Repositories list

• nf-core_vetted_pipelines

  Public
  Parameters, configuration, and instructions for using individual nf-core pipelines

  R

  •

  Artistic License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Dec 16, 2025Dec 16, 2025

• rnaseq_count_nf

  Public
  Nextflow

  •

  GNU General Public License v3.0

  •33 forks•00 stars•00 issues•00 pull requests•Updated Oct 22, 2025Oct 22, 2025

• nextflow_template

  Public
  Config for running non-nf-core Nextflow pipelines on Sasquatch

  Artistic License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 22, 2025Oct 22, 2025

• rare-disease-wf

  Public
  Variant calling with DeepVariant/DeepTrio, and variant filtering in families

  Nextflow

  •

  MIT License

  •00 forks•00 stars•00 issues•00 pull requests•Updated Oct 22, 2025Oct 22, 2025

• nextflow_scri_config

  Public
  An SCRI nextflow profile for NF-Core

  MIT License

  •00 forks•00 stars•11 issue•00 pull requests•Updated Oct 22, 2025Oct 22, 2025

• 2025-05_grundner_gwas_Mtub

  Public
  Association analysis in Mycobacterium tuberculosis

  R

  •

  Artistic License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 26, 2025Sep 26, 2025

• 2024-12_grundner_genotyping_Mtub

  Public
  Genotype calling in 17k Mycobacterium tuberculosis strains

  Nextflow

  •

  Artistic License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Sep 26, 2025Sep 26, 2025

• parers

  Public
  Python

  •

  GNU Affero General Public License v3.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated May 29, 2025May 29, 2025

• RFantibody

  Public
  Copy of RFantibody for use on Sasquatch

  Python

  •

  MIT License

  •155155 forks•00 stars•00 issues•00 pull requests•Updated May 27, 2025May 27, 2025

• kappe_s_2022.04_PF_LiverStage

  Public
  Transcriptome Profiling of bulk RNA-seq from Hepatocytes infected with Plasmodium falciparum.

  Shell

  •

  Artistic License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated Sep 11, 2024Sep 11, 2024

• compareRhythms

  Public
  Approaches to identify Differential Rhythmicity

  TeX

  •

  GNU General Public License v3.0

  •66 forks•00 stars•00 issues•00 pull requests•Updated Jun 18, 2024Jun 18, 2024

• mack_d_2023.04.13_iPSC_neuromuscular_scRNAseq

  Public
  Time-course analysis of scRNA-seq from iPSC motor neurons.

  R

  •

  Artistic License 2.0

  •11 fork•00 stars•00 issues•00 pull requests•Updated May 22, 2024May 22, 2024

• modules

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

  Nextflow

  •

  MIT License

  •1k1k forks•00 stars•00 issues•00 pull requests•Updated Apr 3, 2024Apr 3, 2024

• configs

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

  Nextflow

  •

  MIT License

  •354354 forks•00 stars•00 issues•00 pull requests•Updated Mar 20, 2024Mar 20, 2024

• multi-package-containers

  Public
  Testing building mulled containers for multi-requirement tools.

  236236 forks•00 stars•00 issues•00 pull requests•Updated Mar 19, 2024Mar 19, 2024

• cutandrun_nf

  Public
  Cut&Run Alignment, QC, and Peak Calling Pipeline

  Nextflow

  •

  GNU General Public License v3.0

  •11 fork•00 stars•22 issues•00 pull requests•Updated Jan 30, 2024Jan 30, 2024

• IGNITE

  Public
  repo to demo for 2023.11 IGNITE

  R

  •

  Artistic License 2.0

  •00 forks•00 stars•00 issues•00 pull requests•Updated Jan 25, 2024Jan 25, 2024

• bulk_rnaseq_fusion_nf

  Public
  Jupyter Notebook

  •

  GNU General Public License v3.0

  •22 forks•00 stars•00 issues•00 pull requests•Updated Oct 20, 2023Oct 20, 2023

• sarek_Aug2023

  Public
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

  Nextflow

  •

  MIT License

  •528528 forks•00 stars•00 issues•00 pull requests•Updated Aug 31, 2023Aug 31, 2023

• .github

  Public
  Mission Statement

  00 forks•00 stars•00 issues•00 pull requests•Updated Aug 18, 2023Aug 18, 2023