added changelog and docs#162
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Pull request overview
This PR appears to finalize the v1.1.0 release metadata across the repository (manifest, RO-Crate, nf-core template config, changelog) and updates the nf-test snapshot accordingly.
Changes:
- Bump pipeline version references from
1.1.0devto1.1.0(manifest / RO-Crate / nf-core template metadata). - Update
CHANGELOG.mdfor thev1.1.0release notes. - Update nf-test snapshot output and tweak the Wakhan module container selection logic.
Reviewed changes
Copilot reviewed 6 out of 6 changed files in this pull request and generated 4 comments.
Show a summary per file
| File | Description |
|---|---|
tests/default.nf.test.snap |
Updates stored nf-test snapshot for expected outputs/versions (currently inconsistent with test assertions). |
ro-crate-metadata.json |
Updates RO-Crate release metadata (status, published/modified dates, version, URLs, ids). |
nextflow.config |
Sets manifest version to 1.1.0. |
modules/local/wakhan/main.nf |
Changes container URI selection logic for Singularity vs Docker (currently inverted). |
CHANGELOG.md |
Converts v1.1.0dev entry to a v1.1.0 release entry and expands bullets with authors/PRs. |
.nf-core.yml |
Updates template author and version to 1.1.0. |
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| 'robertaforsyth/wakhan:0.4.2_iss58': | ||
| 'docker://robertaforsyth/wakhan:0.4.2_iss58' }" |
| @@ -307,9 +100,6 @@ | |||
| "sample1/variants/clairs/indel.vcf.gz.tbi", | |||
| "sample1/variants/clairs/snvs.vcf.gz", | |||
| "sample1/variants/clairs/snvs.vcf.gz.tbi", | |||
| "sample3/qc/whatshap_stats/sample3_whatshap_stats.gtf", | ||
| "sample3/qc/whatshap_stats/sample3_whatshap_stats.log", | ||
| "sample3/qc/whatshap_stats/sample3_whatshap_stats.tsv", | ||
| "sample3/variants", |
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| - [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Added DeepVariant and DeepSomatic modules for germline and somatic variant calling from long-read sequencing data (@robert-a-forsyth). | ||
| - [#149](https://github.com/IntGenomicsLab/lrsomatic/pull/149) - Added GPU support for Clair3, DeepVariant, and fibertools (@robert-a-forsyth). |
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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).