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    31 repositories

    • gms-artic

      Public
      A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).
      Nextflow
      •
      GNU Affero General Public License v3.0
      •89•0•0•0•Updated Sep 20, 2024Sep 20, 2024

    • JASEN

      Public
      Epitypification pipeline for clinical NGS data. Written in NextFlow, Python & Bash.
      nextflowmlstantibiotic-resistancecgmlstpubmlst
      Nextflow
      •
      GNU General Public License v3.0
      •11•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • pgx

      Public
      Pharmacogenomics pipeline
      HTML
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Mar 7, 2024Mar 7, 2024

    • Twist_Solid

      Public
      Pipeline for Solid tumours
      Python
      •6•0•0•0•Updated Feb 15, 2023Feb 15, 2023

    • STARlight

      Public
      RNA-seq STAR Pipeline
      Python
      •1•0•0•0•Updated Jan 20, 2023Jan 20, 2023

    • pgx_module

      Public
      Anlysis of pharmacogenomic targets from Genomic Medicine Swedens heamatology panel.
      Python
      •
      MIT License
      •4•0•0•0•Updated Dec 12, 2022Dec 12, 2022

    • raredisease

      Public
      Call and score variants from WGS/WES of rare disease patients.
      Nextflow
      •
      MIT License
      •34•0•0•0•Updated Dec 6, 2022Dec 6, 2022

    • gmsmetapost

      Public
      GMS Metagenomics post-classification
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Sep 26, 2022Sep 26, 2022

    • KITM_fastq_preprocessing

      Public
      QC and trimming of fastq reads
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 26, 2022Sep 26, 2022

    • snakemake-wrappers

      Public
      This is the development home of the Snakemake wrapper repository, see
      CAP CDS
      •186•0•0•0•Updated Sep 23, 2022Sep 23, 2022

    • taxprofiler

      Public
      Highly parallelised multi-taxonomic profiling of shotgun metagenomic data
      Nextflow
      •
      MIT License
      •34•0•0•0•Updated Sep 16, 2022Sep 16, 2022

    • hydra-genetics_qc

      Public
      Collection of rules performing QC and generating reports.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 16, 2022May 16, 2022

    • qiaseq_qc

      Public
      Pipeline based on hydra modules for in-house validation of qiagen's qiaseq bioinformatics pipeline
      Python
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated May 11, 2022May 11, 2022

    • hydra-genetics_snv_indels

      Public
      Collection of rules used to call snv and small indels.
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated May 11, 2022May 11, 2022

    • hydra-genetics_prealignment

      Public
      Snakemake module containing processing steps that should be performed before sequence alignment.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated May 9, 2022May 9, 2022

    • hydra-genetics_alignment

      Public
      Snakemake module containing processing steps that should be performed during sequence alignment.
      Python
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated May 5, 2022May 5, 2022

    • modules

      Public
      Repository to host tool-specific module files for the Nextflow DSL2 community!
      Nextflow
      •
      MIT License
      •713•0•0•0•Updated May 5, 2022May 5, 2022

    • test-datasets

      Public
      Test data to be used for automated testing with the nf-core pipelines
      MIT License
      •351•0•0•0•Updated Apr 19, 2022Apr 19, 2022

    • Twist_RNA

      Public
      Python
      •3•0•0•0•Updated Apr 19, 2022Apr 19, 2022

    • Twist_DNA

      Public
      Python
      •
      GNU General Public License v3.0
      •5•0•0•0•Updated Mar 30, 2022Mar 30, 2022

    • cnv_sv

      Public
      Collection of rules used to call structural variants
      Python
      •
      GNU General Public License v3.0
      •3•0•0•0•Updated Feb 2, 2022Feb 2, 2022

    • bioconda-recipes

      Public
      Conda recipes for the bioconda channel.
      Shell
      •3.3k•0•0•0•Updated Jan 31, 2022Jan 31, 2022

    • parabricks

      Public
      Snakemake module containing different analyses provided by parabricks.
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 27, 2022Jan 27, 2022

    • TNscope

      Public
      Sentieon TNscope basic pipeline
      Python
      •
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 17, 2022Jan 17, 2022

    • LiSC

      Public
      scRNA-seq
      R
      •
      MIT License
      •1•0•0•0•Updated Sep 21, 2021Sep 21, 2021

    • snake_rnaseq

      Public
      STAR pipeline
      Python
      •
      MIT License
      •1•0•0•0•Updated Sep 2, 2021Sep 2, 2021

    • var-genes-ro

      Public
      Virulence and Antibiotic Resistance Genes used with JASEN pipeline at the university hospital of Linköping, Sweden.
      binderjupyter-notebookantibiotic-resistanceclinical-decision-supportbioinformatics
      Jupyter Notebook
      •
      Creative Commons Zero v1.0 Universal
      •0•1•0•0•Updated Aug 31, 2021Aug 31, 2021

    • nextflow_rnaseqfus

      Public
      Perl
      •0•0•0•0•Updated Jun 1, 2021Jun 1, 2021

    • nextstrain-auspice

      Public
      JavaScript
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Jun 1, 2021Jun 1, 2021

    • nf-core-sarek

      Public
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Jun 1, 2021Jun 1, 2021