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    • AWS CloudFormation templates for deploying Nextflow infrastructure
      Python
      Apache License 2.0
      23303Updated Dec 23, 2024Dec 23, 2024
    • Nextflow wrapper for CWL workflows. Intended to enable CWL workflows to be automated to run on Tower
      Nextflow
      Apache License 2.0
      0000Updated Dec 20, 2024Dec 20, 2024
    • This is a repository for storing configurations for custom AWS Bedrock/Synapse chat agent configurations
      Apache License 2.0
      0000Updated Dec 19, 2024Dec 19, 2024
    • eks-stack

      Public
      Kubernetes stack deployed to AWS EKS managed by OpenTofu & Spacelift
      HCL
      1400Updated Dec 19, 2024Dec 19, 2024
    • nf-genie

      Public
      Nextflow workflow for main GENIE processing
      Groovy
      Apache License 2.0
      1300Updated Dec 13, 2024Dec 13, 2024
    • Centralized Repository for Synapse Operations in Nextflow
      Nextflow
      Apache License 2.0
      1210Updated Dec 6, 2024Dec 6, 2024
    • nf-agora

      Public
      Nextflow workflow for agora-data-tools data processing
      Nextflow
      0000Updated Nov 6, 2024Nov 6, 2024
    • Open-source airflow deployment and production DAGs for the DPE team
      Python
      Apache License 2.0
      0000Updated Oct 31, 2024Oct 31, 2024
    • py-orca

      Public
      Python package for connecting services and building data pipelines
      Python
      Apache License 2.0
      1500Updated Oct 31, 2024Oct 31, 2024
    • py-dcqc

      Public
      Python package for performing quality control (QC) for data coordination (DC)
      Python
      Apache License 2.0
      3310Updated Aug 12, 2024Aug 12, 2024
    • Flexible framework for submission evaluation for challenges run on Synapse
      Python
      MIT License
      3500Updated Jul 31, 2024Jul 31, 2024
    • Python script for optimizing resource allocations for Nextflow workflows based on past metrics
      Python
      Apache License 2.0
      0000Updated Jul 29, 2024Jul 29, 2024
    • nf-dcqc

      Public
      Nextflow Workflow for Data Coordination Quality Control
      Nextflow
      MIT License
      1110Updated Jun 25, 2024Jun 25, 2024
    • Annotate VCF files using VEP and generate MAF files using vcf2maf
      Nextflow
      Apache License 2.0
      1030Updated Jun 1, 2024Jun 1, 2024
    • nf-synstage

      Public archive
      Nextflow pipeline for staging files from Synapse
      Nextflow
      Apache License 2.0
      2010Updated Apr 19, 2024Apr 19, 2024
    • nf-synindex

      Public archive
      Nextflow pipeline for indexing S3 objects in Synapse
      Nextflow
      Apache License 2.0
      4000Updated Apr 19, 2024Apr 19, 2024
    • sarek

      Public
      Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
      Nextflow
      MIT License
      417000Updated Apr 2, 2024Apr 2, 2024
    • CWL interface to the Synapse command line.
      Common Workflow Language
      Apache License 2.0
      8443Updated Nov 13, 2023Nov 13, 2023
    • nf-artist

      Public
      A NextFlow pipeline to run image rendering process to generate resources for the HTAN Portal.
      Nextflow
      4202Updated Oct 17, 2023Oct 17, 2023
    • nf-dynamic-challenge

      Public archive
      Data to model framework for Dynamic challenge
      Nextflow
      MIT License
      3100Updated Oct 11, 2023Oct 11, 2023
    • nf-model2data

      Public archive
      Nextflow model 2 data workflow
      Nextflow
      MIT License
      1000Updated Sep 1, 2023Sep 1, 2023
    • Dockerfile
      Apache License 2.0
      3000Updated Jul 18, 2023Jul 18, 2023
    • vcf2maf

      Public
      Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms
      Perl
      Other
      218000Updated Jul 18, 2023Jul 18, 2023
    • A home for experimental scripts used for launching Nextflow Tower workflows for iAtlas
      Python
      Apache License 2.0
      0000Updated Jun 26, 2023Jun 26, 2023
    • Collection of scripts used to manage workflows for the NTAP Addendum 5 project
      Python
      Apache License 2.0
      0000Updated May 15, 2023May 15, 2023
    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      MIT License
      277000Updated Mar 1, 2023Mar 1, 2023
    • orca-recipes-astro

      Public archive
      This will serve as the airflow prototype for the dpe team
      Python
      Apache License 2.0
      0000Updated Feb 15, 2023Feb 15, 2023
    • Common Workflow Language
      MIT License
      3403Updated Feb 15, 2023Feb 15, 2023
    • sagetasks

      Public archive
      Python library for building ETL pipelines involving Synapse and data processing workflows
      Python
      Apache License 2.0
      2202Updated Feb 7, 2023Feb 7, 2023
    • Python's Filesystem abstraction layer
      Python
      MIT License
      177000Updated Jan 28, 2023Jan 28, 2023