Skip to content

@Sage-Bionetworks-Workflows Sage-Bionetworks-Workflows

Change the repository type filter

All

    Repositories list

    55 repositories

    • eks-stack

      Public
      HCL
      •1•4•0•3•Updated Nov 19, 2024Nov 19, 2024

    • nf-genie

      Public
      Nextflow workflow for main GENIE processing
      Groovy
      •
      Apache License 2.0
      •1•3•0•0•Updated Nov 15, 2024Nov 15, 2024

    • nextflow-infra

      Public
      AWS CloudFormation templates for deploying Nextflow infrastructure
      Python
      •
      Apache License 2.0
      •22•3•0•3•Updated Nov 6, 2024Nov 6, 2024

    • nf-agora

      Public
      Nextflow workflow for agora-data-tools data processing
      Nextflow
      •0•0•0•0•Updated Nov 6, 2024Nov 6, 2024

    • orca-recipes

      Public
      Open-source airflow deployment and production DAGs for the DPE team
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

    • py-orca

      Public
      Python package for connecting services and building data pipelines
      Python
      •
      Apache License 2.0
      •1•5•0•0•Updated Oct 31, 2024Oct 31, 2024

    • nf-cwl-wrap

      Public
      Nextflow wrapper for CWL workflows. Intended to enable CWL workflows to be automated to run on Tower
      Dockerfile
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 21, 2024Aug 21, 2024

    • py-dcqc

      Public
      Python package for performing quality control (QC) for data coordination (DC)
      Python
      •
      Apache License 2.0
      •3•3•1•0•Updated Aug 12, 2024Aug 12, 2024

    • nf-synapse-challenge

      Public
      Flexible framework for submission evaluation for challenges run on Synapse
      Python
      •
      MIT License
      •3•5•0•0•Updated Jul 31, 2024Jul 31, 2024

    • py-optimize-nextflow

      Public
      Python script for optimizing resource allocations for Nextflow workflows based on past metrics
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

    • nf-synapse

      Public
      Centralized Repository for Synapse Operations in Nextflow
      Nextflow
      •
      Apache License 2.0
      •1•2•1•0•Updated Jul 25, 2024Jul 25, 2024

    • nf-dcqc

      Public
      Nextflow Workflow for Data Coordination Quality Control
      Nextflow
      •
      MIT License
      •1•1•1•0•Updated Jun 25, 2024Jun 25, 2024

    • nf-vcf2maf

      Public
      Annotate VCF files using VEP and generate MAF files using vcf2maf
      Nextflow
      •
      Apache License 2.0
      •1•0•3•0•Updated Jun 1, 2024Jun 1, 2024

    • nf-synstage

      Public archive
      Nextflow pipeline for staging files from Synapse
      Nextflow
      •
      Apache License 2.0
      •2•0•1•0•Updated Apr 19, 2024Apr 19, 2024

    • nf-synindex

      Public archive
      Nextflow pipeline for indexing S3 objects in Synapse
      Nextflow
      •
      Apache License 2.0
      •4•0•0•0•Updated 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
      •415•0•0•0•Updated Apr 2, 2024Apr 2, 2024

    • cwl-tool-synapseclient

      Public
      CWL interface to the Synapse command line.
      Common Workflow Language
      •
      Apache License 2.0
      •8•4•4•3•Updated Nov 13, 2023Nov 13, 2023

    • nf-artist

      Public
      A NextFlow pipeline to run image rendering process to generate resources for the HTAN Portal.
      Nextflow
      •4•2•0•2•Updated Oct 17, 2023Oct 17, 2023

    • nf-dynamic-challenge

      Public archive
      Data to model framework for Dynamic challenge
      Nextflow
      •
      MIT License
      •3•1•0•0•Updated Oct 11, 2023Oct 11, 2023

    • nf-model2data

      Public archive
      Nextflow model 2 data workflow
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Sep 1, 2023Sep 1, 2023

    • vcf2maf-docker

      Public
      Dockerfile
      •
      Apache License 2.0
      •3•0•0•0•Updated 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
      •217•0•0•0•Updated Jul 18, 2023Jul 18, 2023

    • iatlas-scripts

      Public
      A home for experimental scripts used for launching Nextflow Tower workflows for iAtlas
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated Jun 26, 2023Jun 26, 2023

    • ntap-add5-scripts

      Public
      Collection of scripts used to manage workflows for the NTAP Addendum 5 project
      Python
      •
      Apache License 2.0
      •0•0•0•0•Updated May 15, 2023May 15, 2023

    • configs

      Public
      Config files used to define parameters specific to compute environments at different Institutions
      Nextflow
      •
      MIT License
      •274•0•0•0•Updated 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
      •0•0•0•0•Updated Feb 15, 2023Feb 15, 2023

    • dockstore-workflow-rnaseq

      Public
      Common Workflow Language
      •
      MIT License
      •3•4•0•3•Updated 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
      •2•2•0•2•Updated Feb 7, 2023Feb 7, 2023

    • pyfilesystem2

      Public
      Python's Filesystem abstraction layer
      Python
      •
      MIT License
      •177•0•0•0•Updated Jan 28, 2023Jan 28, 2023

    • nf-dcqc-poc

      Public archive
      Proof of concept demonstrating a Nextflow workflow orchestrated by a Python script for quality control
      Python
      •0•3•0•0•Updated Jan 23, 2023Jan 23, 2023