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@tomkinsc tomkinsc released this 10 Jul 19:48
· 220 commits to master since this release
v1.20.0
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Learn about vigilant mode.

New:

  • WDL workflow added to read_utils.wdl::downsample() [#819, #821, #823]
  • WDL workflows added for iSNV calling/v-phaser [#828]
    • assemble_denovo_with_deplete_and_isnv_calling.wdl
    • assemble_denovo_with_isnv_calling.wdl
    • isnvs_one_sample.wdl
  • WDL workflow to create a DNAnexus applet to launch demultiplexing [#838]
    • demultiplexing on DNAnexus occurs on instances scaled to input run type/size, up to NovaSeq size
    • sequencing_center can be passed as an input to the DNAnexus applet, allowing it to be set for demultiplexing at time of upload [#844]

Changed:

  • optimizations related to bwa-based depletion (output is piped between several steps to avoid disk writes) [#791]
  • ncbi.py:: tbl_transfer() now uses a rewritten feature table parser that is more tolerant of possible edge cases present in feature tables [#826]
  • sampleNamesFile no longer output by interhost.wdl:: multi_align_mafft_ref() [#808]
  • -P removed from snakemake UGER qsub command [#817]
  • intrahost.py::merge_to_vcf now tries to guess sample names to use in creating VCF file, based on v-phaser output [#828]
  • WDL workflows altered for compatibility with dxWDL 0.69
  • illumina.py::illumina_demux updated to allow NovaSeq-format dates [#831]
  • demux.wdl::illumina_demux now allows a custom RunInfo.xml to be passed in [#831]
  • demux.wdl:illumina_demux now allows thread count to be passed to demux [#834]
  • various small documentation updates [#835]
  • gzip replaced with pigz in several external process calls to improve performance [#842]
  • in depletion, post-bwa filter changed from -f0x4 (include unmapped) to -F0x2 (exclude mapped proper pairs) [#791]

Fixed:

  • bwa-depleted bam files are now reverted to remove headers related to human alignment that could cause issues for downstream tools [#791]
  • snakemake config now correctly lists only hg19 in bwa_dbs_remove
  • bugfixes to WDL workflow for demux.wdl:: merge_and_reheader_bams() [#818, #824]
  • fixed bug that caused incorrect encoding of ALT alleles in sample-specific GT columns in intrahost.py::merge_to_vcf [#828]
  • fixed a non-deterministic/intermittent error in kraken call related to pipe closure [#840, #841 ]

Added/upgraded:

  • dxWDL 0.60.2 -> 0.69 [#828, #838]
  • cromwell 30.2 -> 32 [#828, #838] (WDL workflows are still in draft-2 spec)
  • fastqc 0.11.5 -> 0.11.7 [#833] (supports NovaSeq)
  • pigz 2.3.4 -> 2.4 [#842]
  • For viral-ngs Docker image, bumped viral-baseimage 0.1.9 -> 0.1.11 [#811]
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