How to run sarek on AWS with cloudFormation

Modified version of the nextflow "hello" pipeline, that outputs a hello.txt file. For testing the seqera platform.

Scripts to convert mixed genome BMA files to bigwigs, for Richard's CLAPanalysis project

hello world that waits 10 mins

Runs GSEA on a list of ranked genes

Instructions to set up nextflow in AWS

Test datasets

Generate frequency of barcodes on amplicon sequencing data

Nextflow pipeline that runs DESeq2 on data processed with the nextflow RNAseq pipeline

nextflow pipeline for basic variant calling in RNAseq data

Nextflow pipeline to merge FastQ files from different lanes

Nextflow pipeline that runs the commands given in the inputfile

Nextflow pipeline for WGS alignment

Singularity recipes

Stand-alone version of cytofpipe