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v1.19.3
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@tomkinsc tomkinsc released this 30 Mar 18:05
· 288 commits to master since this release
v1.19.3
cd86d7a

New:

  • WDL workflow for Genbank submission [#797, #793, #800]
  • metagenomics.py taxlevel_summary to tabulate taxonomic abundance data from multiple Kraken-format summary files. [#792]
  • WDL workflow spikein to report spike-ins [#796]
  • new contigs WDL workflow that runs depletion, SPAdes, and has a placeholder for future contig-based taxonomic classification steps to be added later [#796]
  • sample name is now reported in Krona reports as the "root"-level name [#785]

Changed:

  • WDL workflows for depletion now default to use an hg19 BWA database instead of an hg19 bmtagger database [#796]
  • WDL assembly.scaffold: change name of final output file from {sample_name}.scaffold.fasta to {sample_name}.scaffolded_imputed.fasta [#796]

Fixed:

  • Fixes and updates to tbl_transfer_prealigned --oob_clip behavior. [#807]
  • Fixes version mismatch for tbl2asn spec [#787]
  • Addresses edge cases of tbl2asn usage [#797]
  • In Snakemake workflow, skip blank lines in samples-*.txt files [#794]
  • bugfix ncbi annotation step in Snakemake workflow for Genbank submission prep [#786]

Added/Upgraded:

  • dxWDL version 0.59->0.60.2 [#797]
  • base image used for Docker container 0.1.8->0.1.9 to include security fixes from upstream [#802]
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