broadinstitute/viral-ngs

Issues

• 怎么在aarch64上安装

  #1013 opened 4 months ago by wwhwwxlz
  1

• intrahost.py and vphaser errors

  #1012 opened a year ago by elasekness
  0

• Can viral-ngs detect virus integration?

  #1011 opened 2 years ago by DAWNkKim
  1

• viral-ngs end to end execution tutorial for viral metagenomics

  #1009 opened 5 years ago by amirshams84
  0

• expose fastq_to_bam via WDL

  #1001 opened 5 years ago by tomkinsc
  0

• intrahost.py error

  #993 opened 5 years ago by mhopken
  7

• update WDL from draft-2 spec to v1.0

  #837 opened 7 years ago by tomkinsc
  5

• WDL type bug in scaffold

  #974 opened 6 years ago by dpark01
  0

• add bbmap tools and allow for clumpify-based dedup of unaligned reads

  #968 opened 6 years ago by tomkinsc
  3

• Changes spades default mode from rna to meta

  #966 opened 6 years ago by yesimon
  1

• add dustmasker as tool

  #962 opened 6 years ago by tomkinsc
  1

• SampleSheet should tolerate windows line endings

  #953 opened 6 years ago by tomkinsc
  1

• in WDLs, sort spike-in reports by read count

  #940 opened 6 years ago by tomkinsc
  0

• ditch py2

  #930 opened 6 years ago by dpark01
  0

• add support for / switch default dbs to zstd

  #929 opened 6 years ago by dpark01
  0

• Pre-formatted nr diamond database link not working

  #803 opened 6 years ago by tyhsu389
  1

• everything is single threaded now?

  #911 opened 6 years ago by dpark01
  2

• expose --skipMarkDupes for WDL align_and_plot

  #924 opened 6 years ago by dpark01
  1

• convert GitHub service integrations to GitHub apps

  #855 opened 6 years ago by dpark01
  1

• Migrate Kraken -> Kraken 2

  #908 opened 6 years ago by tomkinsc
  1

• assemble_spades: add --always_succeed

  #886 opened 6 years ago by dpark01
  1

• WDL workflow: ensure numeric segment ordering for genbank feature tables in multi-segment genomes

  #885 opened 6 years ago by tomkinsc
  0

• Add ability to filter reads based on metagenomic classification

  #875 opened 6 years ago by tomkinsc
  1

• wrap conda builds with retry loop

  #882 opened 6 years ago by tomkinsc
  0

• address snpEff database build failures

  #873 opened 6 years ago by tomkinsc
  0

• Cromwell workflow engine support

  #825 opened 7 years ago by tom-dyar
  7

• Ensure BWA-based depletion is tolerant of unpaired reads

  #779 opened 6 years ago by dpark01
  15

• add length threshold to metagenomics.py::assemble_spades

  #874 opened 6 years ago by tomkinsc
  0

• pytest error: tempfile.py:368: FileNotFoundError

  #862 opened 6 years ago by tomkinsc
  9

• rnaSPAdes sometimes does not emit transcripts.fasta

  #859 opened 6 years ago by dpark01
  1

• update and test Cromwell 32 with Google PAPI v2

  #843 opened 7 years ago by dpark01
  2

• Non-deterministic failure of test_kraken_multi teardown

  #839 opened 7 years ago by dpark01
  15

• Remove human @SQ lines from bwa-depleted bam files

  #814 opened 7 years ago by tomkinsc
  4

• add downsampling util

  #815 opened 7 years ago by tomkinsc
  1

• add ability to pass RunInfo.xml file to illumina_demux

  #830 opened 7 years ago by tomkinsc
  1

• adapt RunInfo parsing code to read NovaSeq date formats

  #829 opened 7 years ago by tomkinsc
  1

• alter kraken.py pipeline() and classify() to tolerate single-end reads

  #820 opened 7 years ago by tomkinsc
  0

• remove -P sabeti_lab from Broad_UGER submission script

  #816 opened 7 years ago by dpark01
  0

• VPHASER 2 for single-end reads?

  #813 opened 7 years ago by aglorias
  0

• add step to break up misassemblies in de novo contigs

  #804 opened 7 years ago by notestaff
  5

• from human depletion databases, mask any sequence similar to viral or bacterial

  #805 opened 7 years ago by notestaff
  1

• Create WDL workflow for Genbank submission

  #793 opened 7 years ago by dpark01
  0

• Change default Hs depletion to BWA?

  #769 opened 7 years ago by dpark01
  1

• Add automated blastx-like LCA of post-spades contigs to demux_plus.wdl

  #784 opened 7 years ago by dpark01
  1

• VPhaser output intepretation - strand bias p value

  #789 opened 7 years ago by cromozome
  3

• Add sample name to Krona output

  #785 opened 7 years ago by dpark01
  0

• bmtagger OOM errors more often than it should

  #780 opened 7 years ago by dpark01
  0

• Change krona wrapper to read from summary report instead of read report

  #777 opened 7 years ago by dpark01
  8

• conda package build failures

  #770 opened 7 years ago by dpark01
  2

• illumina_indices.py "TruSight Amplicon Panels" second item key should be "i5" not "i7"

  #764 opened 7 years ago by myourshaw
  1