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actions-runners

Instructions and scripts for custom GitHub Actions runners

aws_igenomes

configuration for an iGenomes refgenieserver

bioconda-recipes

Conda recipes for the bioconda channel.

configs

Config files used to define parameters specific to compute environments at different Institutions

containers

Bioinformatics containers

crisprseq

[Under construction] A pipeline for all crispr analyses

draw-centromere-with-karyoploter

Drawing centromere constriction at chromosome ideograms, plotted with karyoploteR package from R

flye

De novo assembler for single molecule sequencing reads using repeat graphs

funcscan

(Meta-)genome screening for functional and natural product gene sequences

insertseq

Run INSERT-seq as an nf-core pipeline

masterprojectbioinfo

miod

data base of microindels and microduplications

mirpedrol

modules

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

multi-package-containers

Testing building mulled containers for multi-requirement tools.

nextflow

A DSL for data-driven computational pipelines

nf-co2footprint

nf-validation

Params validation plugin for Nextflow pipelines

paths-filter

Conditionally run actions based on files modified by PR, feature branch or pushed commits

personalweb

DBWsubject - personal website

plugins

Nextflow plugins index repository

protein-interactions-modeler

SBI + PYT project. program to model protein-protein interactions

recipes

recipes & asset classes definitions

refgenconf

A Python object for standardized reference genome assets.

refgenie

Reference genome resource manager

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

solraig

test-datasets

Test data to be used for automated testing with the nf-core pipelines

testpipeline

A small example pipeline used to test new nf-core infrastructure and common code.