Isolated conversion trial: seqkit/stats

Outcome

The model-backed worker completed in 8 minutes 41 seconds, with Planemo lint clean and its single emitted Galaxy test passing on the third attempt. No parent-side artifact repairs or worker hints were supplied. The worker output has not been edited.

This is a held-out module rather than a worked example in the bundled conversion notes. It exercises multi-file sequence inputs, FASTA/FASTQ datatype selection, a non-empty additional-arguments default, and stdout-redirection to one TSV output.

The worker result is successful but is not a complete test-coverage or semantic-equivalence grade: it emitted only one of the five non-stub upstream test cases.

Independent supplemental validation subsequently passed 5/5 Galaxy tests, covering single-end Illumina FASTQ, paired Illumina FASTQ, nanopore FASTQ, genome FASTA, and transcriptome FASTA. The original worker artifact still ships only its one test; the supplemental tests live in a separate copy.

Reproducibility

• Foundry main at merge: f19ad2e0c7949c8583981a3a6fe296bac26b2174; selected cast bundle byte-matches that merge.
• Mold revision: 8; cast adapter: claude.
• Pi: 0.84.4; provider/model: openai-codex/gpt-5.6-terra; reasoning: high.
• Wall budget: 3,600 seconds; actual duration: 521,092 milliseconds.
• nf-core/modules pin: 0befdd9db2975ee04a97decc1672a4304387e9a7.
• Module: modules/nf-core/seqkit/stats.
• nf-core/test-datasets pin: 9e3d19ac85b1f62ce3d4ee6df634d61bc5c7656e.
• Planemo: 0.75.47; wrapper dependency: SeqKit 2.13.0.
• Isolation: fresh process, context, configuration, staged module, and explicit skill; ambient resource discovery disabled. Local mode is not a security boundary. Planemo used local Galaxy and Conda dependency resolution.
• Model usage cost recorded by Pi: approximately USD 0.74; this is the provider estimate, not a full infrastructure cost.

Original worker artifacts

• Tool XML
• Local macros
• Conversion provenance
• Harness run record
• Worker trace
• Final worker Planemo report
• Supplied prompt

These artifacts are in temporary directories, not published wrappers in tools-iwc-lab.

Observed decisions

• Exposed reads as one multiple="true" data input rather than adding an unused single/paired selector; meta.single_end does not drive this module’s command.
• Accepted fasta, fasta.gz, fastqsanger, and fastqsanger.gz; emitted one format="tsv" output.
• Preserved the --all default as the text field’s default value.
• Copied mold_revision: 8 and cast_target: claude from the cast bundle correctly; source file hashes also match.
• Used a stable numeric content assertion for the pinned single-end FASTQ fixture because the nf-test snapshot contains an output MD5 but no downloadable expected output artifact.

Self-corrections

1. The initial command used shell line-continuation backslashes. Galaxy joined command lines with spaces, yielding seqkit stats \\ --tabular ...; SeqKit interpreted a flag as a filename. The worker diagnosed this from the structured report and removed continuation backslashes.
2. The next command staged symlinks on separate lines without shell separators. Galaxy joined the ln and seqkit commands. The worker added explicit semicolons and the third test run passed.

This repeats the line-continuation failure from the samtools/index trial and supports a narrow, general command-rendering correction in the conversion skill.

Parent verification

The final worker report passes the Foundry Planemo report schema validator and records 1/1 successful tests. Artifact hashes match the harness run record and remained unchanged throughout parent verification. A separate validation copy retains the worker command, interface, and macros unchanged and adds the four omitted upstream input shapes. Its final report also passes schema validation and records 5/5 successful tests.

• Supplemental validation wrapper
• Final supplemental Planemo report
• Supplemental run log
• Initial supplemental report

The initial supplemental run executed all five input shapes successfully but failed one parent-authored assertion: the parent assumed the genome FASTA had the canonical 29,903-base length. Direct counting of the pinned FASTA confirmed 29,829 bases; the assertion was corrected to that independently measured value and the full suite rerun. No wrapper command or input/output definition changed. Added tests omit an explicit extra_args value and assert the Q1 column, confirming that the default --all option is applied.

Supplemental assertions check row counts, input multiplicity, sequence format, default statistics columns, and the genome length. They do not assert every statistic, output dataset identifier usability, or all possible CLI flags.

Follow-up candidates

1. Explain Galaxy command whitespace normalization, use explicit shell separators, and inspect the rendered command when shell execution fails.
2. Reconcile the procedure’s “for each” usable upstream fixture instruction with its “at least one” shipment requirement. The worker declared no unresolved problems despite omitting paired, nanopore, genome FASTA, and transcriptome FASTA coverage.
3. Define cast_artifact_sha precisely. The worker populated it with _provenance.json.mold.content_hash (2293453c...), which hashes the Mold source, not the cast bundle. The harness independently records the actual selected bundle hash (3037f19b...).

The default-value behavior for an explicitly empty additional-arguments field and the usability of numeric input filenames in the TSV’s file column have not been graded by this trial.