NF pipelines work by Mery

The Nextflow pipelines themselves live under nextflow_pipelines/ — see nextflow_pipelines/README.md for how to run one, how the config layers work, and how tool modules are shared via the sibling nextflow_process_library repo.

Contributing

This repo gets edited concurrently by different lab members, and often by more than one Claude Code session at once. Before editing a subworkflow, module, or config here:

1. Follow nextflow_pipelines/subworkflows/CLAUDE.md and TEMPLATE.nf for new subworkflows.
2. Follow shared nextflow_process_library's own modules/CLAUDE.md for tool modules there, and keep anything specific to this benchmark (QC/metrics logic, thresholds) in this repo's own nextflow_pipelines/modules/local/ — never in the shared module repo.
3. Verify a changed subworkflow standalone with nextflow run <file>.nf — it should fail only on a missing required parameter, not a compile error.
4. Whatever you change here — a subworkflow, a config, CLAUDE.md, this README, anything — record it in NOTEBOOK.md before you're done (see below), not just in the commit message. The commit says what changed; the notebook says why and what happened (results, errors, decisions, flags for whoever picks this up next).

Lab notebook conventions

NOTEBOOK.md at the repo root is a chronological, append-only log of work sessions on this repo — one dated entry per session, covering what was done, what happened (concrete results/errors, not a diff restatement), and the decision or next step. Never edit or reorder past entries; always append.

If you use Claude Code, this convention is checked in as a project skill at .claude/skills/notebook/ — anyone who clones this repo gets the same /notebook behavior automatically, no setup needed. If you don't use Claude Code, follow the header format documented at the top of NOTEBOOK.md itself.

If you are using Claude code this is an suggested prompt:

Before we wrap up, review what we changed in this session and append one
dated entry to NOTEBOOK.md at the repo root, following the format in its own
header. Cover:
- what was done/tried
- what happened — concrete results, errors, numbers, not a restatement of
  the diff
- any decision made or flags left for whoever works on this next

If today's date already has an entry, add to it rather than starting a new
heading. Never edit or reorder any past entry — only append.

Use the skill present in this repo for lab notebook generation.