--- name: bio-workflow-methods-docwriter description: Generate reproducible Methods from Nextflow, Snakemake, or CWL run artifacts. Use when documenting exact commands, versions, parameters, QC gates, provenance, and outputs. --- # Bio Workflow Methods Docwriter Write Methods text and run documentation from real workflow artifacts. Every command, version, and parameter comes from evidence; nothing is inferred. ## Instructions 1. Collect the evidence package listed in [reference/evidence-checklist.md](reference/evidence-checklist.md): launch command, configs, engine version, tool versions or container digests, input checksums or accessions, reference and database versions, QC reports, and the final output list. 2. Build a draft `run_manifest.yaml` with the extractor for the engine: - Nextflow: `extract_nextflow_run.py` reads `trace.txt` and the `work/` task folders. `--tool-versions` is a JSON mapping of process name to `{"tool": ..., "version": ...}`; `--outputs-manifest` lists one final output path per line. - Snakemake: `extract_snakemake_run.py` reads a JSONL file with one record per job (`rule`, `status`, `tool`, `version`, `command`, `inputs`, `outputs`). Assemble it from `--printshellcmds` logs and the version records; see `fixtures/snakemake/jobs.jsonl`. - CWL: `extract_cwl_run.py` reads one normalized JSON record (run metadata plus `steps` and `outputs`), not a raw CWLProv folder; see `fixtures/cwl/provenance.json`. 3. Fill the remaining fields from evidence only. While drafting, mark a missing value `NOT CAPTURED`; the final manifest must not contain it. If the value cannot be recovered, record the gap under `limitations` and do not call the manifest reproducible. 4. Validate the manifest against [schemas/run-manifest.schema.json](schemas/run-manifest.schema.json) with `validate_run_manifest.py`. 5. Draft `METHODS.md` from [templates/methods_report.md](templates/methods_report.md): workflow summary at the top, then inputs, exact rerun command, environment, steps as executed, QC, outputs, and limitations. 6. For manuscript Methods prose, hand the manifest to `/scientific-writing`. Keep script names, internal flags, and runtime bookkeeping in Methods or the supplement, not in Results. Resolve the installed skill once: ```bash METHODS_SKILL="${METHODS_SKILL:-$HOME/.agents/skills/bio-workflow-methods-docwriter}" ``` Each script declares its dependencies inline (PEP 723), so `uv run --script` needs no separate environment. ## Quick Reference | Task | Action | |------|--------| | Evidence checklist | [reference/evidence-checklist.md](reference/evidence-checklist.md) | | Standards to align with | [reference/standards.md](reference/standards.md) | | Manifest schema | [schemas/run-manifest.schema.json](schemas/run-manifest.schema.json) (LinkML source: [schemas/workflow-run-schema.yaml](schemas/workflow-run-schema.yaml)) | | Drafting templates | [METHODS.md template](templates/methods_report.md), [paper-summary YAML](templates/paper_summary.yaml) | | Extract a Nextflow draft | `uv run --script "$METHODS_SKILL/scripts/extract_nextflow_run.py" --help` | | Extract a Snakemake draft | `uv run --script "$METHODS_SKILL/scripts/extract_snakemake_run.py" --help` | | Extract a CWL draft | `uv run --script "$METHODS_SKILL/scripts/extract_cwl_run.py" --help` | | Validate manifest | `uv run --script "$METHODS_SKILL/scripts/validate_run_manifest.py" run_manifest.yaml` | | Complete example manifest | [examples/run_manifest.example.yaml](examples/run_manifest.example.yaml) | ## Input Requirements - Workflow artifacts (Nextflow/Snakemake/CWL logs and configs) - Tool version records or container digests - QC reports and output manifests ## Output - `METHODS.md` (agent-authored; workflow summary first, then detailed steps) - `run_manifest.yaml` (machine-readable run manifest) - Artifact contract: [schemas/run-manifest.schema.json](schemas/run-manifest.schema.json) - Paper-summary schema: [schemas/bio-paper-schema.yaml](schemas/bio-paper-schema.yaml) ## Quality Gates - [ ] No invented commands, versions, or parameters - [ ] Every step has inputs, outputs, and versions captured - [ ] Commands were sourced from task scripts, not environment-bearing wrappers, and contain no credentials - [ ] No `NOT CAPTURED`, `UNKNOWN`, or `TBD` placeholder remains in a required field - [ ] Workflow summary appears at top of `METHODS.md` - [ ] The final manifest passes `validate_run_manifest.py` ## Examples ### Example 1: Nextflow run to validated manifest ```bash METHODS_SKILL="${METHODS_SKILL:-$HOME/.agents/skills/bio-workflow-methods-docwriter}" uv run --script "$METHODS_SKILL/scripts/extract_nextflow_run.py" \ --trace trace.txt --workdir work --out run_manifest.yaml \ --run-id rnaseq-2026-02-02 --pipeline-name nf-core/rnaseq --pipeline-version 3.14.0 \ --commit-sha --engine-version \ --launch-command "" \ --tool-versions tool-versions.json --outputs-manifest outputs.txt uv run --script "$METHODS_SKILL/scripts/validate_run_manifest.py" run_manifest.yaml ``` ## Troubleshooting **Issue**: Missing tool versions in logs **Solution**: Use `NOT CAPTURED` only while assembling a draft. The final validator rejects it; recover the version from provenance or report the missing evidence in `limitations` without claiming a reproducible manifest. --- Source attribution: fmschulz Original project: https://github.com/fmschulz/omics-skills/blob/493585ac4b5cc032c974273a8c4e8f0458df6c2a/skills/bio-workflow-methods-docwriter/SKILL.md License: MIT License information: https://opensource.org/license/mit Original upstream instructions; downloaded from Dave AI. ## Upstream license notice MIT License Copyright (c) 2026 Frederik Schulz Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. # Dave AI resource metadata Creator / publisher: fmschulz Original project: https://github.com/fmschulz/omics-skills/blob/493585ac4b5cc032c974273a8c4e8f0458df6c2a/skills/bio-workflow-methods-docwriter/SKILL.md Attribution basis: Recovered original package and original project license at a pinned revision Fields of work: Data & Analytics, Education & Research, Product Management, Project & Program Management Roles: Business Intelligence Analyst, Data Scientist, Product Manager, Project Manager, Researcher Specialties: API Tools: Cwl, Nextflow, Snakemake Country applicability: Country not specified Classification basis: Source catalog labels Instruction SHA-256: 44a098660aae466a5471c91974436c7c3c662da30877fcba336dff1855b037b8 Metadata reviewed: 2026-10-27 This metadata supersedes earlier Dave AI catalog attribution. Original instruction and supporting files are preserved.