Important! Template update for nf-core/tools v4.0.2#1827
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…-4.0.2 # Conflicts: # .github/CONTRIBUTING.md # .github/workflows/awsfulltest.yml # .github/workflows/nf-test.yml # .github/workflows/release-announcements.yml # .nf-core.yml # CHANGELOG.md # README.md # assets/multiqc_config.yml # docs/usage.md # main.nf # modules.json # modules/nf-core/fastqc/main.nf # modules/nf-core/fastqc/meta.yml # modules/nf-core/multiqc/environment.yml # modules/nf-core/multiqc/main.nf # modules/nf-core/multiqc/meta.yml # modules/nf-core/multiqc/tests/main.nf.test # modules/nf-core/multiqc/tests/main.nf.test.snap # nextflow.config # nextflow_schema.json # nf-test.config # ro-crate-metadata.json # subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf # tests/nextflow.config # workflows/rnaseq.nf
- restore dev's subworkflows/nf-core/utils_nfcore_pipeline/main.nf so
imNotification() is available again (template-side removal would have
broken PIPELINE_COMPLETION's hook_url branch)
- add hook_url params declaration in nextflow.config (the auto-merge
dropped dev's System.getenv('HOOK_URL') line); schema entry stays
- ignore the removed assets/multiqc_config.yml in lint.files_exist
- accept nf-core lint's ro-crate description normalization against
README content
nf-core pipelines lint --fix container_configs run against the kept-from-dev module pins. The conf/containers_*.config files are static manifests for nf-core tooling and are not includeConfig'd anywhere at runtime, so the regenerated content has no functional impact on pipeline runs.
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- Import imNotification from utils_nfcore_pipeline explicitly. The strict
Nextflow syntax check in CI ('Nextflow Lint' / pre-commit nextflow-lint)
flagged 'imNotification is not defined' on the call site at
utils_nfcore_rnaseq_pipeline/main.nf:166. Implicit cross-include
resolution that worked in earlier Nextflow / Groovy modes is no
longer accepted under the strict parser bundled with this template.
- Run prettier on docs/usage.md (table column padding tweak only).
…tputDir
After cross-checking against the four nf-core 4.0.2 template merges that
landed first (mag, rnavar, bamtofastq, seqinspector), align rnaseq with
the cohort:
- Adopt 'outputDir = params.outdir' and 'workflow.output.mode =
params.publish_dir_mode' in nextflow.config (above the existing
process.publishDir block). All four cohort pipelines added these
lines; they configure the new 4.0 output DSL default without
conflicting with the existing process.publishDir, which is still
what publishes anything with a withName selector.
- Strip the Slack/Teams 'imNotification' notification path. Template
4.0.2 removed this helper from subworkflows/nf-core/utils_nfcore_pipeline
and all four cohort pipelines accepted that removal. Drops:
- hook_url declaration in nextflow.config and nextflow_schema.json
- hook_url take: input + onComplete branch in
subworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf
- imNotification include in the local utils subworkflow
- hook_url positional arg from PIPELINE_COMPLETION call site in main.nf
- hook_url=... entries from awsfulltest.yml + cloud_tests_full.yml
Tower launch parameters (the runs no longer need
MEGATESTS_ALERTS_SLACK_HOOK_URL plumbing).
Restored subworkflows/nf-core/utils_nfcore_pipeline/main.nf to the
template-canonical version (auto-resolved at merge time, then
reverted to dev in 47d5f07). The 'def imNotification' function
is gone; modules.json sha continues to point at the matching
upstream commit.
- Updated tests/main.pipeline_completion.workflow.nf.test to match
the new 9-input PIPELINE_COMPLETION signature (was 10).
CI's check_local_copy lint flagged that the local content didn't match the remote at the dev-recorded sha 65f5e638. Bump to the sha used by the rest of the 4.0.2 cohort (mag, bamtofastq): a3fb7351b1fdb2b1de282b765816bbea190e86a8. Diff vs 65f5e638 is just the 'valid_config = valid_config' default-value tweak and the imNotification removal we already aligned to.
pinin4fjords
reviewed
May 5, 2026
The 8 conf/containers_*.config files (singularity_https/oras/docker/conda_lock,
amd64/arm64) and the modules/nf-core/{fastqc,multiqc}/.conda-lock/ files were
shipped by nf-core/tools 4.0 as scaffolding for a per-process container
override layer fed by committed conda lock files. Nobody is using them yet:
they are not includeConfig'd from nextflow.config or any profile, they only
cover 2 of ~128 processes (fastqc, multiqc), and every other 4.0.2-merged
nf-core pipeline ships them inert too. Until the feature is fleshed out,
they are pure noise.
Disable the container_configs lint rule and add the eight removed conf/containers_*.config paths to the files_exist ignore list, so 'nf-core pipelines lint' stops asking for them. They were dropped in de9c912 as orphaned scaffolding for an unimplemented feature.
erikrikarddaniel
approved these changes
May 5, 2026
Member
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Thanks @erikrikarddaniel ! |
pinin4fjords
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to nf-core/tools
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May 5, 2026
… duplicate 'the') Both typos in nf_core/pipeline-template/docs/CONTRIBUTING.md ship with every pipeline that adopts the 4.0 template. 'focussed' is a less-common British spelling; 'focused' is preferred in modern AmE and BrE style guides. The second hit (line 54) is a duplicated 'the the'. Caught downstream during the nf-core/rnaseq#1827 template merge review.
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pinin4fjords
added a commit
to nf-core/differentialabundance
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May 13, 2026
Resolves conflicts for nf-core/tools v4.0.2 template merge, following nf-core/rnaseq#1827 precedent. Kept from dev (pipeline-specific): - paramsets workflow signature and full workflows/differentialabundance.nf body with output {} blocks - nf-test.config explicit-profile policy and all tests/default.nf.test cases - Pipeline-specific manifest contributors Adopted from template: - nf_core_version 4.0.2, nextflowVersion !>=25.10.4, badge bumps in README and ro-crate-metadata.json - outputDir = params.outdir + workflow.output.mode = params.publish_dir_mode - utils_nfcore_pipeline bumped to a3fb7351b1fdb2b1de282b765816bbea190e86a8 (drops imNotification path) - tests/default.nf.test variable rename stable_name/stable_path -> stable_path/stable_content, applied to all four test cases - .lineage/ added to .gitignore - Template's auto-generated ro-crate-metadata.json (lint will renormalize description from the resolved README) Local touch-ups: - Removed .github/CONTRIBUTING.md from .nf-core.yml files_unchanged (file moved to docs/CONTRIBUTING.md in dev) - Dropped orphan def before_text/after_text declarations in subworkflows/local/utils_nfcore_differentialabundance_pipeline/main.nf - awsfulltest.yml nf-slack channel switched to differentialabundance-dev
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Merges nf-core/tools v4.0.2 template into
dev. Substantial drift (last template merge was v3.5.1), so most conflicts were resolved by keeping rnaseq-specific behaviour and selectively adopting template improvements. After the initial merge, choices were cross-checked against the four 4.0.2 PRs that landed first (nf-core/mag#1030, nf-core/rnavar#303, nf-core/bamtofastq#138, nf-core/seqinspector#233) and aligned where they had reached the same conclusion.Resolution summary
Kept from dev (pipeline-specific)
conf/modules/*.configlayout, ARM/AMD container splits, parabricks/sentieon hooks, prokaryotic test profilenf-test.configwith dynamicSKIP_SENTIEON/SKIP_GPUignore lists and explicit-profilepolicy (CPUtestvs GPUtest_gpu)nf-test.ymlNextflow pin25.04.3(conda--mkdirfix) and NFT0.9.5bumpawsfulltest.ymlaligner matrix andif: always()artifact uploadPREPARE_GENOME28-input call site and rnaseq-specificPIPELINE_COMPLETIONsummary (rnaseqSummarywith per-sample trim/map/strand status)process.publishDirblock withext.publish_prefixfor--skip_quantification_mergeper-sample publishingfastqcandmultiqcmodules at the dev pinned shas (don't churn ARM Wave pins)workflows/rnaseq.nf→workflows/rnaseq/,assets/multiqc_config.yml→workflows/rnaseq/assets/multiqc/,.github/CONTRIBUTING.md→docs/CONTRIBUTING.mdcreativeWorkStatus: InProgress, dev URLs /3.26.0devversion inro-crate-metadata.jsonAdopted from template / aligned with the 4.0.2 cohort
nf_core_version: 4.0.2and template badge updates inREADME.md/ro-crate-metadata.jsonoutputDir = params.outdirandworkflow.output.mode = params.publish_dir_modeinnextflow.config(alongside the existingprocess.publishDirblock, matching mag / rnavar / bamtofastq / seqinspector)imNotificationnotification path: removedhook_urlparam + schema entry, removedimNotificationimport + workflow plumbing, droppedhook_url=...fromawsfulltest.yml+cloud_tests_full.yml. The four cohort pipelines all dropped the same path. Bumpedsubworkflows/nf-core/utils_nfcore_pipelinetoa3fb7351b1fdb2b1de282b765816bbea190e86a8(the cohort sha) socheck_local_copypasses; the only difference vs the previous dev sha is thisimNotificationremoval plus avalid_config = valid_configdefault-value tweak.rzr/fediverse-actioninrelease-announcements.ymlandactions/upload-artifact@v7inawsfulltest.ymldocs/CONTRIBUTING.md(new) - the rnaseq-specific note about not setting a defaultprofile "test"was ported acrosscontributorgraph inro-crate-metadata.json(Harshil / Phil / Rickard from.nf-core.ymltemplate.author);#pinin4fjordsPerson preserved becausemaintainerreferences it.github/CONTRIBUTING.mdfromlint.files_unchanged(file no longer exists)tests/default.nf.testvariable rename (stable_name/stable_path→stable_path/stable_content); applied to both test cases for consistency> [!WARNING]block indocs/usage.md(replaces Docusaurus:::warning)Cleanups (post-merge fixes spotted during conflict review)
def before_text = ""/def after_text = ""orphan declarations insubworkflows/local/utils_nfcore_rnaseq_pipeline/main.nf; the heredoc assignments below now declare withdeftests/main.pipeline_completion.workflow.nf.testafter droppinghook_urlfrom PIPELINE_COMPLETIONLint follow-ups
assets/multiqc_config.ymltolint.files_existignore list in.nf-core.yml(we removed the file because dev moved its content toworkflows/rnaseq/assets/multiqc/).ro-crate-metadata.json'sdescriptionfield against the README content (URL anchors and unicode escaping); accepted as-is.Deliberate divergence: dropped orphaned
conf/containers_*.configscaffoldingThe 4.0 template ships eight
conf/containers_<engine>_<arch>.configfiles plus committedmodules/nf-core/{fastqc,multiqc}/.conda-lock/*.txtlock files as scaffolding for a per-process container override layer. The four cohort pipelines (mag, rnavar, bamtofastq, seqinspector) all kept these files inert at template-shipped sizes, but in every case they:includeConfig'd fromnextflow.configor any profile,Rather than carry a half-implemented feature, this PR removes them and disables the
container_configslint rule via.nf-core.yml. When somebody actually implements the feature properly (committed conda lock files for every module, profile wiring, CI coverage), regenerate vianf-core pipelines lint --fix container_configsand drop the lint opt-out. Note: the next template-sync PR will re-add these files; they should be deleted again until the underlying feature is real.Files resolved
.github/CONTRIBUTING.md,.github/workflows/awsfulltest.yml,.github/workflows/cloud_tests_full.yml,.github/workflows/nf-test.yml,.github/workflows/release-announcements.yml,.nf-core.yml,CHANGELOG.md,README.md,assets/multiqc_config.yml,conf/containers_*.config(8 files),docs/usage.md,main.nf,modules.json,modules/nf-core/fastqc/{main.nf,meta.yml},modules/nf-core/multiqc/{environment.yml,main.nf,meta.yml,tests/main.nf.test,tests/main.nf.test.snap},nextflow.config,nextflow_schema.json,nf-test.config,ro-crate-metadata.json,subworkflows/local/utils_nfcore_rnaseq_pipeline/{main.nf,tests/main.pipeline_completion.workflow.nf.test},subworkflows/nf-core/utils_nfcore_pipeline/main.nf,tests/default.nf.test,tests/nextflow.config,workflows/rnaseq.nf.Test plan
nf-testsmoke (CPU shards, docker)References