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* feat: adding rose and its files * feat: adding the required scripts * refactor: move rose files to standard ccbr_tool layout Reorganize rose into <tool>/ccbr_tool_<optional tool version>/Dockerfile.<version>. * docs: 🤖 update readme for rose/ccbr_rose/Dockerfile.v1 (#353) Co-authored-by: kopardev <kopardev@users.noreply.github.com> * docs: 🤖 update readme for rose/ccbr_rose/Dockerfile.v1 (#356) Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> ---------
* feat: new dockerfile and JSON for rseqc * docs: 🤖 update readme for rseqc/ccbr_rseqc_4.0.0/Dockerfile.v1 (#187) Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> * chore: version 1 thru 3 already exist! * feat: adding original version of ROSE for CARLISLE pipeline * fix: syntax to work with buildx in GHA * fix: adding the missing wrapper scripts * feat: adding chipenrich required by CARLISLE * chore: remove obsolete tool version commands file * chore: update chipenrich Dockerfile * chore: remove rose from chipenricher branch * ci: run on patch for fixed entrypoint * refactor: reorganize chipenrich into ccbr_tool layout * ci: test fix-print-versions branch * ci: use latest release of ccbr/actions * docs: 🤖 update readme for chipenrich/ccbr_chipenrich/Dockerfile.v1 (#357) Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
* feat: updated shiver dockerfile with more libs and gatk4 * docs: 🤖 update readme for shiver/ccbr_shiver_1.7.3/Dockerfile.v2 (#362) Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> ---------
* feat: added R docker for phlyogenetic analysis * docs: 🤖 update readme for phylo/ccbr_r_phylo/Dockerfile.v1 (#364)
Co-authored-by: github-actions[bot] <github-actions[bot]@users.noreply.github.com>
* feat: create ubuntu 26.04 base image resolves #367 * chore: update CHANGELOG.md * chore: drop argparse.bash * fix: drop python2 * fix: use venv to install python deps * fix: install venv * docs: 🤖 update readme for base_images/ccbr_ubuntu_26.04/Dockerfile.v1 (#369) Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
…#373) Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>
Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Kelly Sovacool, PhD <kelly-sovacool@users.noreply.github.com>
…#374) Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
…#380) Co-authored-by: 41898282+github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
- Replace knu/changed-files@v1 with git diff HEAD~1 HEAD to scope file detection to the latest commit only (not full PR diff) - Add fetch-depth: 2 to get-files checkout for parent commit access - Guard build-docker job with if condition to skip when matrix is empty Agent-Logs-Url: https://github.com/CCBR/Dockers2/sessions/40678bbc-3f69-4380-95b3-9af2a243041a Co-authored-by: copilot-swe-agent[bot] <198982749+Copilot@users.noreply.github.com> Co-authored-by: kelly-sovacool <17768269+kelly-sovacool@users.noreply.github.com>
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Strikethroughany points that are not applicable.)CHANGELOG.mdwith a short description of any user-facing changes and reference the PR number. Guidelines: https://keepachangelog.com/en/1.1.0/