Fix .bed input path handling and reference_data paths#1373
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normalize_output_prefix now strips exactly 3 extensions (mirroring SOS :bnnn) instead of pattern-matching known suffixes, so .bed inputs like protocol_example.rnaseq.tpm_matrix.bed correctly resolve to protocol_example rather than the full basename. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…nnotation notebook Update all example command paths from reference_data/ to input/reference_data/ to match the actual tutorial directory layout. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…n notebook Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
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Summary
normalize_output_prefixto strip exactly 3 extensions (mirroring SOS:bnnn), so.bedinputs likeprotocol_example.rnaseq.tpm_matrix.bedresolve toprotocol_exampleinstead of the full basename. Previously qc_1 wrote output to the wrong path, causing SOS to report the expected output file missing.reference_data/toinput/reference_data/to match the actual tutorial directory layout.Test plan
sos run pipeline/bulk_expression_QC.ipynb qcwith a.bedTPM input and verifyprotocol_example.low_expression_filtered.tpm.gct.gzis created at the expected pathinput/reference_data/paths🤖 Generated with Claude Code