Christopher Hakkaart's repositories
analysis-scripts
Analysis scripts
dualrnaseq
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
website
Nextflow public web site
demo
An nf-core demo pipeline
hello-actions
Hello actions!
hello-nextflow
Training materials for a Nextflow beginners workshop 2024
modules
Repository to host tool-specific module files for the Nextflow DSL2 community!
myfirstpipeline
My first pipeline GA
mypipeline
My first pipeline
mypipeline2
My second pipeline
mypipeline3
This doesn't matter today
nanogenvar
Pipeline for variant calling nanopore data.
nextflow
A DSL for data-driven computational pipelines
Nextflow-Developer-Workshop
Best practices for developing your pipelines with Nextflow and nf-core
nf-core-demo
Demo nf workflow for unlocking nf-core workshop
nf-workshops
Map of Nextflow and nf-core workshops
patterns
A curated collection of Nextflow implementation patterns
poc
Proof of concept pipeline
poc-training
3 hour Nextflow training
pocrnaseq
Proof of concept rnaseq pipeline
rewarewaannotation
Nextflow pipeline for the annotation of the rewarewa (Knightia excelsa) genome.
rnafusion
RNA-seq analysis pipeline for detection gene-fusions
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
sarek
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
templateswebinar
Templates webinar
test-data
Files for dev testing
training
Nextflow training material
vanilla
Vanilla Gitpod dev env