feat: bring local modules to nf-core 4.0 compliance#152
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Convert all 10 local modules (9 fgbio + align_bam) from 'path versions.yml'
to topic-based version emission (tuple(task.process, tool, eval(cmd)),
topic: versions), and remove the obsolete per-process .out.versions mixing in
the workflow. Versions now flow entirely through channel.topic('versions');
the collated versions YAML is byte-identical (snapshots unchanged).
…ules
Bring the 10 local modules toward nf-core compliance: add environment.yml
(conda packages) and reference it via conda "${moduleDir}/environment.yml";
add meta.yml with name/description/keywords/tools/input/output and a
containers: block (docker + singularity-oras, amd64+arm64) sourced from
Seqera Containers builds.
With local-module meta.yml containers: blocks present, generation now emits docker and singularity-oras entries for all fgbio/align_bam processes (https and conda-lock configs keep nf-core modules only).
The inline container directives in the local modules' main.nf disagreed with the generated conf/containers_* source of truth: - align_bam pinned bwa_fgbio_samtools (stale name/digest from before the environment.yml existed) instead of fgbio_bwa_samtools. - 8 fgbio modules pointed their singularity ref at a community-cr-prod https blob that now 404s; filterconsensusreads used a divergent https blob. Point every local module's main.nf container at the oras refs from conf/containers_singularity_oras_amd64.config (durable, lint-validated, and CI-exercised) plus the matching amd64 docker tags. CI did not catch the dead blobs because the generated oras config overrides main.nf on real runs. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
… ch_versions FilterConsensusReads pipes into `samtools sort`, so emit its samtools version to the versions topic (mirroring align_bam), in addition to fgbio. Remove the now-empty ch_versions scaffold from the workflow (all versions flow through the topic; the workflow's `versions` emit was unconsumed). Regenerate RD-mode software-version snapshots accordingly. Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
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SPPearce
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Jun 16, 2026
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Please swap to check for apptainer (as in my previous comment).
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Also please update the CHANGELOG |
Co-Authored-By: Claude Opus 4.8 (1M context) <noreply@anthropic.com>
SPPearce
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Stacked on #151 (nf-core component updates). This PR updates the local modules, split out per review feedback (easier to review in stages).
Changes
tuple(task.process, tool, eval(cmd)), topic: versions); remove the obsolete.out.versionsmixing (and the now-vestigialch_versionsscaffold) in the workflow.FILTERCONSENSUSREADSnow also reports the samtools version (it pipes intosamtools sort), matchingALIGN_BAM's multi-tool reporting.environment.ymlto each local module and reference it viaconda "${moduleDir}/environment.yml".meta.ymlto each local module (name/description/keywords/tools/input/output) with acontainers:block (docker + singularity-oras://, amd64 + arm64) built via Seqera Containers for the 3 distinct environments (fgbio,fgbio+samtools,bwa+fgbio+samtools).conf/containers_*.configso the docker + singularity-oras configs include all local processes (https/conda-lock configs keep nf-core modules only — those wave artifacts weren't generated for the local containers).Verification (nextflow 25.10.4)
nf-core pipelines lint— 0 failuresnf-test test --profile debug,test,docker— full suite passes. The versions YAML matches pre-migration output except for the newly addedsamtoolsline underFILTERCONSENSUSREADS(snapshots updated accordingly).🤖 Generated with Claude Code