broadinstitute / viral-core / 20938129427

Builds Branch Commit Type Ran Committer Via Coverage
20938129427 v2.5.22 Merge pull request #162 from broadinstitute/fix-ci-docker-tag-race-condition Fix CI race condition when release tag created during build push web-flow github
72.03
20938129426 v2.5.22 Merge pull request #162 from broadinstitute/fix-ci-docker-tag-race-condition Fix CI race condition when release tag created during build push web-flow github
71.85
20938110603 master Merge pull request #162 from broadinstitute/fix-ci-docker-tag-race-condition Fix CI race condition when release tag created during build push web-flow github
72.03
20937751859 fix-ci-docker-tag-race-condition Fix CI race condition when release tag created during build Pass Docker tag as job output from build_docker to test_in_docker and test_docs, ensuring downstream jobs pull the exact image that was built rather than recalculating the tag independen... Pull #162 dpark01 github
71.86
20937760795 fix-ci-docker-tag-race-condition Merge 461f4b592 into ec375fcae Pull #162 web-flow github
71.97
20933450853 v2.5.21 Merge pull request #161 from broadinstitute/trim-rmdup-subsamp Add trim_rmdup_subsamp_reads function push web-flow github
71.8
20933450851 v2.5.21 Merge pull request #161 from broadinstitute/trim-rmdup-subsamp Add trim_rmdup_subsamp_reads function push web-flow github
71.97
20932853990 trim-rmdup-subsamp Add trim_rmdup_subsamp_reads function to read_utils Move trim_rmdup_subsamp_reads from viral-assemble/assembly.py to read_utils.py. - Add threading support to Trimmomatic tool - Convert manual temp file cleanup to context managers - Add command-l... Pull #161 dpark01 github
72.03
20932864025 trim-rmdup-subsamp Merge f48219da9 into 589f1a1fe Pull #161 web-flow github
72.01
20931749004 master Merge pull request #160 from broadinstitute/issue-159-align-and-fix-optimization Optimize align_and_fix runtime with sambamba and skip_realign option push web-flow github
70.97
20919342230 issue-159-align-and-fix-optimization Fix sambamba index to create .bai instead of .bam.bai Sambamba index command creates {file}.bam.bai by default, but WDL workflows expect {file}.bai naming convention. This caused Terra workflow failures where the task succeeded (exit code 0) but ... Pull #160 dpark01 github
70.79
20919343111 issue-159-align-and-fix-optimization Merge f9b616da0 into dd823d605 Pull #160 web-flow github
70.77
20899680251 issue-159-align-and-fix-optimization Disable sambamba merge due to segfault bug in v1.0.1 - Raise NotImplementedError in sambamba.merge() with explanation - Skip TestSambambaMerge tests with pytest.mark.skip - Bug occurs on both ARM emulation and native x86 platforms - Recommend usi... Pull #160 dpark01 github
70.95
20896743977 issue-159-align-and-fix-optimization Add sambamba dependency for align_and_fix optimization Issue #159: Adding sambamba to support faster duplicate marking and BAM operations in align_and_fix pipeline. Co-Authored-By: Claude Opus 4.5 <noreply@anthropic.com> push dpark01 github
70.58
20865577961 v2.5.20 Merge pull request #158 from broadinstitute/perf-hybrid-v2 Optimize filter_bam_by_ids: 13% faster with samtools pipes + SQLite batching push web-flow github
70.6