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fix(plugin_development): correct errors found in tutorial walkthrough (… …#1013) - Make the Part 5 task counter thread-safe with AtomicInteger. Nextflow can report task completions concurrently, and the plain int counter intermittently undercounted (e.g. "Final task count: 3" for 5 tasks). - Tell learners to update the template's GreetingObserverTest in Part 5 (factory now returns two observers) and Part 6 (navigate() on a bare Mock(Session) throws an NPE). The solutions already contained these edits but the lessons never mentioned them, so `make test` failed. - Fix a 404 link to the "Using plugins" docs page. Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com> Co-authored-by: Adam Talbot <12817534+adamrtalbot@users.noreply.github.com>
fix(nfcore_build): correct Build with nf-core materials for the train… …ing environment (#1012) * fix(nfcore_build): correct Hello nf-core materials for the training environment Fix bugs and inaccuracies in the Build with nf-core course against the training image (Nextflow 26.04.4, nf-core/tools 4.0.2), found in Friederike's walkthrough (#1005-#1011) and re-verified on 4.0.2: - Demo symlink: Nextflow 26.04 stores pulled pipelines under assets/.repos/<org>/<name>/clones/<commit>, so the old assets symlink left pipelines/nf-core/demo missing. - nf-core/demo now ships modules/local/cowpy; update the modules tree. - Line numbers, highlights and Before blocks that did not match the files produced by the 4.0.2 template and the lesson steps. - modules create: tool name must be lowercase, document the Bioconda prompt, and show the generated main.nf as 4.0.2 writes it. - find/concatenate excerpt now matches the installed module signature. - Part 4: declare batch in nextflow.config before schema build, and pass --batch in the invalid-input test so the output shows only file errors. - Solutions: part4 validate_params = true, composable-hello docker config, and FIND_CONCATENATE include order matching Part 2. Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io> Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(nfcore_build): align solutions with lesson end state and document install traceback - Solutions part1-4: workflows/hello.nf and the utils_nfcore_hello_pipeline subworkflow now match what the 4.0.2 template plus the lesson edits produce, so the "start fresh" boxes give files that match the Before blocks and line numbers. - Part 2: show the long traceback that `nf-core modules install` prints before NotADirectoryError on 4.0.2, and drop the claim that `info` writes no files (it rewrites modules.json). Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io> Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(nfcore_build): have attendees switch their scaffold to nf-schema 2.7.2 The nf-core/tools pipeline template pins nf-schema 2.5.1, which prints `WARN: Unrecognized config option 'validation.*'` on every run under Nextflow 26.04. The solutions and the Part 2-4 docs are written against 2.7.2, but nothing told attendees to switch, so their runs never matched the documented output. Part 1 §2.2 now has them update the pin, the §5.5 output shows the one-off plugin download, and the stray download line in Part 3 §1.2.4 is removed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * fix(nfcore_build): clone nf-core/demo for browsing instead of symlinking the asset cache `nextflow clone` puts the default revision directly at pipelines/nf-core/demo, so the setup no longer depends on the Nextflow 26.04 per-revision clone layout. The course only reads the demo code, so the pull is not needed. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * docs(nfcore_build): point Part 1 file-explorer instruction at pipelines/nf-core/demo Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io> Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com> * chore(nfcore_build): bump nf-core/tools to 4.1.0 (#1014) * chore(nfcore_build): bump nf-core/tools to 4.1.0 Update the devcontainer pin, the required-version text in the orientation page, and the nf-core/tools banners in lesson output. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * fix(nfcore_build): update command output and line numbers for nf-core/tools 4.1.0 - Part 1 §2.1: pipelines create no longer prints the container-config line - Part 1 §5.1-5.2: input-channel block starts at line 84 in the 4.1.0 template - Part 2 §1.4: modules install no longer fails with NotADirectoryError on single-file local modules; it now prints the include statement Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> * fix(nfcore_build): update solutions to the nf-core/tools 4.1.0 template Apply the 4.0.2 -> 4.1.0 template changes to core-hello-part1..4: updated utils_nfschema_plugin subworkflow (cli_typecast input, parameters_schema option keys), the extra argument passed to it from the local utils subworkflow, the process_low_memory label, new subworkflow SHAs in modules.json, and nf_core_version in .nf-core.yml. Update the docs that show these files: the modules.json SHAs in Part 2, and the utils_nfcore_hello_pipeline line numbers and the utils_nfschema_plugin error line in Part 4. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Claude Opus 5.5 (1M context) <noreply@anthropic.com> --------- Co-authored-by: Friederike Hanssen <friederike.hanssen@seqera.io> Co-authored-by: Claude Opus 5.5 <noreply@anthropic.com>
Restrict heading-numbering checks to docs/en and fix orphan frontmatt… …er dashes (#988) * Only enforce heading numbering against docs/en check_headings.py's numbering validation was being triggered by translations that reorder heading text: English's "#### Part 1: ..." doesn't start with a digit, so is_heading() ignores it, but Turkish's natural "#### 1. Bölüm: ..." does, so the checker tries to validate it as a real "1." numbered heading and reports spurious level/sequencing errors. The one file this was previously known to hit (side_quests/plugin_development/index.md) was worked around with a per-file, all-languages entry in check-headings.yml's files_ignore. That doesn't scale: the same "Part N" -> "N. <word>" reordering can happen anywhere non-English content uses numbered part/step labels, and CI only checks files that actually changed in a given PR, so nio one would have noticed until this exact file changed again. Heading numbering is a source-content convention anyway, so only docs/en/ needs to be checked. Confirmed a mixed docs/en + docs/tr + docs/de) file, only the English entry gets validated. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> * Fix orphan frontmatter dashes in 3 pre-existing translated files Same bug as the one just fixed in PR #987 (translation pipeline's fix_frontmatter() left an unclosed leading "---" in place when the English source has no frontmatter), found by a site-wide sweep after that fix landed. These three predate #987's changes entirely: - docs/tr/docs/seqera_scale/next_steps.md - docs/tr/docs/nfcore_use/00_orientation.md - docs/de/docs/seqera_scale/01_run_with_seqera.md (also had a second, related issue: the file's own legitimate "---" horizontal rule was missing its preceding blank line, which is markdown-ambiguous with a Setext heading underline; added the blank line to match the English source's spacing) Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> --------- Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
Update translations (manual) (#975) * Update translations * Exclude plugin_development index page from heading check The Turkish translation phrases "Part N" as "N. Bölüm", which matches the numbered-heading regex and gets flagged as a heading-level mismatch (h4 vs expected h2). The Part N labels are TOC-style links to separate lesson files, not part of a sequential numbering scheme, so the page doesn't need heading-number validation in any language. Co-Authored-By: Claude Sonnet 5 <noreply@anthropic.com> --------- Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com> Co-authored-by: Geraldine Van der Auwera <geraldinevdauwera@gmail.com> Co-authored-by: Claude Sonnet 5 <noreply@anthropic.com>
Post-Summit fixes + Fix issues found via container-verified tutorial … …walkthroughs (#945) Fixes found during Summit training + fresh pass of validation with Claude: Walked through hello_nextflow, hello_nf-core, and six side quests end-to-end in the real training container, fixing confirmed doc/behavior mismatches: - hello_nextflow: broken -resume cache-hit example, stale before/after snippet - hello_nf-core: module-install output, hl_lines, backticks, JSON/YAML formatting, and a Channel.topic -> channel.topic regression in the solution checkpoints - Side quests (working_with_files, metadata, splitting_and_grouping, nf_test, workflows_of_workflows, dev_environment): naming consistency, hl_lines, broken snippets, nf-test version-compatibility note - docker-setup skill: pull the image tag pinned by the branch's own devcontainer.json instead of a hardcoded tag
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