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7 changes: 7 additions & 0 deletions .github/copilot-instructions.md
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@@ -1,25 +1,32 @@
# Custom Instructions

(Migrated from old file)

<!-- SUPERPOWERS-START -->

# SUPERPOWERS PROTOCOL

You are an autonomous coding agent operating on a strict "Loop of Autonomy."

## CORE DIRECTIVE: The Loop

For every request, you must execute the following cycle:

1. **PERCEIVE**: Read `plan.md`. Do not act without checking the plan.
2. **ACT**: Execute the next unchecked step in the plan.
3. **UPDATE**: Check off the step in `plan.md` when verified.
4. **LOOP**: If the task is large, do not stop. Continue to the next step.

## YOUR SKILLS (Slash Commands)

VS Code reserved commands are replaced with these Superpowers equivalents:

- **Use `/write-plan`** (instead of /plan) to interview me and build `plan.md`.
- **Use `/investigate`** (instead of /fix) when tests fail to run a systematic analysis.
- **Use `/tdd`** to write code. NEVER write code without a failing test.

## RULES

- If `plan.md` does not exist, your ONLY valid action is to ask to run `/write-plan`.
- Do not guess. If stuck, write a theory in `scratchpad.md`.

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2 changes: 1 addition & 1 deletion .github/workflows/draft-release.yml
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Expand Up @@ -24,7 +24,7 @@ jobs:
- uses: actions/checkout@v7
with:
fetch-depth: 0 # required to include tags
- uses: CCBR/actions/draft-release@v0.7
- uses: CCBR/actions/draft-release@v0.8
with:
github-token: ${{ github.token }}
version-tag: ${{ github.event.inputs.version-tag }}
2 changes: 1 addition & 1 deletion .github/workflows/post-release.yml
Original file line number Diff line number Diff line change
Expand Up @@ -17,6 +17,6 @@ jobs:
- uses: actions/checkout@v7
with:
fetch-depth: 0
- uses: CCBR/actions/post-release@v0.7
- uses: CCBR/actions/post-release@v0.8
with:
github-token: ${{ github.token }}
1 change: 0 additions & 1 deletion CHANGELOG.md
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Expand Up @@ -7,7 +7,6 @@
- Detect SLURM-killed Snakemake child jobs in classic cluster mode by adding a `--cluster-status` hook and `scancel` integration, so timed out, OOM-killed, cancelled, or otherwise failed child jobs now retry/fail cleanly instead of leaving the master workflow hanging indefinitely. (#148, @kopardev)
- Clarify motif enrichment outputs and interpretation in the documentation: fix the reported location of HOMER/AME result folders, explain how ASPEN reuses HOMER-generated `target.fa`/`background.fa` in AME, document the AME parallelization strategy, and add simpler guidance for interpreting `knownResults.txt` and `ame_results.txt`. (#146, @kopardev)


## ASPEN 1.4.0

- Add structured pipeline state tracking: a `pipeline.status.json` sidecar and `pipeline.{running,completed,failed,canceled}` marker files are now written to `WORKDIR` during `run`, with a live progress monitor that periodically updates `pipeline.running` with a step-completion percentage; a best-effort `jobby` TSV summary (`snakemake.log.jobby`) is now also generated when Slurm submission fails before Snakemake starts. Consolidated shared logging/banner/version-tag helper functions into a new staged library (`workflow/scripts/ccbr_pipeline_logging.sh`, slated for future migration to `ccbr_tools`); redesigned the `--version`/banner output. (#119, @kopardev)
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