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@tomkinsc tomkinsc released this 03 Oct 16:38
· 29 commits to master since this release
v1.24.0
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Learn about vigilant mode.

New:

  • binned coverage plot option in reports.py align_and_plot via --binLargePlots (#957) (thanks to @lakras)
  • metagenomics.py taxlevel_summary can now also aggregate reports in KrakenUniq format (#948)
  • krakenuniq WDL task (and demux_plus, etc.) writes a viral summary tsv, aggregating kraken reports from all input samples (#948)
  • add aggregate_spike_count function to reports.py to write a tsv table of spike-ins seen in all samples, aggregating separate spike-in reports (#955, #973, #981)
  • an optional QC check has been added to taxon_filter.py filter_lastal_bam (#961)
    • raises a QCError() if the sample name (bam file basename) begins with any number of negative control prefixes ("neg", "water", "NTC") and lastal has identified reads to keep after filtering
  • add WDL task to aggregate spikein reports (#965)
  • add tool wrapper for BBMap (#969)

Changed:

  • for more stringent demux, change max_mismatches=0, from max_mismatches=1 (#960)
  • malformed kraken reports now result in warnings (#958)
  • default reference used in DNAnexus WDL pipeline for ERCC seqs updated from from 32-seq file to 96-seq file (#959, #972)
  • metagenomics.py taxlevel_summary call moved to separate WDL task and called after kraken where it is called; this beak-out allows aggregation of kraken reports created previously or elsewhere (#964)
  • fasta ID is now sanitized for picard CreateSequenceDictionary calls to adhere to character set restrictions in SAM/BAM RNAME spec. see: samtools/hts-specs#333 (#977)
  • Adding spec for timeouts when running WDL on DNAnexus (#983; thanks @godotgildor)
  • install conda packages to separate environment within Docker container (#980)

Fixed:

  • quieted conda warnings related to use of -V (#947)
  • genome feature table parser for reading tsv/Sequin formatted-files now handles feature qualifiers that consist of only a key, fixing observed issue with ribosomal_slippage occurring without a value; qualifier-parsing regex also more robust (#949)
  • KrakenUniq Krona report now correctly reports "unique kmers" rather than "genome coverage" (#950)
  • in WDL KrakenUniq task, declared vars with defaults are now non-optional (#951)
  • Fixed WDL assemble task assembler parameterization for the joint trinity-spades case (#952)
  • The SampleSheet and tabfile readers are now tolerant of a BOM being present—seen in output written by some editors (#954)
  • In WDL for assembly scaffolding, contig alignment threshold changed from Int to Float (#975)
  • specify USE_JDK_DEFLATER=true and USE_JDK_INFLATER=true for picard until bug in Intel deflator is fixed to prevent sporadic crashes (#977)

Added/Upgraded:

  • matplotlib 1.5.3 -> 2.2.4 (#948, #977)
  • bedtools 2.27.1 -> 2.28.0 (#977)
  • blast 2.6.0 -> 2.7.1 (#977)
  • lxml 4.3.0 -> 4.3.3 (#948)
  • switch from picard to picard-slim package (sans 'r') (#977)
  • update picard 2.18.11 -> 2.20.5 (#977)
  • krona 2.7 -> 2.7.1
  • bump Docker viral-baseimage 0.1.14 -> 0.1.15 (#979)
  • added bbmap 38.56
  • change lz4 dependency from lz4-bin sourced from bioconda to lz4-c from conda-forge, 131 -> 1.9.1 (#977)
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