broadinstitute/viral-ngs: v1.23.0

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