broadinstitute viral-ngs issues

broadinstitute / viral-ngs

Viral genomics analysis pipelines

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issues

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intrahost.py and vphaser errors

#1012 elasekness opened 7 months ago
0
Can viral-ngs detect virus integration?

#1011 doeun99 opened 11 months ago
1
update instance type to v2 for consolidate_run_tarballs

#1010 tomkinsc opened 3 years ago
0
viral-ngs end to end execution tutorial for viral metagenomics

#1009 amirshams84 opened 3 years ago
0
do not discard read IDs for single-end reads after running mvicuna

#1008 tomkinsc opened 4 years ago
0
ensure read_structure override works for CheckIlluminaDirectory

#1007 tomkinsc closed 4 years ago
0
bump cromwell/womtool/dxWDL/dx-toolkit versions

#1006 tomkinsc closed 4 years ago
0
allow `do_not_sanitize` arg to be passed to revert_bam_picard entrypoint

#1005 tomkinsc closed 4 years ago
0
More robust determination of GATK version

#1004 notestaff opened 4 years ago
0
update source url for obtaining gatk 3.8

#1003 tomkinsc closed 4 years ago
0
expose read_utils.py::fastq_to_bam in wdl task and workflow

#1002 tomkinsc opened 4 years ago
0
expose fastq_to_bam via WDL

#1001 tomkinsc opened 4 years ago
0
add code to illumina.py::RunInfo() to infer instrument model

#1000 tomkinsc opened 4 years ago
1
remove py2

#999 tomkinsc closed 4 years ago
0
add krakenuniq summary kmer filter

#998 tomkinsc opened 4 years ago
5
handle when gatk jar is in subdir

#997 tomkinsc closed 4 years ago
0
pin snakemake to 5.6.0

#996 tomkinsc closed 4 years ago
0
bugfixes and deoptimize

#995 dpark01 closed 4 years ago
0
dxWDL upgrade

#994 dpark01 closed 4 years ago
0
intrahost.py error

#993 mhopken closed 4 years ago
7
escape vcf path passed to snpeff

#992 tomkinsc closed 4 years ago
4
picard 2.20.5 -> 2.21.1

#991 tomkinsc closed 4 years ago
0
pin attrs=19.1.0 for now

#990 tomkinsc closed 4 years ago
0
pytest 4.2.0 -> 5.2.0

#989 tomkinsc opened 4 years ago
0
mention where to find latest version of viral-ngs on DNAnexus

#988 tomkinsc closed 4 years ago
0
docs: more generic dsub example

#987 tomkinsc closed 4 years ago
0
update rundocker.sh

#986 tomkinsc closed 4 years ago
0
skip build_conda stage in travis build matrix

#985 tomkinsc closed 4 years ago
1
whitespace bugfix

#984 dpark01 closed 4 years ago
0
Adding logic for default timeouts when running WDL on DNAnexus.

#983 godotgildor closed 4 years ago
0
conda config --set anaconda_upload no

#982 tomkinsc closed 4 years ago
0
do not strip "ERCC" from samples reported in aggregate spike-in report

#981 tomkinsc closed 4 years ago
0
install conda packages to separate environment within Docker container

#980 tomkinsc closed 4 years ago
0
bump Docker viral-baseimage 0.1.14 -> 0.1.15

#979 tomkinsc closed 4 years ago
0
add .git to .dockerignore

#978 tomkinsc closed 4 years ago
2
update picard 2.18.11 -> 2.20.3

#977 tomkinsc closed 4 years ago
2
fix wdl type bug in tasks_assembly task scaffold

#976 notestaff closed 4 years ago
1
s/Int/Float/ for contig alignment threshold

#975 tomkinsc closed 4 years ago
0
WDL type bug in scaffold

#974 dpark01 closed 4 years ago
0
add loglevel to parsers lacking it in reports.py

#973 tomkinsc closed 4 years ago
0
update DNAnexus object referenced for the spike-ins DB

#972 tomkinsc closed 4 years ago
0
update to dxWDL 1.11, dx 0.285.0, cromwell 43. update some dx URLs.

#971 notestaff closed 4 years ago
0
add clumpify-based dedup

#970 tomkinsc opened 4 years ago
3
add tool wrapper for BBMap

#969 notestaff closed 4 years ago
0
add bbmap tools and allow for clumpify-based dedup of unaligned reads

#968 tomkinsc opened 5 years ago
3
add custom demux settings for NextSeq, more stringent barcode Q score threshold for all systems but NovaSeq

#967 tomkinsc closed 4 years ago
0
Changes spades default mode from rna to meta

#966 yesimon opened 5 years ago
1
add WDL task to aggregate spikein reports

#965 tomkinsc closed 4 years ago
0
move metagenomics.py taxlevel_summary to separate task

#964 tomkinsc closed 5 years ago
0
repair malformed zip files in extract_tarball

#963 tomkinsc closed 5 years ago
0