*nf-core/tools Issue Triage — Likely Already Fixed (~67 issues)*

  These issues appear to be addressed in the current codebase and may be candidates for closing:

  *🟢 Likely Fixed*
  • https://github.com/nf-core/tools/issues/4076 Old non-topic fastqc/multiqc channels — topic channel
  commits `d5785ae43`, `c02f3d9f7`
  • https://github.com/nf-core/tools/issues/4073 Subworkflow lint converts underscores to slashes — commit
   `0cf9275e5`
  • https://github.com/nf-core/tools/issues/4066 Subworkflows lint not comparing output channels —
  `subworkflows/lint/meta_yml.py:98-110`
  • https://github.com/nf-core/tools/issues/4062 Multi-line tuple as multiple inputs —
  `modules/lint/main_nf.py:127-133`
  • https://github.com/nf-core/tools/issues/4041 Container linting for modules — commits `683e26a9a`,
  `454816236`
  • https://github.com/nf-core/tools/issues/3985 Support `val` in version topic channels —
  `main_nf.py:745` uses `(?:eval|val)` regex
  • https://github.com/nf-core/tools/issues/3979 No `test_full` profile fails download CI —
  `download_pipeline.yml` only uses `test` profile
  • https://github.com/nf-core/tools/issues/3972 `modules lint --fix` mangled output (follow-up) — commits
   `f0a7dad92`, `677915a2f`
  • https://github.com/nf-core/tools/issues/3952 Implement wave.yml as tools command — commits
  `08a08d0a7`, `809723f3d`, `0df4fe913`
  • https://github.com/nf-core/tools/issues/3941 Linter drops trailing double quote in topics — commits
  `f0a7dad92`, `cda268c75`, `23d980bcb`
  • https://github.com/nf-core/tools/issues/3932 Remove latest-everything from PR CI — commit `68661d3e8`
  • https://github.com/nf-core/tools/issues/3927 `files_unchanged` broken for custom pipelines —
  `files_unchanged.py:79-85`
  • https://github.com/nf-core/tools/issues/3901 `modules lint --fix` produces mangled output — commits
  `f0a7dad92`, `677915a2f`
  • https://github.com/nf-core/tools/issues/3889 `task.process` without quotes crashes linting —
  `main_nf.py:744-746` fails gracefully
  • https://github.com/nf-core/tools/issues/3844 Subworkflow meta YML components mismatch —
  `meta_yml.py:132`
  • https://github.com/nf-core/tools/issues/3794 Schema error for integer with empty string default —
  `schema.py:204-207`
  • https://github.com/nf-core/tools/issues/3772 `modules lint` fails on patched modules —
  `main_nf.py:52-60`
  • https://github.com/nf-core/tools/issues/3771 Error when no versions emitted but topics are —
  version/topic emit logic handles this
  • https://github.com/nf-core/tools/issues/3768 Remove nf-test latest for PRs — commit `68661d3e8`
  • https://github.com/nf-core/tools/issues/3751 Add Codespaces badge to pipeline template — commits
  `08524eb76`, `4dacc4a3a`
  • https://github.com/nf-core/tools/issues/3740 Social media releases include pipeline description —
  commit `1d3f4de1c`
  • https://github.com/nf-core/tools/issues/3738 Add example assertions into nf-test template —
  `module-template/tests/main.nf.test.j2`
  • https://github.com/nf-core/tools/issues/3728 Fill out empty tests — commit `d6c1f65bc`
  • https://github.com/nf-core/tools/issues/3724 `pipelines lint` and `modules install` disagree on
  modules.json format — commit `fdeddeece`
  • https://github.com/nf-core/tools/issues/3710 Update rich-click to 1.9 — `pyproject.toml` has
  `"rich-click==1.9.*"`
  • https://github.com/nf-core/tools/issues/3684 Docker build fails due to 403 from nf-test — nf-test
  install method changed
  • https://github.com/nf-core/tools/issues/3679 Make ro-crate updated with README during sync — commit
  `2b6b60cf6`
  • https://github.com/nf-core/tools/issues/3655 Allow user names with dots when creating modules —
  `create.py:336-348`
  • https://github.com/nf-core/tools/issues/3644 Exclude entire directories from linting —
  `merge_markers.py:39-54`
  • https://github.com/nf-core/tools/issues/3573 `.nf-core.yml` errors give unhelpful message —
  `utils.py:1462-1468`
  • https://github.com/nf-core/tools/issues/3540 Linting of patched module fails — commit `25940f7e9`
  • https://github.com/nf-core/tools/issues/3530 Linting incorrectly parses output path with arity —
  commit `520386aa5`
  • https://github.com/nf-core/tools/issues/3487 Add subcommand for searching nf-core test-datasets —
  `nf_core/test_datasets/search.py` exists
  • https://github.com/nf-core/tools/issues/3430 Institutional configs not included when NXF_OFFLINE —
  commit `f13bdefb2`
  • https://github.com/nf-core/tools/issues/3420 False positive merge markers due to .venv —
  `merge_markers.py:41`
  • https://github.com/nf-core/tools/issues/3365 Remove hyphens from pipeline names — `create.py:348`
  • https://github.com/nf-core/tools/issues/3360 Add CITATION.cff to pipeline template — commit
  `165d78ee6`
  • https://github.com/nf-core/tools/issues/3288 Lint pipelines schema against meta schema — commit
  `9fe1c3e66`
  • https://github.com/nf-core/tools/issues/3264 CI failing due to bug fetching repo releases —
  `get_repo_releases_branches` in `utils.py`
  • https://github.com/nf-core/tools/issues/3259 Template GENERATE_DOWNSTREAM_SAMPLESHEETS — subworkflow
  exists in template
  • https://github.com/nf-core/tools/issues/3254 Pipeline creation should specify branch name on git init
  — `--initial-branch` in `git_init_pipeline()`
  • https://github.com/nf-core/tools/issues/3172 `--show-hidden` comment misleading — properly implemented
   in `params_file.py`
  • https://github.com/nf-core/tools/issues/3123 Add `--fail-warned` to `nf-core schema lint` —
  `fail_warned` in `commands_pipelines.py`
  • https://github.com/nf-core/tools/issues/3056 modules test on private server requires `--git-remote` —
  `--git-remote` exists in `components/info.py`
  • https://github.com/nf-core/tools/issues/2944 nfcore/tools docker image permission denied — commits
  `1f1c34648`, `6795985b1`
  • https://github.com/nf-core/tools/issues/2855 Remove `tags.yml` from module template — no `tags.yml` in
   `nf_core/module-template/`
  • https://github.com/nf-core/tools/issues/2788 Pipelines with unpinned nf-validation plugin —
  `nf-schema@2.5.1` pinned in template
  • https://github.com/nf-core/tools/issues/2784 Update schema builder to JSON draft 2020-12 —
  `schema.py:110,433`
  • https://github.com/nf-core/tools/issues/2650 modules test fails with custom repo — `install.py:56-59`
  • https://github.com/nf-core/tools/issues/2596 Renovate Dashboard — `.github/renovate.json5` exists
  • https://github.com/nf-core/tools/issues/2536 Add TODO comment when no meta present —
  `module-template/main.nf:127`
  • https://github.com/nf-core/tools/issues/2501 Make sure there's a snapshot — `test_snapshot_exists`
  check in `module_tests.py`
  • https://github.com/nf-core/tools/issues/2427 Schema: Support `anyOf`, `allOf` and `oneOf` —
  implemented in `schema.py`
  • https://github.com/nf-core/tools/issues/2408 nf-core container download — `docker.py` and
  `container_fetcher.py`
  • https://github.com/nf-core/tools/issues/2357 Use singularity containers for apptainer profile —
  `nextflow.config:180-181`
  • https://github.com/nf-core/tools/issues/2309 Download Docker images via API — `docker.py` implements
  Docker API download
  • https://github.com/nf-core/tools/issues/2142 `modules install` fails with custom remote path — custom
  remote handling in `install.py`
  • https://github.com/nf-core/tools/issues/2018 Bump-versions for all subcommands — `ModuleVersionBumper`
   and `PipelineVersionBumper` exist
  • https://github.com/nf-core/tools/issues/2009 Jinja template strings only linted in template files —
  `pipelines/lint/template_strings.py`
  • https://github.com/nf-core/tools/issues/1915 Handling patched modules in subworkflows —
  `subworkflows/lint/module_patch.py`
  • https://github.com/nf-core/tools/issues/1911 nf-core tools in docker is broken — Dockerfile actively
  maintained
  • https://github.com/nf-core/tools/issues/1824 Updating modules.json new format causes branch lookup
  error — format migration in `modules_json.py`
  • https://github.com/nf-core/tools/issues/1737 Speed up `nf-core modules` pytests — extensive mock usage
   in `tests/`
  • https://github.com/nf-core/tools/issues/1703 pathlib adoption roadmap — `pathlib.Path` pervasive
  throughout codebase
  • https://github.com/nf-core/tools/issues/1697 Tests slow due to web queries — mock/patch patterns in
  `tests/test_utils.py`
  • https://github.com/nf-core/tools/issues/1689 Too many commented out tests — no significant
  commented-out tests found
  • https://github.com/nf-core/tools/issues/1627 Add automated tests for nf-core download —
  `tests/pipelines/download/test_download.py`
  • https://github.com/nf-core/tools/issues/1554 Schema: Support nested parameters (objects) — `$defs`
  support in `schema.py`
  • https://github.com/nf-core/tools/issues/1534 More consistent logging — consistent patterns throughout
  `nf_core/`
  • https://github.com/nf-core/tools/issues/1529 Docstring format convention — consistent format in
  `bump_versions.py`, `schema.py`
  • https://github.com/nf-core/tools/issues/1527 Use `pathlib.Path` instead of `os.path` — largely done
  • https://github.com/nf-core/tools/issues/1524 Subworkflow handling and custom modules —
  `get_components_to_install()` in `components_utils.py`
  • https://github.com/nf-core/tools/issues/1318 Write permission error with docker non-root user — fixed
  in `pipelines/download/docker.py`
  • https://github.com/nf-core/tools/issues/112 Refactor pipeline emails — email subworkflow architecture
  now standard

  *🟡 Likely Outdated* (superseded by newer approaches)
  • https://github.com/nf-core/tools/issues/3668 Modules yaml schemes don't follow nf-core releases
  • https://github.com/nf-core/tools/issues/3656 Enable configurations for module linting — superseded by
  `.nf-core.yml` config
  • https://github.com/nf-core/tools/issues/3222 nf-core pipelines launch CLI issue — `launch.py` fully
  functional; likely stale
  • https://github.com/nf-core/tools/issues/3044 Subworkflow install failure results in 0 exit code —
  likely resolved
  • https://github.com/nf-core/tools/issues/2940 Refactor SyncedRepo class — done, now separate
  `workflow_repo.py`, `modules_repo.py`
  • https://github.com/nf-core/tools/issues/2928 Subworkflow installation bug — general bug; install now
  mature
  • https://github.com/nf-core/tools/issues/2860 Add support for xz-compression — not widely needed for
  nf-core use case
  • https://github.com/nf-core/tools/issues/2854 Update CI workflow for pipelines — CI has been updated;
  superseded
  • https://github.com/nf-core/tools/issues/2774 Have module_changes.py check test.nf and environment.yml
  — approach changed
  • https://github.com/nf-core/tools/issues/2058 Using CVMFS for storing reference genome data —
  cloud-native approach adopted
  • https://github.com/nf-core/tools/issues/1992 Add institutes.md to pipeline template — superseded by
  RO-Crate metadata
  • https://github.com/nf-core/tools/issues/1249 Default parameters not showing up on NF Tower URL — NF
  Tower replaced by Seqera Platform
  • https://github.com/nf-core/tools/issues/1239 Refgenie Integration — RefGenie approach abandoned
  • https://github.com/nf-core/tools/issues/1086 RefGenie - add assets from AWS-iGenomes — RefGenie
  abandoned
  • https://github.com/nf-core/tools/issues/1084 Use RefGenie for pipeline template genomes.conf —
  RefGenie abandoned
  • https://github.com/nf-core/tools/issues/797 Add nf-core lint to super-linter — standalone linting
  preferred

  *🟠 Partially Fixed / Needs Verification*
  • https://github.com/nf-core/tools/issues/4049 `subworkflows lint <name> --local` — `--local` alone
  works; named+local combo may still fail
  • https://github.com/nf-core/tools/issues/3316 Make `main` default for all nf-core repos — `tools` done;
   `modules`/`configs` still on `master`

  _~240 remaining issues confirmed still open. Analysis based on codebase at nf-core/tools main branch._