Apply 2.0.3 to dev#243
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Agent-Logs-Url: https://github.com/sanger-tol/readmapping/sessions/a61689a5-a2a7-402a-bd52-58075aec1701 Co-authored-by: sainsachiko <134130358+sainsachiko@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
Co-authored-by: Copilot Autofix powered by AI <175728472+Copilot@users.noreply.github.com>
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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: 3.5.2. For more documentation on how to update your pipeline, please see the nf-core documentation and Synchronisation documentation. |
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Pull request overview
This PR applies the v2.0.3 release metadata and updates PacBio barcode handling so empty barcode values are accepted and covered by refreshed snapshots.
Changes:
- Bumped pipeline metadata and release references from 2.0.2 to 2.0.3.
- Updated PacBio adapter YAML handling to avoid barcode substitution when barcode is empty.
- Updated samplesheet documentation, example data, and nf-test snapshots.
Reviewed changes
Copilot reviewed 14 out of 14 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
.nf-core.yml |
Updates template version to 2.0.3. |
CHANGELOG.md |
Adds v2.0.3 release notes. |
CITATION.cff |
Updates citation release metadata. |
assets/samplesheet.csv |
Adds an empty-barcode PacBio example case. |
docs/usage.md |
Documents required and optional samplesheet columns. |
nextflow.config |
Bumps manifest version. |
nextflow_schema.json |
Clarifies input CSV may have at least four columns. |
ro-crate-metadata.json |
Updates RO-Crate context and release metadata. |
subworkflows/local/align_long.nf |
Branches PacBio YAML handling by barcode presence. |
tests/default.nf.test.snap |
Refreshes default snapshot outputs for v2.0.3 and empty barcode behavior. |
tests/short_aligner_minimap2.nf.test.snap |
Refreshes workflow version snapshot. |
tests/uli.nf.test.snap |
Refreshes workflow version snapshot. |
tests/uli_no_lima.nf.test.snap |
Refreshes workflow version snapshot. |
tests/untrim.nf.test.snap |
Refreshes workflow version snapshot. |
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muffato
approved these changes
May 15, 2026
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Apply 2.0.3 to dev
PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).