القائمة
Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks).
التثبيت باستخدام Codex أو Claude انسخ هذا Prompt والصقه في Codex أو Claude أو مساعد آخر ليراجع صفحة Skill ويثبّتها لك.
استنادا إلى تصنيف SOC المهني
Carry an existing Galaxy workflow's tests forward as a regression baseline and augment them for a change-set's deltas, emitting a Galaxy test plan.
Triage failing Galaxy run outputs; classify the failure surface and capture evidence before recommending repairs.
Synthesize a Galaxy workflow test plan from a free-form summary and the Galaxy design briefs.
Assemble Galaxy workflow test fixtures and assertions.
Execute a workflow's tests via Planemo; emit structured pass/fail and outputs.
Path from a CWL Workflow to a Galaxy gxformat2 workflow — orchestrates the Foundry skills of the CWL → GALAXY pipeline in order, in a per-run working directory.
| name | convert-nfcore-module-to-galaxy-tool |
| description | Convert one nf-core module dir into a Galaxy tool wrapper (tool.xml + macros.xml + _provenance.yml + remote-URL <test> blocks). |
Follow the procedure below and use the artifact/reference sections as the runtime contract.
planemo (planemo). uv tool install planemo==0.75.45 (or pip install planemo==0.75.45).
Ephemeral run: uvx --from planemo==0.75.45 planemo.
Check: planemo --version.
Docs: https://planemo.readthedocs.io/
Bundled reference: references/cli/planemo.md.references/cli/planemo.md: CLI tool reference copied verbatim into the bundle. Install metadata for the planemo CLI invoked by the convergence loop. Use when: always — the cast skill needs planemo on PATH before running lint/test.references/notes/nfcore-channel-input-to-galaxy-collection.md: Research note copied verbatim into the bundle. Map process input channels (tuple(meta, path)) to Galaxy / . Use when: emitting for a module.references/notes/nfcore-meta-map-to-galaxy-params.md: Research note copied verbatim into the bundle. Triage meta-map keys: behavior-driving keys become Galaxy s; identity keys are dropped. Use when: a process consumes a meta-map and any meta keys influence the script: body.references/notes/nfcore-stub-block-to-galaxy-noop-test.md: Research note copied verbatim into the bundle. Document the intentional drop of stub: blocks; rely on planemo test for fixture coverage. Use when: the module's main.nf contains a stub: block.references/notes/nfcore-task-ext-args-to-galaxy-additional-options.md: Research note copied verbatim into the bundle. Surface task.ext.args as a single Galaxy text param; do not enumerate per-flag inputs. Use when: the upstream script: body interpolates ${task.ext.args} (or args2/args3).references/notes/nfcore-versions-emit-to-galaxy-version-command.md: Research note copied verbatim into the bundle. Translate the versions.yml emit block (or topic: versions) into Galaxy's <version_command>. Use when: the script: body or output: declarations contain a versions emit.references/cli/planemo-lint.json: CLI command reference packaged as a sidecar. Reference for planemo lint flags and output classification; first gate in the convergence loop. Use when: step 10.1 — after every // emission.references/cli/planemo-test.json: CLI command reference packaged as a sidecar. Reference for planemo test --test_output_json invocation, exit codes, and the JSON report path. Use when: step 10.2 — after lint clears.references/notes/component-nextflow-containers-and-envs.md: Research note copied verbatim into the bundle. Resolve the container directive (mulled, biocontainer, Wave) and environment.yml into a Galaxy block with matching bioconda pins. Use when: emitting and the module's container directive is non-trivial (ternary or mulled).references/notes/component-nextflow-containers-and-envs.yml: Companion file copied verbatim into the bundle. Sibling of references/notes/component-nextflow-containers-and-envs.md; read it where that note directs.references/notes/component-nf-core-tools.md: Research note copied verbatim into the bundle. Reference for nf-core module conventions: meta.yml shape, modules.json, environment.yml posture, test layout, container directive idioms. Use when: parsing meta.yml, environment.yml, or main.nf and a convention is unclear; when populating _provenance.yml.references/notes/galaxy-discover-datasets.md: Research note copied verbatim into the bundle. Reference for the <discover_datasets> XML element: attributes, named/regex patterns, vs contexts, test-side <discovered_dataset>. Use when: translating a Nextflow output: channel that uses a glob path or runtime-interpolated filenames into a Galaxy or multi-output .references/schemas/planemo-test-report.schema.json: Schema file copied verbatim into the bundle. Validate planemo test --test_output_json output before classifying failures; the JSON gate that replaces free-text parsing. Use when: step 10.2 — after every planemo test invocation.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 skill 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 skill summarizes whole pipelines, the wrong granularity for one module.
The skill is run per module by an outer harness (a script or human loop). Cross-module batches are not its concern.
The skill expects:
modules/nf-core/<name>/, or any local clone of that shape).nf-core/modules. When absent, the 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 skill resolves to a recent SHA on the module's pipeline-of-record branch (best-effort; recorded in _provenance.yml either way).The skill 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 skill 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_at
tool.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 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 ${task.ext.args} / args2 / args3.
<outputs>For each output: channel that isn't the versions emit, decide cardinality first, then shape (per galaxy-discover-datasets §Convert skill posture). The Nextflow glob alone is not enough — path('*.bam') (N files, one per element of an upstream collection) and path('*.{bai,csi,crai}') (exactly one file, alternation across mutually-exclusive extensions) look the same but map to different Galaxy idioms.
path("${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 skill 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 skill 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 skill'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 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 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 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 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 skill (not in this plan).nextflow-to-galaxy; this skill runs at the module tier..shed.yml and shed publication live in the new repo's CI, not in this skill.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 skill 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.research → the 5 nf-core→Galaxy translation notes (nfcore-channel-input-to-galaxy-collection, nfcore-meta-map-to-galaxy-params, nfcore-task-ext-args-to-galaxy-additional-options, nfcore-versions-emit-to-galaxy-version-command, nfcore-stub-block-to-galaxy-noop-test) plus component-nf-core-tools, component-nextflow-containers-and-envs, galaxy-discover-datasets. All copied verbatim into the cast bundle under references/notes/, loaded per each ref's used_at/load.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.examples — pending: 3 hand-picked Wave 1 modules (one trivial, one paired-aware, one with conditional). Used for round-trip smoke testing before this skill 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.mode: condense → mode: verbatim (matching every other skill; the prior condense was always a verbatim passthrough), so the cast is fully deterministic and the notes land under references/notes/. planemo ref now sources released 0.75.44 (jmchilton fork retired).