nygenome

E2e Pipeline Test — Testing skill for Claude Code

Testing community

Run the full Lancet2 pipeline on both test profiles back-to-back.

How to install E2e Pipeline Test

Installs to ~/.claude/commands/nygenome-lancet2-e2e-pipeline-test.md

Terminal

mkdir -p ~/.claude/commands && curl -fsSL https://raw.githubusercontent.com/nygenome/Lancet2/HEAD/.claude/commands/e2e-pipeline-test.md -o ~/.claude/commands/nygenome-lancet2-e2e-pipeline-test.md

Restart Claude Code, or start a new session, for it to be picked up.

What E2e Pipeline Test does

description: Run the full Lancet2 pipeline on both test profiles back-to-back. Germline (NA12878 / chr1) then somatic (HCC1395 tumor + HCC1395BL normal / chr4). Confirms exit-0 and a reasonable variant count for each; truth comparison is out of scope. allowed-tools: Bash

/e2e-pipeline-test — end-to-end smoke test

Run the full Lancet2 pipeline twice in succession against the project's test data. The germline stage exercises the single-sample (case-only) code path on `NA12878.final.cra

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