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@tomkinsc tomkinsc released this 25 Jul 16:03
· 189 commits to master since this release
v1.21.0
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New:

  • added a new utility function to merge a group of separate tarballs into one single tarball: file_utils.py::merge_tarballs() [#853]
    • useful for consolidating sequencing runs that have been uploaded in chunks
    • data can be piped in and/or out
    • tarball content can be extracted to disk during the repack
  • added WDL workflow, isnvs_merge_to_vcf.wdl, to perform multiple alignment on assembled sequences, call iSNVs, and produce a VCF with variants seen in across all samples relative to a reference [#864]

Changed:

  • WDL task files renamed to have tasks_ prefix [#865]
  • dxWDL 0.72: revert WDLs to unbound task inputs [#857, #860]

Fixed:

  • WDL dx-launcher: consolidate_run_tarballs is now executed as a separate top-level job to allow uploading of the output [#858]
  • Broad UGER: allow run-pipe.sh to be called when a conda env is active [#851]
  • remove build_lastal_db as a Snakemake local rule [#849]
  • testing: fixed an issue with the handling of tempdirs [#866]

Added/upgraded:

  • mafft 7.221 -> 7.402 [#863]
  • gatk 3.6 -> 3.8 [#863, #867]
  • bwa 0.7.15 -> 0.7.17 [#863]
  • blast 2.6.0 -> 2.7.1 [#863]
  • trimmomatic 0.36 -> 0.38 [#863]
  • bedtools 2.26.0 -> 2.27.1 [#863]
  • biopython 1.70 -> 1.72 [#863]
  • snakemake 4.1.0 -> 5.2.0 [#852]
  • pytest 3.0.5 -> 3.6.3 [#856]
  • update Dockerfile viral-baseimage 0.1.11 -> 0.1.12 [#861]
  • dxWDL 0.69 -> 0.72 (soon to be merged in to dx-toolkit) [#857]
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