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Releases: broadinstitute/viral-assemble

v2.3.0.0

11 Mar 18:11
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Full Changelog: v2.2.4.0...v2.3.0.0

v2.2.4.0

09 Jan 15:43
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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

v2.1.33.0

12 Dec 16:07
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Full Changelog: v2.1.20.2...v2.1.33.0

v2.1.20.2

02 Dec 02:19
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Update to SPAdes 3.15.0, change default invocation from RNAspades to RNAviralspades.

v2.1.20.1

01 Dec 20:26
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Expose parameters for SPAdes:

  • allow for override of default rnaSPAdes mode
  • expose kmer values

v2.1.20.0

23 Mar 18:03
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Bump viral-core (picard, samtools, pysam, zstandard)

v2.1.16.1

15 Jan 04:03
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  • 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

14 Jan 03:41
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  • bump viral-core to 2.1.16

v2.1.12.1

22 Dec 20:30
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  • 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

14 Dec 21:17
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Updated:

  • bump docker base image viral-core v2.1.10.0 -> v2.1.12.0