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@tomkinsc tomkinsc released this 10 Apr 22:08
· 96 commits to master since this release
v1.23.0
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Learn about vigilant mode.

New:

  • scaffolder uses ambiguous alignments when no unambiguous ones exist (#904)
  • add function to assist Illumina index correction (#917)
    • illumina.py::guess_barcodes identifies barcodes with outlier counts after demux, and suggests possible corrections
  • Testing migrated from travis-ci.ORG -> travis-ci.COM (#910)
  • the Snakemake and WDL pipelines now create a file of the top spikeins seen (#909)
  • functionality reporting outlier_barcodes can now act on single-index runs (#932)
  • the viral-ngs version is out emitted as a string output of WDL workflows (#928)
  • The params --skipMarkDupes and --plotOnlyNonDuplicates are now exposed in the WDL task plot_coverage in tasks_reports.wdl (#925)

Changed:

  • testing-related performance improvements (#915)
  • changes related to the use of conda v4 (#922, #923)
  • new stub CondaPackage for use with tests (#916)
  • conda fixes related to changed bioconda guidelines (#906)
    • primarily with respect to package channel priorities

Fixed:

  • changes related to conda on travis (#944)
  • Corrections to Broad index sequences listed in illumina_indices.py (#941)
  • update tasks_taxon_filter.wdl to respect tags_to_clear_space_separated param (#919)
  • illumina.py fixed small bug where exception was not raised for missing files (#926)
  • memory spec corrections in UGER job submission script; JVM memory update for demux (#920)
  • fix util.misc.available_cpu_count() (#912)
  • add guardrails to barcode_helper for the case where observed barcodes are null (#946)

Added/Upgraded:

  • update PyYAML to v5.1 to address CVE-2017-18342
  • perl 5.22.0 -> 5.26 to support conda build 3 and current conda-forge pinnings (#922, #945 )
  • java-jdk==8.0.112 -> openjdk==8.0.112
  • downgrade of blast 2.7.1 -> 2.6.0 due to upstream boost incompatibilities
    Within docker image (#906):
  • pysam 3.11 -> 3.12
  • biopython 1.68 -> 1.72
  • samtools 1.6 -> 1.9
  • pigz 2.3.4 -> 2.4
  • picard 2.9.0 -> 2.18.11
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