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52 Open 188 Closed
52 Open 188 Closed
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Issues list

intrahost.py and vphaser errors
#1012 opened Nov 8, 2023 by elasekness
Can viral-ngs detect virus integration?
#1011 opened Jul 10, 2023 by DAWNkKim
1
viral-ngs end to end execution tutorial for viral metagenomics
#1009 opened Jul 10, 2020 by amirshams84
expose fastq_to_bam via WDL
#1001 opened Feb 5, 2020 by tomkinsc
add bbmap tools and allow for clumpify-based dedup of unaligned reads
#968 opened Jun 28, 2019 by tomkinsc
3
Changes spades default mode from rna to meta
#966 opened Jun 14, 2019 by yesimon
@notestaff
1
add dustmasker as tool
#962 opened Jun 11, 2019 by tomkinsc
@yesimon
1
ditch py2
#930 opened Feb 22, 2019 by dpark01
add support for / switch default dbs to zstd
#929 opened Feb 20, 2019 by dpark01
WDL workflow: ensure numeric segment ordering for genbank feature tables in multi-segment genomes
#885 opened Sep 14, 2018 by tomkinsc
wrap conda builds with retry loop
#882 opened Aug 24, 2018 by tomkinsc
add length threshold to metagenomics.py::assemble_spades enhancement
#874 opened Jul 31, 2018 by tomkinsc
@notestaff
rnaSPAdes sometimes does not emit transcripts.fasta
#859 opened Jul 23, 2018 by dpark01
@notestaff
1
update and test Cromwell 32 with Google PAPI v2
#843 opened Jul 10, 2018 by dpark01
2
update WDL from draft-2 spec to v1.0
#837 opened Jul 5, 2018 by tomkinsc
5
Cromwell workflow engine support
#825 opened Jun 21, 2018 by tom-dyar
7
alter kraken.py pipeline() and classify() to tolerate single-end reads
#820 opened Jun 5, 2018 by tomkinsc
VPHASER 2 for single-end reads?
#813 opened May 4, 2018 by aglorias
from human depletion databases, mask any sequence similar to viral or bacterial
#805 opened Mar 29, 2018 by notestaff
@notestaff
1
add step to break up misassemblies in de novo contigs bug
#804 opened Mar 29, 2018 by notestaff
@notestaff
5
VPhaser output intepretation - strand bias p value
#789 opened Feb 9, 2018 by cromozome
3
Add automated blastx-like LCA of post-spades contigs to demux_plus.wdl
#784 opened Feb 6, 2018 by dpark01
@tomkinsc
1
Change krona wrapper to read from summary report instead of read report
#777 opened Jan 31, 2018 by dpark01
8
use *.bam intermediary files rather than *.sam
#763 opened Jan 25, 2018 by tomkinsc
2
snakemake pipeline viral genome pipe
#749 opened Jan 3, 2018 by jb013b
2
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