bihealth snappy-pipeline issues

bihealth / snappy-pipeline

SNAPPY Nucleic Acid Processing in Python

MIT License

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issues

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fix: mehari wrapper fix_manta_invs.py requires python >=3.11, update conda env

#542 tedil closed 1 month ago
1
chore: add nodefaults to conda env.yaml channels

#541 tedil closed 1 month ago
1
chore(main): release 0.2.2

#540 bihealth-bot opened 1 month ago
1
chore(main): release 0.2.2

#539 tedil closed 1 month ago
1
chore: Replace mutect2_par wrapper with snakemake scattergather

#538 tedil opened 2 months ago
1
feat: Replace mutect2_par with snakemake scattergather

#537 tedil closed 2 months ago
1
chore: move config accesses in wrappers to params

#536 tedil opened 2 months ago
0
Revamp somatic CNV calling

#535 ericblanc20 opened 2 months ago
0
Unclear error messages when GCNV model paths don't resolve

#534 Nicolai-vKuegelgen opened 2 months ago
1
fix: improve env.yaml and requirements compatibility

#533 tedil closed 2 months ago
0
docs: Check & update of configuration defaults (first part)

#532 ericblanc20 opened 3 months ago
2
feat: automatically retrieve references/annotations and cache them

#531 tedil opened 3 months ago
2
chore: remove unused workflows

#530 tedil closed 3 months ago
2
fix: chr format detection in gcnv wrappers needs to always use egrep

#529 Nicolai-vKuegelgen closed 2 months ago
2
Check and update config defaults

#528 ericblanc20 opened 3 months ago
0
chore(main): release 0.2.1

#527 tedil closed 3 months ago
2
fix: switch from setup.py to pyproject toml

#526 tedil closed 3 months ago
11
chore(main): release 0.2.0

#525 tedil closed 3 months ago
2
chore(main): release 1.0.0

#524 tedil closed 3 months ago
0
chore: release 0.2.0

#523 tedil closed 3 months ago
1
chore(main): release 1.0.0

#522 tedil closed 3 months ago
2
fix: rename _version.py to version.py

#521 tedil closed 3 months ago
2
chore(main): release 0.1.0

#520 tedil closed 3 months ago
3
refactor: remove versioneer, update release-please

#519 tedil closed 3 months ago
3
Error when using bwa with the mbcs ngs mapping meta-tool

#518 ericblanc20 closed 3 months ago
0
refactor ngs_mapping

#517 ericblanc20 opened 4 months ago
0
fix: Always include alfred qc files in input for varfish export bam QC #511

#516 Nicolai-vKuegelgen closed 4 months ago
1
Cache reference downloads / index builds, provide snakemake profile with default cache dir

#515 tedil opened 4 months ago
1
Make use of snakemake storage plugins

#514 tedil opened 4 months ago
0
Wrappers: Move config accesses to params

#513 tedil opened 4 months ago
0
Add genome/reference definition section to configuration

#512 tedil opened 4 months ago
0
`varfish_export_mehari_bam_qc` fails for WGS workflow due to undefined exon bed file

#511 Nicolai-vKuegelgen closed 4 months ago
1
fix: bump mehari to v0.25.5 for bugs fixed there

#510 holtgrewe closed 4 months ago
0
Feature: Generate QC file from GeneCount.tab file of star

#509 giacuong171 opened 5 months ago
0
fix: move config access in gcnv/contig_ploidy wrapper to params

#508 tedil opened 5 months ago
1
fix: set locale to C in bcftools/TMB wrapper

#507 tedil closed 5 months ago
0
fix: eb_filter wrapper assuming ANN/CSQ is present

#506 tedil closed 5 months ago
1
fix: missing check for `has_annotation` in somatic_variant_filtration rules

#505 tedil closed 5 months ago
2
The mehari wrapper for new versions (>=0.25) needs to always run bcftools norm

#504 Nicolai-vKuegelgen opened 5 months ago
2
feat: support for somatic variant calling without normal

#503 ericblanc20 closed 5 months ago
1
somatic variant calling without normal

#502 ericblanc20 closed 5 months ago
0
fix: gcnv wrapper regex curly-brackets parsed by python string formatting (#489 )

#501 Nicolai-vKuegelgen closed 5 months ago
2
The gcnv `contig_ploidy` wrapper hardcodes config paths

#500 Nicolai-vKuegelgen opened 5 months ago
2
feat: add CI for a scaled down version of a cancer WES pipeline

#499 tedil closed 5 months ago
3
fix: explicitly require gawk in mutect2/filter wrapper environment

#498 tedil closed 5 months ago
1
refactor: supply pre-commit-hooks and replace flake8+isort+black with ruff

#497 tedil closed 3 months ago
3
refactor!: use pydantic models for validation

#496 tedil closed 3 months ago
3
feat: Adding somatic neoepitope preparation workflow

#495 giacuong171 opened 6 months ago
2
refactor: Schema validation for config files

#494 tedil closed 6 months ago
1
feat!: Update snakemake to v8

#493 tedil opened 6 months ago
5