mjakobs's repositories
EXCAVATOR2_free
A modified version of the EXCAVATOR2 copy number caller that can be run from any directory.
fastqsplit_singularity
A singularity container for `fastqsplit`: https://github.com/supernifty/fastqsplit
HCMM_CNVs
HCMMCNVs is a browser-based software for detecting copy number variants (CNVs) using whole exome sequencing (WES) technology.
HCMM_CNVs_wrapper
This is a fork of lunching/HCMM_CNVs. This code has been edited to include wrapper functions so it can be run as a command line tool rather than a shiny app.
MutationTimeR_ppcg
An fork of the R package to time somatic mutations customised for ppcg consensus files
nf-core_modules
This is a fork of the nf-core/modules repository, which hosts tool-specific module files for the Nextflow DSL2 community!
sarek_custom_CN_ghm
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
singularity-deploy
Build and deploy Singularity containers to GitHub releases, and pull with the singularity-hpc client
skills-hello-github-actions
My clone repository
skills-test-with-actions
My clone repository
variant_calling
Group pipeline for variant calling