fix: insert '--' before snakemake targets to prevent --rerun-triggers consuming them#89
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… consuming them snakemake's --rerun-triggers uses nargs=+ in argparse, causing it to greedily consume the first target path as an extra trigger value when targets immediately follow the trigger list. Extract _build_snakemake_cmd() helper and append '--' before any target paths so argparse stops flag processing before the targets are seen. Add three regression tests that directly exercise the command-building logic. Fixes #87 Co-authored-by: Francois Lanusse <EiffL@users.noreply.github.com>
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Fixes #87
Summary
_build_snakemake_cmd()helper incommands.pythat owns snakemake argv construction--before any target paths to terminate argparse flag processingRoot cause
snakemake's
--rerun-triggersusesnargs=+in argparse, so it greedily consumes the first positional argument after the trigger list as another trigger value. Whenlc run <output>appends target paths immediately after the trigger values, snakemake rejects the path as "invalid choice".Test plan
test_run_cmd_inserts_separator_before_targets— reproduces the bug; asserts--appears between triggers and targetstest_run_cmd_no_separator_when_no_targets— no--when running rule alltest_run_cmd_multiple_triggers_all_before_separator— all trigger tokens precede--Generated with Claude Code