will be automatically closed once a newer template PR has been merged.