chore: update nf-core modules and subworkflows to latest#151
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@znorgaard , is there a reason to add more to this branch? It is easier to review in stages. |
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I can keep it split. In this one: update all the nf-core pieces. |
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Can we remove the name line from the environment.yml files, and then we don't need the patches.
And update the Changelog please.
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nh13
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Updated subworkflow adds a 10th 'cli_typecast' take parameter; pass null (default) from the PIPELINE_INITIALISATION call site. utils_nextflow_pipeline is intentionally NOT updated: its latest revision requires nextflow 26.04 for 'nextflow lint', which breaks the container_configs check; kept at the 25.10.4-compatible template version.
… fastqc to latest
- Reapply each module's name: patch (auto-reapplied on update)
- Adapt call sites to new input signatures: samtools/faidx now takes
(meta, fasta, fai) + get_sizes; samtools/merge now takes
(meta, input, index) + (meta2, fasta, fai, gzi)
- Modules now emit versions via the 'versions' topic; remove the obsolete
.out.versions mixing for FASTQC, MERGE_BAM, BWAMEM1_INDEX, SAMTOOLS_FAIDX
(collected via channel.topic('versions'))
- Refresh tiny snapshot: prepare_genome tool versions now reported via topic
…gnature The 4.0 multiqc module takes a single tuple input (meta, files, config, logo, replace_names, sample_names) and emits report as (meta, html). Build the input tuple in the workflow (always applying the base assets/multiqc_config.yml, plus params.multiqc_config when set), and map the report output accordingly.
Version strings now reflect updated bwa/index (0.7.19), samtools (1.23.1), and multiqc (1.35), with bwa/samtools index-step versions now collected via the versions topic. MultiQC 1.35 no longer writes standalone multiqc_plots/ exports (the interactive report is unchanged); the default test file list is updated accordingly. No consensus BAM/content changes.
nf-core 4.0.2's container_configs lint check runs 'nextflow inspect', whose JSON output is broken under nextflow 26.04 (uncaught JSONDecodeError). Pin the linting job to 25.10.4 (the pipeline's declared minimum and the required nf-test matrix version) so the check runs cleanly.
Now that the updated nf-core modules expose a containers: meta block, the container_configs lint check generates non-empty configs (FASTQC, MULTIQC); commit them so the check passes. Local fgbio modules will be added once they gain meta.yml containers blocks.
…shot MultiQC renders multiqc_plots/ (pdf/png/svg) on linux/amd64 (CI) but not on all local archs, so the file-list (stable_name) snapshot of the default test was env-dependent and failed on CI. Exclude multiqc_plots/ from stable_name (stable_path already ignores the plot files via .nftignore).
Removing the name line from each nf-core module environment.yml makes the local files match upstream, so the corresponding .diff patches are no longer needed. Delete the patches and their modules.json entries. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Reference the upstream Nextflow bug (nextflow-io/nextflow#7116) and its fix (#7121) inline so the pin's rationale and unpin condition are clear. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
…napshots MultiQC only renders multiqc_plots/ where its kaleido backend works (linux/amd64) and silently skips it on other archs (e.g. arm64, or amd64 under Rosetta), which made the default test's file-list snapshot environment-dependent. Instead of excluding the plots from the assertion, disable export_plots for tests via a new assets/multiqc_test_config.yml wired through the test profile's multiqc_config. Production runs keep export_plots: true. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
Stale blocks carried nf-test 0.8.4/0.9.0/0.9.2 version stamps because nf-test only rewrites a snapshot block when its content changes, and these deterministic md5 blocks had not changed since earlier runs. Drop and regenerate them so all stamps reflect the pinned 0.9.4. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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Updates all nf-core modules and subworkflows to their latest versions, on top of the 4.0.2 template branch (#150). Stage 1 of 2 — local-module compliance is split into #152 (stacked on this branch) for easier staged review.
Changes
utils_nfcore_pipeline,utils_nfschema_pluginupdated to latest (+cli_typecastcall-site arg).utils_nextflow_pipelineintentionally kept at the 25.10.4-compatible version (its latest needs nextflow 26.04 fornextflow lint, which breaks thecontainer_configscheck).bwa/index,samtools/{dict,faidx,merge},fastqc,multiqcupdated; patches reapplied;samtools/faidx+samtools/mergecall signatures adapted; MULTIQC call migrated to the 4.0 single-tuple input.versionstopic; obsolete.out.versionsmixing removed (local modules stay onversions.ymlhere — migrated in feat: bring local modules to nf-core 4.0 compliance #152).multiqc_plots/exports — report unchanged; no consensus-BAM changes); default test ignores the environment-dependentmultiqc_plots/tree.conf/containers_*.configfor fastqc/multiqc.linting.ymlnextflow to 25.10.4 socontainer_configsdoesn't crash on a 26.04 runner.Verification (nextflow 25.10.4)
nf-core pipelines lint— 0 failuresnf-test test --profile debug,test,docker— full suite (26) passes🤖 Generated with Claude Code