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    83 repositories

    • gwas

      Public
      A pipeline for Genome Wide Association Studies
      Nextflow
      •
      MIT License
      •17•0•1•0•Updated May 10, 2022May 10, 2022

    • mtbseq-nf

      Public
      MTBSeq made simple and easy using Nextflow.
      Nextflow
      •1•0•0•0•Updated Apr 15, 2022Apr 15, 2022

    • rita_bahia_analysis_nf

      Public
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Apr 6, 2022Apr 6, 2022

    • nf-gwas

      Public
      A nextflow pipeline to perform genome-wide association studies using regenie.
      Nextflow
      •
      MIT License
      •21•0•0•0•Updated Mar 21, 2022Mar 21, 2022

    • h3agwas

      Public
      GWAS Pipeline for H3Africa
      Nextflow
      •
      Other
      •66•0•0•0•Updated Mar 17, 2022Mar 17, 2022

    • nf-gwas-pipeline

      Public
      A Nextflow Genome-Wide Association Study (GWAS) Pipeline
      R
      •
      GNU General Public License v3.0
      •20•0•0•0•Updated Feb 12, 2022Feb 12, 2022

    • Imputation-nf

      Public
      Imputation pipeline
      Nextflow
      •
      GNU General Public License v3.0
      •4•0•0•0•Updated Feb 5, 2022Feb 5, 2022

    • chipimputation

      Public
      Genotype Imputation Pipeline for H3Africa
      Nextflow
      •
      MIT License
      •20•0•0•0•Updated Feb 5, 2022Feb 5, 2022

    • gwas_scripts

      Public
      Codebook from my GWAS cookbook
      R
      •
      MIT License
      •111•0•0•0•Updated Feb 5, 2022Feb 5, 2022

    • imputation_accuracy_calculator

      Public
      Python
      •
      MIT License
      •6•0•0•0•Updated Dec 15, 2021Dec 15, 2021

    • NGS-analysis-from-TB-sputum

      Public
      A pipeline to remove contaminant NGS reads from TB-sputum samples
      Makefile
      •
      GNU General Public License v3.0
      •2•0•0•0•Updated Oct 25, 2021Oct 25, 2021

    • HHS

      Public
      Hungry-Hungry SNPos
      Rust
      •1•0•0•0•Updated Oct 20, 2021Oct 20, 2021

    • gentb-nf

      Public
      The Nextflow version of https://github.com/farhat-lab/gentb-snakemake
      Mozilla Public License 2.0
      •1•0•0•0•Updated Sep 7, 2021Sep 7, 2021

    • bactopia

      Public
      A flexible pipeline for complete analysis of bacterial genomes
      HTML
      •
      MIT License
      •71•1•1•0•Updated Aug 19, 2021Aug 19, 2021

    • mtb_mono_inh_nf

      Public
      Nextflow
      •2•1•0•0•Updated Aug 19, 2021Aug 19, 2021

    • pipelines-nextflow

      Public
      A set of workflows written in Nextflow for Genome Annotation.
      Nextflow
      •
      GNU General Public License v3.0
      •18•0•0•0•Updated Aug 13, 2021Aug 13, 2021

    • nextflow-spark

      Public
      Nextflow
      •3•0•0•0•Updated Aug 4, 2021Aug 4, 2021

    • Genotype_Imputation_Pipeline

      Public
      Final version of the pipeline for processing TOPMED and other dbGaP datasets, includes: automatic identification of reference genome build and selection of correct chain file, mapping to GRCh37 reference build, initial quality control, ancestry analysis, post-ancestry quality control, phasing, imputation, post-imputation quality control.
      FreeBasic
      •6•1•0•1•Updated Jul 27, 2021Jul 27, 2021

    • wgs_lineage1_phylogenetic_nf

      Public
      Nextflow
      •2•0•0•0•Updated Jul 14, 2021Jul 14, 2021

    • dandrea_legionella_nf

      Public
      Nextflow
      •
      MIT License
      •2•0•0•1•Updated Jun 24, 2021Jun 24, 2021

    • bioinfo_rio_vagrant

      Public
      A vagrant version of the amazing ITGE2017 analysis machine
      Ruby
      •
      MIT License
      •0•1•0•0•Updated Jun 16, 2021Jun 16, 2021

    • k8s_test_nf

      Public
      Nextflow
      •0•0•0•0•Updated Jun 15, 2021Jun 15, 2021

    • clockwork

      Public
      CRyPTIC data processing pipelines
      HTML
      •
      MIT License
      •22•0•0•0•Updated Jun 3, 2021Jun 3, 2021

    • bov_human_nf

      Public
      Nextflow
      •1•0•0•0•Updated May 26, 2021May 26, 2021

    • multi-projects

      Public
      Nextflow
      •2•0•0•0•Updated May 18, 2021May 18, 2021

    • tractoflow

      Public
      TractoFlow: A robust, efficient and reproducible diffusion MRI pipeline leveraging Nextflow & Singularity
      Nextflow
      •
      Other
      •22•0•0•0•Updated May 17, 2021May 17, 2021

    • wf-hap-snps

      Public
      Small variant calling for haploid samples
      Nextflow
      •
      Mozilla Public License 2.0
      •8•0•0•0•Updated May 17, 2021May 17, 2021

    • chipimputation_evaluate_chips

      Public
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated May 14, 2021May 14, 2021

    • uceasy

      Public
      UCEasy: a wrapper for the phyluce software package.
      Python
      •
      MIT License
      •4•0•0•0•Updated May 13, 2021May 13, 2021

    • fastqwiper

      Public
      A workflow to recover corrupted fastq.gz files, drop wrong lines and remove unpaired reads
      Python
      •
      MIT License
      •3•0•0•0•Updated May 13, 2021May 13, 2021