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108 Open 164 Closed
108 Open 164 Closed
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Issues list

Preparation for somatic CNV
#587 opened Dec 23, 2024 by ericblanc20
@ericblanc20
Absolute path_link_in in ngs_mapping step in config.yaml
#578 opened Dec 11, 2024 by DivyaratanPopli
revamp somatic sv calling & purity/ploidy estimation
#573 opened Dec 10, 2024 by ericblanc20
1
ngs_data_qc - pydantic throws error when parameters for picard are not defined
#556 opened Dec 2, 2024 by mbenary
panel of normals step always requires e.g. pure_cn config bug Something isn't working
#550 opened Nov 15, 2024 by tedil
@tedil
2
Consistently use get_args xor get_params backlog postponed and put to backlog
#543 opened Nov 4, 2024 by tedil
Revamp somatic CNV calling
#535 opened Jul 25, 2024 by ericblanc20
1
Unclear error messages when GCNV model paths don't resolve
#534 opened Jul 16, 2024 by Nicolai-vKuegelgen
1
Check and update config defaults
#528 opened Jul 5, 2024 by ericblanc20
8 tasks
1
refactor ngs_mapping
#517 opened Jun 7, 2024 by ericblanc20
@tedil @ericblanc20
Cache reference downloads / index builds, provide snakemake profile with default cache dir
#515 opened Jun 3, 2024 by tedil
@tedil
1
Make use of snakemake storage plugins
#514 opened Jun 3, 2024 by tedil
@tedil
Wrappers: Move config accesses to params
#513 opened Jun 3, 2024 by tedil
1
@tedil @ericblanc20
Add genome/reference definition section to configuration
#512 opened May 30, 2024 by tedil
@tedil @ericblanc20
Feature: Generate QC file from GeneCount.tab file of star
#509 opened May 6, 2024 by giacuong171
The mehari wrapper for new versions (>=0.25) needs to always run bcftools norm
#504 opened Apr 29, 2024 by Nicolai-vKuegelgen
2
The gcnv contig_ploidy wrapper hardcodes config paths
#500 opened Apr 15, 2024 by Nicolai-vKuegelgen
1
@tedil
2
Better error messages when config.yaml is faulty
#486 opened Jan 25, 2024 by Nicolai-vKuegelgen
2
Switch to using the Snakemake builtin slurm executor rather than relying on profiles
#475 opened Dec 2, 2023 by holtgrewe
@tedil
The melt merge_vcf step fails if all input files are empty.
#473 opened Nov 27, 2023 by Nicolai-vKuegelgen
Adding neoepitope prediction pipeline
#472 opened Nov 27, 2023 by giacuong171
1
The dataset config pedigree_field should not be empty by default
#471 opened Nov 22, 2023 by Nicolai-vKuegelgen
Create tests for gcnv_merge_vcfs tool
#467 opened Nov 15, 2023 by Nicolai-vKuegelgen
Re-activate freebayes wrapper
#466 opened Nov 14, 2023 by holtgrewe
Fix tests for sv_calling_wgs
#463 opened Nov 3, 2023 by holtgrewe
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