broadinstitute viral-ngs issues

broadinstitute / viral-ngs

Viral genomics analysis pipelines

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repair malformed zip files in extract_tarball

#963 tomkinsc closed 5 years ago
0
add dustmasker as tool

#962 tomkinsc opened 5 years ago
1
add optional QC check to filter_lastal_bam

#961 tomkinsc closed 5 years ago
1
in picard demux set max_mismatches=0

#960 tomkinsc closed 5 years ago
0
update default ERCC seq file for WDL

#959 tomkinsc closed 5 years ago
1
emit log warnings for malformed kraken reports

#958 tomkinsc closed 5 years ago
0
binned coverage plot option in align_and_plot

#957 lakras closed 5 years ago
0
update GATK version mentioned in Install section of the docs

#956 tomkinsc closed 5 years ago
0
add aggregate_spike_count to reports.py

#955 tomkinsc closed 5 years ago
0
remove BOM from first line of samplesheet file, if present

#954 tomkinsc closed 5 years ago
0
SampleSheet should tolerate windows line endings

#953 tomkinsc closed 5 years ago
1
Fixed WDL of task assemble for the trinity-spades case. Removed workaround for a now-fixed Cromwell issue.

#952 notestaff closed 5 years ago
0
in metagenomics WDL task, make declared vars with defaults non-optional

#951 tomkinsc closed 5 years ago
0
Fix s/genome coverage/unique kmers/ in krakenuniq Krona report

#950 yesimon closed 5 years ago
0
handle feature qualifiers that consist of only a key

#949 tomkinsc closed 5 years ago
0
aggregate viral summary from krakenuniq WDL task

#948 tomkinsc closed 5 years ago
0
Fix conda -V log warnings

#947 yesimon closed 5 years ago
0
add guardrails for the case where observed barcodes are null

#946 tomkinsc closed 5 years ago
0
update version of perl used when building viral-ngs conda package for release

#945 tomkinsc closed 5 years ago
0
travis conda debug

#944 tomkinsc closed 5 years ago
0
Revert "Remove merge_compressed_files because they are cattable"

#943 yesimon closed 5 years ago
1
have WDL task and Snakemake rule "spikein_report" produce sorted report and file of top N hits

#942 tomkinsc closed 5 years ago
0
Update illumina_indices.py

#941 09aaronl closed 5 years ago
0
in WDLs, sort spike-in reports by read count

#940 tomkinsc closed 5 years ago
0
Correct "seq_in_adapter"s in illumina_indices.py

#939 09aaronl closed 5 years ago
0
Kraken2 depletion for human reads as alternative to bmtagger

#938 yesimon opened 5 years ago
2
open_or_gzopen -> compressed_open. Add support for zstd.

#937 yesimon opened 5 years ago
2
Remove merge_compressed_files because they are cattable

#936 yesimon closed 5 years ago
0
Split out TaxonomyDB into a separate python lib

#935 yesimon opened 5 years ago
1
Upgrade pytest

#934 yesimon closed 5 years ago
0
Update illumina_indices.py

#933 09aaronl closed 5 years ago
1
allow outlier_barcodes to act on single-index runs

#932 tomkinsc closed 5 years ago
0
Follow conda solver recommendations.

#931 yesimon closed 5 years ago
0
ditch py2

#930 dpark01 opened 5 years ago
0
add support for / switch default dbs to zstd

#929 dpark01 opened 5 years ago
0
output viral-ngs version as string in WDL workflows

#928 tomkinsc closed 5 years ago
5
Revamp of metagenomics rules

#927 yesimon closed 5 years ago
4
illumina.py: fixed small bug where exception was not raised for missing files

#926 notestaff closed 5 years ago
0
expose --skipMarkDupes and --plotOnlyNonDuplicates in WDL

#925 tomkinsc closed 5 years ago
0
expose --skipMarkDupes for WDL align_and_plot

#924 dpark01 closed 5 years ago
1
Update CondaPackage InstallMethod for overwritten envs.

#923 yesimon closed 5 years ago
2
Bump CONDA_PERL 5.22 -> 5.26 to match conda-forge pins in CB3

#922 yesimon closed 5 years ago
7
retry conda environment install on Travis

#921 tomkinsc closed 5 years ago
3
memory spec corrections in UGER job submission script; JVM memory for demux

#920 tomkinsc closed 5 years ago
0
update tasks_taxon_filter.wdl

#919 tomkinsc closed 5 years ago
0
Hyperlink DOI to preferred resolver

#918 katrinleinweber closed 5 years ago
1
add function to assist Illumina index correction

#917 tomkinsc closed 5 years ago
3
Create a stub CondaPackage for use with tests.

#916 yesimon closed 5 years ago
0
Replace remote S3 paths with local paths for test_snake dryruns.

#915 yesimon closed 5 years ago
0
exclude secondary alignments and unaligned reads in flagstat output from WDLs

#914 tomkinsc closed 5 years ago
0

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