Snakemake pipeline fixes and downstream data updates from PR #166#197
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Snakemake pipeline fixes and downstream data updates from PR #166#197elewis2 wants to merge 1 commit into
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- Replace dedent/cd/wget pattern with curl --create-dirs throughout Snakefile to fix silent failures where shell sections would exit without running commands - Update Ensembl download to use may2025.archive.ensembl.org (main site broken) and move query string to download_ensembl_curl_config.txt - Update CGI biomarkers download URL (changed upstream, no longer zipped) - Add Dockerfile.snakemake: multi-stage build with npm rebuild to fix Node version compilation issues with native deps (node-expat/xml-stream) - Add downloadCosmic.sh helper script for COSMIC download auth flow - Fix fdaSrs/index.js: UNII file header renamed 'PT' -> 'Display Name' upstream, causing all 168k records to be skipped silently - Update data/signatures.json: add sourceIdVersion '3' to all COSMIC signatures (DBS/ID/SBS series) and add name field for proper versioned record lookup Co-authored-by: Matthew Stuart-Edwards <m.stuartedwards@uleth.ca>
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