amalgkit rerun

Overview

amalgkit rerun reads sanity_report.json, resolves failed pipeline targets, and reruns the selected commands. It also writes a manifest so the rerun plan can be inspected or archived.

Run amalgkit sanity first:

amalgkit sanity --out_dir ./ --all

Then preview rerun targets:

amalgkit rerun --out_dir ./ --dry_run yes

Default paths

Report:   out_dir/sanity/sanity_report.json
Manifest: out_dir/sanity/rerun_manifest.json

--metadata report uses the metadata path stored in the sanity report. This is the default and is usually the safest choice.

Examples

Rerun all failed targets recorded by the report:

amalgkit rerun --out_dir ./

Rerun only selected target families:

amalgkit rerun --out_dir ./ --check getfastq,quant

Limit by run:

amalgkit rerun --out_dir ./ --check getfastq,quant --run SRR000001,SRR000002

Limit by species:

amalgkit rerun --out_dir ./ --check merge,busco,finalize --species "Homo sapiens"

Include warning-level issues, such as missing global summary PDFs:

amalgkit rerun --out_dir ./ --include_warnings yes

Disable manifest output:

amalgkit rerun --out_dir ./ --manifest none

Supported targets

• getfastq
• index
• quant
• merge
• busco
• finalize
• all

If --check is omitted, rerun uses the checks recorded in sanity_report.json.

Notes

• --redo yes is the default for rerun so broken outputs can be overwritten.
• --download_dir and --download_lock_dir are shared with download-heavy targets.
• Use --dry_run yes before large cluster reruns.