Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).
Directory Mold with only index.md frontmatter.
target-specific fields are coherent.
eval.md declares cases and check type.
12 typed references; 0 resolver issues.
All on-demand references describe triggers.
Hypothesis references include verification.
Typed Mold references describe what casting consumes and when the generated skill should load each artifact.
Workflow-construction idiom. Usually condensed during casting.
Workflow-construction idiom. Usually condensed during casting.
Workflow-construction idiom. Usually condensed during casting.
Workflow-construction idiom. Usually condensed during casting.
Workflow-construction idiom. Usually condensed during casting.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Background synthesis loaded by explicit progressive-disclosure metadata.
Tool-level install metadata. Aggregated into the cast bundle's Required Tools section.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Command reference. Usually cast to a sidecar and loaded only when invoked.
Structured contract copied for validation or lookup.
Convert one nf-core module directory into a Galaxy tool wrapper. Input is a path to modules/nf-core/<name>/ (or any directory of the same shape: main.nf + meta.yml + environment.yml + optional tests/). Output is a self-contained tool dir: tool.xml, macros.xml, _provenance.yml, with <test> blocks pinned to remote nf-core/test-datasets URLs.
The Mold authors a Galaxy tool XML wrapper directly from the nf-core module shape — the regular structure (tuple(meta, path) channels, task.ext.args escape hatch, versions emit, environment.yml bioconda pin) makes a mechanical mapping practical. It does not depend on [[summarize-nextflow]] — that Mold summarizes whole pipelines, the wrong granularity for one module.
The Mold is run per module by an outer harness (a script or human loop). Cross-module batches are not its concern.
The Mold expects:
modules/nf-core/<name>/, or any local clone of that shape).nf-core/modules. When absent, the cast skill resolves to git rev-parse HEAD of the dir’s containing repo.nf-core/test-datasets to use for <test> block location URLs. When absent, the cast skill resolves to a recent SHA on the module’s pipeline-of-record branch (best-effort; recorded in _provenance.yml either way).The Mold does not accept “convert a subworkflow” — meta.yml with a populated components: field is out of scope (composes other modules; route to a separate subworkflow Mold not in this plan).
Three files in a sibling output directory the harness specifies:
<output_dir>/
<name>.xml # primary wrapper
macros.xml # tool-local macros (token, requirements, version_command, citations)
_provenance.yml # nfcore source SHA, file hashes, mold revision, generated_attool.xml shape (skeleton; idiomatic IUC layout):
<tool id="<name>" name="<name>" version="@TOOL_VERSION@+galaxy@VERSION_SUFFIX@" profile="23.1">
<description><!-- meta.yml description, first sentence --></description>
<macros>
<import>macros.xml</import>
</macros>
<expand macro="requirements"/>
<expand macro="version_command"/>
<command detect_errors="exit_code"><![CDATA[
<!-- script: body translated, $task.ext.args → $extra_args -->
]]></command>
<inputs>
<!-- per nfcore-channel-input-to-galaxy-collection + nfcore-meta-map-to-galaxy-params -->
<param name="extra_args" type="text" optional="true" .../> <!-- per task.ext.args pattern -->
</inputs>
<outputs>
<!-- one Galaxy <data> / <collection> per output: channel, minus the versions channel -->
</outputs>
<tests>
<test>
<param name="reads_1" location="https://raw.githubusercontent.com/nf-core/test-datasets/<sha>/.../test_1.fastq.gz"/>
<output name="trimmed" location="https://raw.githubusercontent.com/nf-core/test-datasets/<sha>/.../trimmed.fastq.gz"
checksum="sha256$..."/>
</test>
</tests>
<help><!-- meta.yml description --></help>
<expand macro="citations"/>
</tool>_provenance.yml shape (canonical):
nfcore_source:
modules_repo: nf-core/modules
module_path: modules/nf-core/<name>
branch: master
git_sha: <sha at conversion time>
meta_yml_hash: <sha256 of meta.yml at conversion>
main_nf_hash: <sha256 of main.nf at conversion>
environment_yml_hash: <sha256 of environment.yml at conversion>
test_datasets_sha: <sha of nf-core/test-datasets pin>
generated:
by_mold: convert-nfcore-module-to-galaxy-tool
mold_revision: 1
cast_target: claude
cast_artifact_sha: <sha of cast bundle used>
on_date: 2026-05-10
overrides: []The cast skill is not a single LLM prompt. It is a small program with embedded LLM calls:
process block for input/output channels; resolve container directive into bioconda packages; compute file hashes; resolve git SHAs; emit _provenance.yml and the static portions of <requirements>, <citations>, <version_command>.script: body into Galaxy <command> Cheetah; pick <inputs> shapes (data vs collection; conditional gating); name and document outputs; humanize <help>; place <test> block fixtures.The boundary mirrors [[summarize-nextflow]] §Procedure: enumerated artifacts deterministic, free-text fields LLM.
Open meta.yml, main.nf, environment.yml, and tests/main.nf.test (when present). Reject early if meta.yml.components: is populated (subworkflow composing other modules; out of scope — see Non-goals).
Compute sha256 of each file and capture for _provenance.yml.
<requirements>Walk environment.yml.dependencies:. Each bioconda::<name>=<version> becomes a Galaxy <requirement type="package" version="<version>"><name></requirement> entry. For mulled / multi-package environments, declare every package — bioconda’s mulled-resolution produces an equivalent image (per [[component-nextflow-containers-and-envs]]).
Record any forced divergence from upstream container choice in _provenance.yml.overrides.
<inputs>Per [[nfcore-channel-input-to-galaxy-collection]], decide the Galaxy input shape from the process’s input channel cardinality. Per [[nfcore-meta-map-to-galaxy-params]], triage meta-map keys into Galaxy params, conditionals, or drops.
Emit a final extra_args text param per [[nfcore-task-ext-args-to-galaxy-additional-options]] if (and only if) the script body interpolates ${task.ext.args} / args2 / args3.
<outputs>For each output: channel that isn’t the versions emit, decide cardinality first, then shape (per [[galaxy-discover-datasets]] §Convert Mold posture). The Nextflow glob alone is not enough — path('*.bam') (N files, one per element of an upstream collection) and path('*.{bai,csi,crai}') (exactly one file, alternation across mutually-exclusive extensions) look the same but map to different Galaxy idioms.
path("${prefix}.json")) → <data name="..." format="json" from_work_dir="${prefix}.json"/>. No <discover_datasets>.path("*.{bai,csi,crai}"), or path("${prefix}.${ext}") where ext is computed): the channel emits one file whose extension depends on inputs or args. Map to a <data> with the most-common extension as format=, plus a <change_format> block that flips on the input ext or the responsible param. Preserve the upstream invocation byte-for-byte and capture the result with a tight mv — ln -s '$input' 'input.${input.ext}' to stage with the upstream-expected name, run the tool exactly as the nf-core script: body does, then mv 'input.${input.ext}'.{bai,csi,crai} '$output_name'. Do not use <collection> + <discover_datasets> for this shape — there is no list. Direct write to '$output_name' (instead of mv) is the secondary form, used only when the upstream script: body itself passes an output-path arg to the tool. See [[galaxy-discover-datasets]] §Convert Mold posture Rule 2 for the full pattern, including the variant and the from_work_dir callout.path('*.bam') where the upstream process emits N files keyed by element identifier) → <collection type="list" name="..." format="bam"> with <discover_datasets pattern="__name_and_ext__" visible="true"/>.tuple val(meta), path("*_R{1,2}.fastp.fastq.gz")) → <collection type="paired" ...> with a custom (?P<name>...)_R(?P<identifier_1>[12])... regex.versions channel → drop; the <version_command> carries that load (per [[nfcore-versions-emit-to-galaxy-version-command]]).Cardinality heuristic: if the upstream input: channel is tuple(meta, path) (one item per process invocation) and output: emits one path per concept, the output is single — even when the path is glob-shaped. Process cardinality = output cardinality unless the script explicitly fans out.
script: to <command>LLM step. Pass:
script: body.<inputs> and <outputs> already chosen.task.ext.args mapping (text param → $extra_args).Ask only for the Cheetah-flavored Galaxy command. Wrap in <![CDATA[...]]>. Set detect_errors="exit_code" unless a comment in the original script: argues otherwise.
<version_command>Per [[nfcore-versions-emit-to-galaxy-version-command]]: extract the primary tool’s version-emit line from the heredoc or topic: versions annotation, strip Nextflow escaping (\$( → $( etc.), and wrap in <![CDATA[...]]>.
<citations> and <help><citations> are DOIs from meta.yml.tools[].doi (one <citation type="doi">…</citation> per tool). <help> is the meta.yml.description (humanized one-liner; expanded into a paragraph if meta.yml has a longer prose block).
<test> blocks (remote URLs)Read tests/main.nf.test. For each test that asserts a successful run with a non-trivial fixture:
raw.githubusercontent.com/nf-core/test-datasets/<test_datasets_sha>/... URL. Pin <test_datasets_sha> upfront — never use a branch ref.<param ... location="https://..."/> for inputs.<output name="..." location="https://..." checksum="sha256$..."/> (compute checksum from the upstream snapshot file when one exists; omit if not).When tests/main.nf.test has no usable fixture (stub-only coverage, missing test file), the convert Mold does not ship a placeholder <test>. It surfaces the gap in _provenance.yml.overrides and exits with a non-zero status; the harness escalates to human review. Every shipped wrapper carries at least one <test> block backed by a real fixture (per [[nfcore-stub-block-to-galaxy-noop-test]] and the reviewer Mold’s dimension #6).
_provenance.ymlCollect: nf-core module source (repo, path, branch, git_sha), file hashes, test-datasets pin, mold metadata, any overrides (forced divergence from upstream container, dropped stub block, hand-edits the cast skill chose to apply).
Iterate until clean. Both gates exit on structured signals — never free-text grep.
planemo lint <output_dir> (see planemo-lint). Treat by exit code:
<help>, missing <citations>) are fixed in place by the cast skill, then loop.planemo test <output_dir> --test_output_json <output_dir>/_planemo_test_report.json (see planemo-test). Always pass --test_output_json; planemo’s stdout is for humans and intentionally not part of the cast skill’s parsing surface.
After the run:
validate-planemo-test-report CLI from @galaxy-foundry/planemo-test-report-schema). A schema-invalid report means the pinned planemo SHA drifted or the run aborted before writing the report — escalate to human triage; do not classify.tests[].data.job is dict[str, Any] (extra-allow) — its inner keys come from the Galaxy job state and are not constrained by planemo-test-report, so treat them as best-effort signals:
tests[].data.status == "success" → pass.tests[].data.status == "failure" + data.problem_log matches an output-discovery pattern (<discover_datasets> mismatch, missing dataset name, format mismatch) → adjust the corresponding <output> / <discover_datasets> block.tests[].data.status == "failure", and data.job.stderr (when present) carries upstream tool stderr → the <command> Cheetah translation is wrong; LLM revises.tests[].data.status == "error" with HTTP/URL signals → fixture-availability fault; verify the nf-core/test-datasets URL resolves and consider a local test-data/ fallback, recording the divergence in _provenance.yml.overrides.The convergence loop is bounded (default 3 attempts). On exhaustion, the cast skill writes whatever it has and surfaces the final _planemo_test_report.json (plus the lint diagnostics) for human triage.
meta.yml.components: populated → out of scope. Routed to a separate Mold (not in this plan).[[nextflow-to-galaxy]]; this Mold runs at the module tier..shed.yml and shed publication live in the new repo’s CI, not in this Mold.meta.yml may lie. Hand-authored, can drift from script: IO. When the LLM-inferred IO disagrees with meta.yml, prefer meta.yml and surface the disagreement in _provenance.yml.overrides.environment.yml is the source of truth for <requirements>. Don’t substitute a hand-picked container source.task.ext.args with embedded Groovy logic can’t be cleanly mapped to a single text param. Surface as a text param plus a heavy <help> block; document the divergence in _provenance.yml.overrides.tests/main.nf.test has only stub-mode coverage (-stub-run), the convert Mold cannot derive a Galaxy <test> from it (per [[nfcore-stub-block-to-galaxy-noop-test]]). Surface the gap; let the harness decide whether to author a <test> by hand.patterns → 5 nf-core→Galaxy translation patterns (see frontmatter references[]). LLM-condensed into the cast skill.cli-tool → planemo carries the pinned install metadata; flows into the cast bundle’s _required_tools.json via the PR #235 mechanism.cli-command → planemo-lint and planemo-test cast to JSON sidecars; consulted on-demand inside the §10 loop.schema → planemo-test-report copied verbatim into the cast bundle; the convergence loop AJV-validates --test_output_json output against it before classifying failures.research → [[component-nf-core-tools]], [[component-nextflow-containers-and-envs]], [[galaxy-discover-datasets]]. On-demand, condensed into runtime context when triggered.examples — pending: 3 hand-picked Wave 1 modules (one trivial, one paired-aware, one with conditional). Used for round-trip smoke testing before this Mold ships.evidence: hypothesis.planemo test --test_output_json validated against planemo-test-report; pulled in cli-tool/cli-command/schema references for planemo, planemo-lint, planemo-test, planemo-test-report. Deferred-manpages caveat removed.