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bioconda-recipes

Conda recipes for the bioconda channel.

cnv_sv

Collection of rules used to call structural variants

dnaseq

Sentieon DNAseq basic pipeline

gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).

gmsmetapost

GMS Metagenomics post-classification

hydra-genetics_alignment

Snakemake module containing processing steps that should be performed during sequence alignment.

hydra-genetics_prealignment

Snakemake module containing processing steps that should be performed before sequence alignment.

hydra-genetics_qc

Collection of rules performing QC and generating reports.

hydra-genetics_snv_indels

Collection of rules used to call snv and small indels.

jasen

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

kitm_fastq_preprocessing

QC and trimming of fastq reads

lisc

scRNA-seq

modules

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

nextflow_rnaseqfus

nextstrain-auspice

nf-core-sarek

parabricks

Snakemake module containing different analyses provided by parabricks.

pgx

Pharmacogenomics pipeline

pgx_module

Anlysis of pharmacogenomic targets from Genomic Medicine Swedens heamatology panel.

qiaseq_qc

Pipeline based on hydra modules for in-house validation of qiagen's qiaseq bioinformatics pipeline

raredisease

Call and score variants from WGS/WES of rare disease patients.

snake_rnaseq

STAR pipeline

snakemake-wrappers

This is the development home of the Snakemake wrapper repository, see

starlight

RNA-seq STAR Pipeline

taxprofiler

Highly parallelised multi-taxonomic profiling of shotgun metagenomic data

test-datasets

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

tnscope

Sentieon TNscope basic pipeline

twist_dna

twist_rna

twist_solid

Pipeline for Solid tumours