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