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    20 repositories

    • nf-core_vetted_pipelines

      Public
      Parameters, configuration, and instructions for using individual nf-core pipelines
      R
      •
      Artistic License 2.0
      •0•0•0•0•Updated Dec 16, 2025Dec 16, 2025

    • rnaseq_count_nf

      Public
      Nextflow
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • nextflow_template

      Public
      Config for running non-nf-core Nextflow pipelines on Sasquatch
      Artistic License 2.0
      •0•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • rare-disease-wf

      Public
      Variant calling with DeepVariant/DeepTrio, and variant filtering in families
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Oct 22, 2025Oct 22, 2025

    • nextflow_scri_config

      Public
      An SCRI nextflow profile for NF-Core
      MIT License
      •0•0•1•0•Updated Oct 22, 2025Oct 22, 2025

    • 2025-05_grundner_gwas_Mtub

      Public
      Association analysis in Mycobacterium tuberculosis
      R
      •
      Artistic License 2.0
      •0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • 2024-12_grundner_genotyping_Mtub

      Public
      Genotype calling in 17k Mycobacterium tuberculosis strains
      Nextflow
      •
      Artistic License 2.0
      •0•0•0•0•Updated Sep 26, 2025Sep 26, 2025

    • parers

      Public
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated May 29, 2025May 29, 2025

    • RFantibody

      Public
      Copy of RFantibody for use on Sasquatch
      Python
      •
      MIT License
      •130•0•0•0•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
      •1•0•0•0•Updated Sep 11, 2024Sep 11, 2024

    • compareRhythms

      Public
      Approaches to identify Differential Rhythmicity
      TeX
      •
      GNU General Public License v3.0
      •6•0•0•0•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
      •1•0•0•0•Updated May 22, 2024May 22, 2024

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •952•0•0•0•Updated Apr 3, 2024Apr 3, 2024

    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •339•0•0•0•Updated Mar 20, 2024Mar 20, 2024

    • multi-package-containers

      Public
      Testing building mulled containers for multi-requirement tools.
      232•0•0•0•Updated Mar 19, 2024Mar 19, 2024

    • cutandrun_nf

      Public
      Cut&Run Alignment, QC, and Peak Calling Pipeline
      Nextflow
      •
      GNU General Public License v3.0
      •1•0•2•0•Updated Jan 30, 2024Jan 30, 2024

    • IGNITE

      Public
      repo to demo for 2023.11 IGNITE
      R
      •
      Artistic License 2.0
      •0•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • bulk_rnaseq_fusion_nf

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •2•0•0•0•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
      •500•0•0•0•Updated Aug 31, 2023Aug 31, 2023

    • .github

      Public
      Mission Statement
      0•0•0•0•Updated Aug 18, 2023Aug 18, 2023