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aggregate_vcf

Script to aggregate vcfs from different callers

annotsv_container

Container for AnnotSV software.

bonsai

Visualize and analyze resistance and outbreak of bacterial pathogen

bonsai-prp

Pipeline output Processing Program for Bonsai

cadd-container

Singularity container recipe for CADD v1.5

chanjo-report

chanjo-report fork

cll_genie

cmd_vcf

python implementation of cmd vcf module

compare-vcf

Compare and visualize VCF files and rank scores

coyote_cli

command line interface for coyote

cronjobs_lennart

Cronjobs run by worker@lennart

ffpe-nextflow

NextFlow pipeline: fastq -> SNV CNV -> loqusdb

fluentcontrol_scripts

Scripts used in Fluent Control methods on the TECAN Fluent 480 robot.

fluffy

FetaL AneUploidy and FetalFraction analYsis Pipeline

gens

grapejuice

GrapeTree is a fully interactive, tree visualization program, which supports facile manipulations of both tree layout and metadata. Click the first link to launch: https://achtman-lab.github.io/GrapeTree/MSTree_holder.html

jasen

Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.

kvartalsrapport_clarity

Ett enkelt skript för att generera en rapport över externa prover analyserade vid CMD under en definierad tidsperiod

modify_vcf_scout

Script to modify vcfs for genmod rank models

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

nexomeflow

NextFlow pipeline for Exome samples

nextflow-modules

Shared nextflow modules and assets

nextflow_microwgs

nextflow_myeloid

Nextflow pipeline for analysis of the twist myeloid panel

nextflow_oxfordnanopore_sv

Nextflow pipeline for detection of structural variants from Oxford Nanopore data

nextflow_rnaseqfus

Fusion genes identification pipeline

nextflow_st_rnaseqfus

A rnaseq fussion detection assay at CMD

nextflow_test

Proof-on-concept pipeline using Nextflow + Singularity + SLURM

nextflow_tumwgs

nextflow_twist-brca

Nextflow pipeline for TWIST-BRCA