Releases: broadinstitute/viral-core
Releases · broadinstitute/viral-core
v2.1.15
Accept .tsv
as a possible line ending for custom samplesheets in illumina demux [#47]
v2.1.14
- adds --max_barcodes option (default 10000) to cap common barcodes output file length from
illumina.illumina_demux
[#46]
v2.1.13
- bugfixes for file_utils.tsv_join -- make it behave more unix-like instead of excel-like [#45]
v2.1.11
JVMmemory
is now passed to additional picard tools in read_utils.py align_and_fix
v2.1.10
- bump
viral-baseimage
0.1.17 -> 0.1.18 (includes faster miniconda and mamba)
- use bioconda-sourced GATKv3
v2.1.9
- Adjust output filter of
read_utils.align_and_fix()
to remove marked pcr duplicates, mapped singletons, supplementary (chimeric) alignments, secondary alignments, and improperly paired reads. single-end reads are allowed through if mapped.
v2.1.8
Addition of a few scripts: tsv_join, tsv_derived_cols, and priorities.py [#37]
v2.1.7
- bugfix for read_utils.py align_and_fix when empty input and aligner = minimap2 [#36]
v2.1.6
- bugfix: minimap2 behavior when given empty bam input with exactly one read group [#35]