vgteam/toil-vg issues and pull requests

#860 - Fix testing

Pull Request - State: open - Opened by adamnovak 15 days ago

#859 - Log errors better and update Tidyverse

Pull Request - State: closed - Opened by adamnovak 10 months ago - 1 comment

#842 - add --ref_paths_file option to surject

Pull Request - State: open - Opened by glennhickey about 3 years ago

#841 - fix toil-vg map's giraffe support

Pull Request - State: closed - Opened by glennhickey about 3 years ago

#840 - Use UCSC-hosted copies of CI data

Pull Request - State: closed - Opened by adamnovak about 3 years ago

#839 - switch default vg docker image to latest release (v1.34.0)

Pull Request - State: closed - Opened by glennhickey about 3 years ago

#838 - Update combine

Pull Request - State: closed - Opened by glennhickey about 3 years ago

#837 - Vg pedigree workflow deepvariant grch38

Pull Request - State: open - Opened by cmarkello about 3 years ago

#836 - Vg pedigree workflow deepvariant dev

Pull Request - State: closed - Opened by cmarkello over 3 years ago

#835 - unused argument : `min.cov` in toil-vg vcfeval

Issue - State: open - Opened by zqfang over 3 years ago - 2 comments

#834 - genotype calling for structral variants

Issue - State: open - Opened by zqfang over 3 years ago - 4 comments

#833 - Make more features work with region coalescing

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#832 - Tolerate OSError even on Python 3

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#831 - Singularity code can fail when sandbox_dirname is taken

Issue - State: closed - Opened by adamnovak over 3 years ago

#830 - Support coalescing contigs

Pull Request - State: closed - Opened by adamnovak over 3 years ago

#829 - Use a jq that should come as a v2 manifest

Pull Request - State: closed - Opened by adamnovak almost 4 years ago - 2 comments

#828 - Use a Docker Hub mirror

Pull Request - State: closed - Opened by adamnovak almost 4 years ago - 2 comments

#827 - toil-vg construct fails at building the GBWT index if you haven't specially specified --vcf_phasing files

Issue - State: open - Opened by ruolin almost 4 years ago - 1 comment

#826 - Update commands for new mpmap interface

Pull Request - State: closed - Opened by jeizenga about 4 years ago

#825 - Pass ID range components around as strings

Pull Request - State: open - Opened by adamnovak about 4 years ago

#824 - Encoding issues with coordinates in id_ranges?

Issue - State: open - Opened by mlinderm about 4 years ago - 1 comment

#823 - Note new bcftools will reject the broken 1KG VCFs

Pull Request - State: closed - Opened by adamnovak about 4 years ago

#822 - Chromosome X GRCh38 coordinate handling.

Issue - State: closed - Opened by yassineS over 4 years ago - 5 comments

#821 - Make mkdir in dragen job fault tolerant

Issue - State: open - Opened by cmarkello over 4 years ago

#820 - Use os.makedirs(exits_ok=True) for Toil mkdir_p

Pull Request - State: closed - Opened by adamnovak over 4 years ago

#819 - Vg pedigree workflow dev

Pull Request - State: closed - Opened by cmarkello over 4 years ago

#818 - Vg pedigree workflow dev

Pull Request - State: closed - Opened by cmarkello over 4 years ago

#817 - Need better name for analysis subcommand

Issue - State: open - Opened by cmarkello over 4 years ago - 1 comment

#816 - Vg pedigree workflow dev

Pull Request - State: closed - Opened by cmarkello over 4 years ago - 3 comments

#815 - Allow toil-vg sim to use a --gbwt_index and a --sample_name

Pull Request - State: closed - Opened by adamnovak over 4 years ago - 1 comment

#814 - update to latest sveval

Pull Request - State: closed - Opened by glennhickey over 4 years ago

#813 - strtobool lives in a distutils.util submodule

Pull Request - State: closed - Opened by adamnovak over 4 years ago

#812 - Merges to master time out in the CI tests

Issue - State: open - Opened by adamnovak over 4 years ago

#811 - Changed vg gaffe to vg giraffe

Pull Request - State: closed - Opened by xchang1 over 4 years ago

#810 - move back to dev version

Pull Request - State: closed - Opened by glennhickey over 4 years ago

#809 - update vg docker, and make pypi release

Pull Request - State: closed - Opened by glennhickey over 4 years ago

#808 - toil-vg not working with singularity on kubernetes

Issue - State: closed - Opened by glennhickey over 4 years ago - 3 comments

#807 - switch back to development version

Pull Request - State: closed - Opened by glennhickey over 4 years ago

#806 - run_whole_alignment doesn't output chromosomal BAMs

Issue - State: open - Opened by cmarkello over 4 years ago - 4 comments

#805 - Version 1.6.0

Pull Request - State: closed - Opened by glennhickey over 4 years ago - 1 comment

#804 - pip not python3 compatible

Issue - State: open - Opened by wharvey31 over 4 years ago - 6 comments

#803 - vg_construct.py python3 compatibility

Pull Request - State: closed - Opened by cmarkello over 4 years ago - 2 comments

#802 - Added singularity support for Rscript container

Pull Request - State: closed - Opened by cmarkello over 4 years ago - 3 comments

#801 - Vg pedigree workflow

Pull Request - State: closed - Opened by cmarkello over 4 years ago - 2 comments

#800 - fix typo

Pull Request - State: closed - Opened by glennhickey over 4 years ago

#799 - Function call typo in vg_mapeval.py

Issue - State: closed - Opened by cmarkello over 4 years ago - 1 comment

#798 - Fix when run on Courtyard

Pull Request - State: open - Opened by adamnovak over 4 years ago

#797 - All tests fail on Courtyard

Issue - State: closed - Opened by cademirch over 4 years ago - 2 comments

#796 - Set up CI to run on Kubernetes-based runners

Pull Request - State: closed - Opened by adamnovak over 4 years ago

#795 - Add a couple singularity tests

Pull Request - State: closed - Opened by glennhickey over 4 years ago - 1 comment

#794 - Configure singularity for NIH Biowulf compatibility

Pull Request - State: closed - Opened by cmarkello over 4 years ago - 4 comments

#793 - update sveval image

Pull Request - State: closed - Opened by glennhickey over 4 years ago

#792 - Allow Giraffe to exist in paired-end conditions in mapeval

Pull Request - State: closed - Opened by adamnovak almost 5 years ago

#791 - Python 3

Pull Request - State: closed - Opened by glennhickey almost 5 years ago - 2 comments

#790 - fix typo where gam_chunking option gets forgotten

Pull Request - State: closed - Opened by glennhickey almost 5 years ago

#789 - Fix calling with augmenting but no gam chunking

Pull Request - State: closed - Opened by glennhickey almost 5 years ago

#788 - update vg docker

Pull Request - State: closed - Opened by glennhickey almost 5 years ago

#787 - Small fixes

Pull Request - State: closed - Opened by glennhickey almost 5 years ago

#786 - Account for vg producing multiple types of HandleGraphs

Pull Request - State: closed - Opened by adamnovak almost 5 years ago - 7 comments

#785 - update vg docker image

Pull Request - State: closed - Opened by glennhickey almost 5 years ago

#784 - Revise chunking options for toil-vg call

Issue - State: closed - Opened by glennhickey almost 5 years ago

#783 - [WIP] Add a new disk ensurer that is easier to call and use it for GAM merging

Pull Request - State: open - Opened by adamnovak almost 5 years ago

#782 - Allow passing options like k and w to vg minimizer

Pull Request - State: closed - Opened by adamnovak almost 5 years ago

#781 - WIP: Rewrite toil-vg call

Pull Request - State: closed - Opened by glennhickey almost 5 years ago

#780 - Remove the right directory when someone else has downloaded a tool

Pull Request - State: closed - Opened by adamnovak almost 5 years ago

#779 - Kubernetes patches

Pull Request - State: closed - Opened by adamnovak almost 5 years ago

#778 - Make --force_phasing also ignore overlaps

Pull Request - State: closed - Opened by adamnovak almost 5 years ago

#777 - --force_phasing True on toil-vg construct doesn't work

Issue - State: open - Opened by adamnovak almost 5 years ago - 2 comments

#776 - Skip minimizer without gbwt

Pull Request - State: closed - Opened by adamnovak about 5 years ago - 1 comment

#775 - Make sure we don't forget about chr22 when rewriting contig names

Pull Request - State: closed - Opened by adamnovak about 5 years ago

#774 - Using --add_chr_prefix gives me `22` instead of `chr22`

Issue - State: closed - Opened by adamnovak about 5 years ago - 2 comments

#773 - Flat requirements for whole genome mode are wasteful

Issue - State: open - Opened by adamnovak about 5 years ago

#772 - Phasing VCF argument validation fixes, and Kubernetes compatibility patches

Pull Request - State: closed - Opened by adamnovak about 5 years ago