Release 2.1.0 - #65
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Version bump: 2.1.0dev
Documents pipeline architecture and common dev commands for coding agents; nf-core pipeline repos use AGENTS.md instead of CLAUDE.md. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Adopts the template's nf-test.yml/pr-comment.yml CI infrastructure, retiring the legacy ci.yml and linting_comment.yml that had been kept around unintentionally after an earlier, incomplete migration. Also drops the unused fastqc module/schema scaffold and picks up the utils_nextflow_pipeline vendored subworkflow update. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
…ne subworkflow Metadata-only updates (ontologies, identifiers) for the two modules, no tool version bumps. The mafft/align patch (renaming variables to avoid shadowing process inputs) is dropped since upstream fixed the same bug independently using different variable names. Patches two nf-test snapshots whose embedded mafft version string went from the old "v7.520 (2023/Mar/22)" format to a bare numeric 7.52, matching the module's updated version-reporting eval expression. All 6 nf-test profiles verified passing against real Docker containers. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
The template sync and module/subworkflow updates are one PR-sized unit of work; list them as a single Changed entry rather than one line per commit. No Dependencies rows needed since no tool version actually changed in this batch. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
- Ignore conf/igenomes_ignored.config in files_exist, matching the existing conf/igenomes.config entry, since this pipeline has no igenomes feature at all. - Drop the stale "customise AWS full pipeline tests" TODO in awsfulltest.yml; test_full.config already has real pipeline-specific data. - Drop the empty "Pipeline specific contribution guidelines" TODO section in CONTRIBUTING.md; nothing pipeline-specific to add. schema_lint's "Parameter input not found in schema" warning is left as is: this pipeline intentionally has no generic --input parameter, and schema_lint has no per-item ignore mechanism (only an all-or-nothing toggle that would also disable its other, useful checks). Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Template update to 4.0.3, module/subworkflow updates
Closes the remaining ask in #3: MultiQC runs, but only ever aggregated software versions, the workflow summary, and the methods description — none of the actual tool logs. None of hmmer/epa-ng/gappa/mafft/clustalo have a native MultiQC module, so this wraps three outputs as MultiQC custom content instead: - hmmbuild's *.hmmbuild.txt build stats (only produced when no --hmmfile is given for the hmmer alignment method) - EPA-NG's *.epa_info.log placement run summary - GAPPA's heat tree SVG, showing where query sequences landed in the reference phylogeny; skipped above 1 MiB (falls back to a note pointing at the real output file) since large reference trees can produce very large SVGs that would bloat the report Raw tool logs can't be fed to MultiQC's custom content module directly: it always tries to parse leading '#' lines as a YAML header, which breaks on hmmbuild's own descriptive comments. Each is instead wrapped in a small self-describing custom content yaml (id/section_name/ plot_type: html), matching the pattern already used for methods_description_mqc.yaml. Verified real rendering (not just that MultiQC didn't error) via the actual container against real pipeline output. fasta_newick_epang_gappa (a pipeline-authored subworkflow vendored through the nf-core/modules registry) needed two new emits (hmmbuild_log, epang_log) to expose these; patched and tracked via nf-core subworkflows patch rather than edited unpatched. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Report hmmbuild, EPA-NG and GAPPA heat tree output in MultiQC
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Bump version for 2.1.0 release
Resolves .nf-core.yml conflict between master's PR-comment security hotfix (#61, ignore entries for the hand-patched workflow files) and dev's newer 4.0.3 template sync / 2.1.0 version bump: keep the union of both branches' lint-ignore entries and dev's newer version fields. Verified clean with `nf-core pipelines lint --release`.
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❌ nf-test failed with latest Nextflow versionNote Tests with Nextflow's latest version failed but it will not cause a CI workflow failure.
See the full run for details. |
…tion in CI Singularity/Apptainer's unprivileged execution mode fails with "Failed to create user namespace: Permission denied" on the current RunsOn AMI (runs-on-v2.2-ubuntu24-full-x64-20260717095855), regardless of Nextflow version - confirmed by the identical error underlying the "latest-everything" matrix leg, which only appears green because of its continue-on-error. Since singularity/conda only run on release-targeting PRs, this had gone unnoticed since the AMI update. Disable the sysctl restriction before each singularity nf-test run rather than waiting on an AMI-side fix. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
Per nf-core Slack: nf-core/tools 4.0.3 bumped eWaterCycle/setup-apptainer to a faulty digest that causes "Failed to create user namespace: Permission denied" in some pipelines (not all). The correct fix is reverting the digest, not working around it at the kernel/AppArmor level as previously done here. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com>
erikrikarddaniel
marked this pull request as ready for review
July 28, 2026 14:08
charles-plessy
approved these changes
Jul 29, 2026
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It looks good to me but pay attention that your changelog is not ready.
| The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) | ||
| and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). | ||
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| ## v2.1.0 - [yyyy-mm-dd] |
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You still have boilerplate for the date
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Intentional, but thanks for reminding me.
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| ### `Dependencies` | ||
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| | software | previously | now | |
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Maybe the empty table can go away?
scwatts
self-requested a review
August 3, 2026 02:52
scwatts
approved these changes
Aug 3, 2026
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This is a tidy release, and other than the already mentioned CHANGELOG.md changes I didn't see anything blocking
| def alignment = write_align ? "-A ${prefix}.sto" : '' | ||
| def target_summary = write_target ? "--tblout ${prefix}.tbl" : '' | ||
| def domain_summary = write_domain ? "--domtblout ${prefix}.domtbl" : '' | ||
| def to_gzip = ["${prefix}.txt"] |
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Consider apply whitespace alignment here equally amongst variable definitions
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Thanks @scwatts and @charles-plessy ! |
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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: 4.0.3. For more documentation on how to update your pipeline, please see the Synchronisation documentation. |
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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).Description
Release PR for v2.1.0.
Since the last release (v2.0.1, 2026-06-16):
nf-core pipelines lint --releasepasses cleanly.Note: the
CHANGELOG.mdrelease date (## v2.1.0 - [yyyy-mm-dd]) will be finalized with the actual merge date once this PR is approved, in a follow-up commit before merging.