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broadinstitute
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viral-ngs
Viral genomics analysis pipelines
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testing-related fixes
#913
notestaff
opened
5 years ago
0
fix util.misc.available_cpu_count()
#912
notestaff
closed
5 years ago
2
everything is single threaded now?
#911
dpark01
closed
5 years ago
2
travis-ci.ORG -> travis-ci.COM
#910
tomkinsc
closed
5 years ago
0
update PyYAML to fix CVE-2017-18342
#909
tomkinsc
closed
5 years ago
1
Migrate Kraken -> Kraken 2
#908
tomkinsc
closed
5 years ago
1
Adding verbose output to debug on GCP
#907
tom-dyar
closed
5 years ago
0
conda fixes related to changed bioconda guidelines
#906
notestaff
closed
5 years ago
1
When determining available memory and cores, take into account cgroup limits
#905
notestaff
closed
5 years ago
2
let scaffolder use ambiguous alignments when no unambiguous ones exist
#904
notestaff
closed
5 years ago
5
update to use viral-baseimage 0.1.14
#903
notestaff
closed
5 years ago
0
add fallback method for bioconda wrapper of gatk v3
#902
tomkinsc
closed
5 years ago
0
Set timeouts for dx jobs launched from travis-ci .
#901
notestaff
closed
5 years ago
0
Fix issues with Trinity
#900
notestaff
closed
5 years ago
2
fix ncbi tbl parser for refseq accessions
#899
dpark01
closed
5 years ago
0
do not check for chromosome names in bam_is_sorted
#898
tomkinsc
closed
5 years ago
0
respec snakemake per-rule mem requirement: s/mem/mem_mb/g
#897
tomkinsc
closed
5 years ago
0
Fix typo
#896
pvanheus
closed
6 years ago
0
allow ints in remote protocols ("s3://"...)
#895
tomkinsc
closed
6 years ago
0
use python3 in easy-deploy script if available
#894
tomkinsc
closed
6 years ago
0
update easy-deploy docs
#893
tomkinsc
closed
6 years ago
0
increase memory headroom requested for UGER jobs by 10%
#892
tomkinsc
closed
6 years ago
0
allow runinfo override in demux WDL task
#891
tomkinsc
closed
6 years ago
0
change dotkit providing python-yaml
#890
tomkinsc
closed
6 years ago
0
assembly.assemble_spades: added option to drop contigs shorter than given length.
#889
notestaff
closed
6 years ago
2
assembly.py - added --alwaysSucceed option to SPAdes
#888
notestaff
closed
6 years ago
0
preserve Unmatched.bam in illumina_demux WDL task
#887
tomkinsc
closed
6 years ago
0
assemble_spades: add --always_succeed
#886
dpark01
closed
5 years ago
1
WDL workflow: ensure numeric segment ordering for genbank feature tables in multi-segment genomes
#885
tomkinsc
opened
6 years ago
0
update viral-baseimage 0.1.12 -> 0.1.13
#884
tomkinsc
closed
6 years ago
0
add metagenomics.py::filter_bam_to_taxa
#883
tomkinsc
closed
6 years ago
0
wrap conda builds with retry loop
#882
tomkinsc
opened
6 years ago
0
safely build snpEff database
#881
tomkinsc
closed
6 years ago
0
add --no-same-owner to tar -x in WDL tasks
#880
tomkinsc
closed
6 years ago
1
only upload conda packages for tags (#872)
#879
notestaff
closed
6 years ago
0
update spades to 3.12.0
#878
notestaff
closed
6 years ago
0
misc small fixes
#877
notestaff
closed
5 years ago
1
bumped testing-related packages to current versions: coveralls to 1.3.0, coverage to 4.5.1, pytest-xdist to 1.22.5, pytest-mock to 1.10.0, pytest to 3.7.1
#876
notestaff
closed
6 years ago
0
Add ability to filter reads based on metagenomic classification
#875
tomkinsc
closed
6 years ago
1
add length threshold to metagenomics.py::assemble_spades
#874
tomkinsc
opened
6 years ago
0
address snpEff database build failures
#873
tomkinsc
closed
6 years ago
0
only upload conda packages for tags
#872
tomkinsc
closed
6 years ago
0
debug demux
#871
tomkinsc
closed
6 years ago
0
bump pysam, samtools
#870
tomkinsc
closed
6 years ago
0
picard 2.18.9 -> 2.18.11
#869
tomkinsc
closed
6 years ago
0
demux changes to support novaseq
#868
tomkinsc
closed
6 years ago
4
fixes related to GATK bump to 3.8
#867
notestaff
closed
6 years ago
12
testing: fixed an issue with the handling of tempdirs
#866
notestaff
closed
6 years ago
5
rename task WDL files to have "tasks_" prefix
#865
tomkinsc
closed
6 years ago
0
add workflows for isnvs_merge_to_vcf
#864
tomkinsc
closed
6 years ago
3
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