Releases: broadinstitute/viral-assemble
Releases · broadinstitute/viral-assemble
v2.2.4.0
What's Changed
New functionality
- add --allow_incomplete_output option to order_and_orient and add tests and support for empty fasta inputs/outputs throughout the scaffolding/gapfil/impute/refine pipeline by @dpark01 in #36
CI and Build updates
- migration from Travis CI to GitHub Actions by @tomkinsc in #30
- update python modules evaluated for test coverage by @tomkinsc in #33
- rename test action in CI by @tomkinsc in #34
- Update conftest.py to account for breaking changes in the newer version of pytest by @tomkinsc in #35
Docker updates
- update viral-core base image to 2.2.3 (in #35) and 2.2.4 (in #36)
Full Changelog: v2.1.33.0...v2.2.4.0
v2.1.20.2
Update to SPAdes 3.15.0, change default invocation from RNAspades to RNAviralspades.
v2.1.20.1
Expose parameters for SPAdes:
- allow for override of default rnaSPAdes mode
- expose kmer values
v2.1.20.0
Bump viral-core (picard, samtools, pysam, zstandard)
v2.1.16.1
- bug fix:
refine_assembly --already_realigned_bam <no alignments.bam> --outVcf <out.vcf.gz>
was not producing a proper outVcf [#26]
v2.1.16.0
- bump
viral-core
to 2.1.16
v2.1.12.1
- bug fix: refine_assembly now works with empty read input when
--already_realigned_bam
is specified [#23]
- build fix: restore a few integration tests that were being skipped [#24]
v2.1.12.0
Updated:
- bump docker base image
viral-core
v2.1.10.0 -> v2.1.12.0