broadinstitute viral-core issues

broadinstitute / viral-core

viral-ngs: read QC, barcode metrics, spike-in metrics, Illumina metrics and demux

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in util.version.py::get_project_path(), consider calling modules to report VERSION correctly

#109 tomkinsc closed 3 weeks ago
0
inference of sequencer model needs updating

#108 dpark01 opened 1 month ago
1
more ReadTheDocs fixes

#107 dpark01 closed 1 month ago
0
fix docbuild

#106 dpark01 closed 1 month ago
0
Replace custom custom mode selection in zstd_open() with zstandard.open()

#105 tomkinsc opened 1 month ago
0
In cmd.py argparse common_args(), set default number of threads to all available if --threads is unspecified

#104 tomkinsc closed 3 months ago
0
add fgbio to conda dependencies

#103 tomkinsc closed 3 months ago
0
index bam before calling samtools idxstats; warn user if input lacks reads

#102 tomkinsc closed 3 months ago
0
Fail gracefully on bam with no reads in viral-core::read_utils::minimap2_idxstats(), and/or provide informative error message

#101 tomkinsc opened 4 months ago
0
update viral-baseimage 0.2.2 -> 0.2.3 (with fully-featured qsv)

#100 tomkinsc closed 1 month ago
0
update coverage config and testing config inherited by derived docker images

#99 tomkinsc closed 5 months ago
0
bump python version 3.8 -> 3.10

#98 tomkinsc closed 6 months ago
0
bump viral-baseimage 0.2.1 -> 0.2.2

#97 tomkinsc closed 6 months ago
0
update conda python version

#96 dpark01 opened 6 months ago
2
bump viral-baseimage 0.2.0 -> 0.2.1

#95 tomkinsc closed 6 months ago
0
add parameter to remove duplicate bit as exclusion criterion in filter_bam_to_proper_primary_mapped_reads

#94 tomkinsc closed 6 months ago
0
add unit test for TestBwamemIdxstats

#93 tomkinsc closed 6 months ago
0
help text correction for filter_to_proper_primary_mapped_reads

#92 tomkinsc closed 6 months ago
0
add read_utils.py::filter_bam_to_proper_primary_mapped_reads(); add same and expose in minimap2_idxstats and bwamem_idxstats

#91 tomkinsc closed 6 months ago
0
in illumina.py guess_barcodes, count NTCs by prefix if their count is not specified

#90 tomkinsc closed 10 months ago
0
change jvm heap limit for GitHub actions in response to recent build failures

#89 tomkinsc closed 10 months ago
0
add firecloud to requirements-conda.txt

#88 tomkinsc closed 10 months ago
0
bump pytest version; update related deprecated functionality

#87 tomkinsc closed 10 months ago
0
change TravisCI badge to Actions badge in readme

#86 tomkinsc closed 10 months ago
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add jq to conda packages

#85 tomkinsc closed 10 months ago
0
rename test action in CI

#84 tomkinsc closed 11 months ago
0
Preserve read pairing information in FastqToSamTool when provided single fastq with interleaved reads

#83 tomkinsc opened 1 year ago
0
Eliminate ExtractIlluminaBarcodes call by default prior to IlluminaBaseCallsToSam

#82 tomkinsc opened 1 year ago
1
bump pysam pin to >=0.20.0

#81 tomkinsc closed 1 year ago
0
uncomment PyYAML in docs/requirements and bump version

#80 tomkinsc closed 1 year ago
0
Handle more date formats from RunInfo.xml

#79 dpark01 opened 1 year ago
0
fix for failure in illumina.py::guess_barcodes on single-index paired-end data

#78 tomkinsc closed 9 months ago
1
push R fix into docker image

#77 dpark01 closed 2 years ago
0
plot_coverage: do not eval() input to set plot binning function; add mean() and median() to options for binning stat

#76 tomkinsc closed 3 years ago
0
picard 2.25.5 -> 2.25.6

#75 tomkinsc closed 3 years ago
0
GitHub Actions CI ported from TravisCI

#74 tomkinsc closed 1 year ago
0
picard 2.25.4 -> 2.25.5

#73 tomkinsc closed 3 years ago
0
add "IDT for Illumina UD" Indexes

#72 tomkinsc closed 3 years ago
0
remove deprecated "max_reads_in_ram_per_tile" from picard opts, expose opt "sort"

#71 tomkinsc closed 3 years ago
0
bump picard 2.24.0 -> 2.25.4

#70 tomkinsc closed 3 years ago
0
illumina_demux runinfo json output

#69 dpark01 closed 3 years ago
0
convert all json map values to strings

#68 dpark01 closed 3 years ago
0
rewrite main_flowcell_metadata() to return "UNKNOWN" rather than error if sequencer model could not be determined

#67 tomkinsc closed 3 years ago
1
remove sequencer_model from illumina_demux run_info output

#66 dpark01 closed 3 years ago
0
bugfix

#65 dpark01 closed 3 years ago
0
extract more runinfo metadata

#64 dpark01 closed 3 years ago
0
correct arg name to in_dir

#63 tomkinsc closed 3 years ago
0
bump picard 2.24.0 -> 2.25.3

#62 tomkinsc closed 3 years ago
2
pin picard version

#61 dpark01 closed 3 years ago
0
revert Picard to v2.22.2 known to work with NovaSeq runs (NextSeq 2k unknown)

#60 tomkinsc closed 3 years ago
0