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Last edited by Alex Kanitz

ZARP wiki

Meeting notes

Scope statement

What similar workflows are out there?

Design discussions

Discussion points

  • What is the user story?
  • What are the defined use cases?
  • What sets ZARP apart from other similar efforts?

Road map

  • Test current version with real-world data
  • In the meantime: Plan future development
    • Plan upstream API
      • Interface with SRA
      • Derive library params from data
      • Plan user interaction (CLI, UI, website)
      • Prepare for integration into web service?
    • Discuss code organization, especially with respect to extending functionality
      • Tools for individual samples
      • Tools for multiple samples
      • Tools for comparing groups of samples
    • Discuss reuse and storage of results
      • Minimize storage
      • Minimize reruns
      • How to determine whether samples have been run (database, folder structure, hashes)
      • How to pass data between consecutive stages/pipelines (compare code organization)
    • Plan downstream API
      • How to extend MultiQC report?
      • Snakemake report?
      • Directory and file naming structure
      • Prepare for integration into web service?
    • Overall code organization
      • How to coordinate different pipelines
      • How to deal with interactive parts in between

Other RNA-Seq analysis pipelines

Pipeline comparison in table https://docs.google.com/spreadsheets/d/1P4eefWLBTbCLYizajXTrG6lC016ASDMEuW06makzZvo/edit?usp=sharing

Published

date name - link
2017 aRNApipe - https://academic.oup.com/bioinformatics/article/33/11/1727/2929343
2017 RNACocktail - https://www.nature.com/articles/s41467-017-00050-4
2018 VIPER - https://link.springer.com/article/10.1186/s12859-018-2139-9
2018 hppRNA - https://academic.oup.com/bib/article-abstract/19/4/622/2918128 
2019 ARMOR - https://www.g3journal.org/content/9/7/2089
2019 UTAP - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2728-2
2019 BISR - https://link.springer.com/article/10.1186/s12859-019-3251-1
2019 GEO2RNAseq - https://www.biorxiv.org/content/10.1101/771063v1
2019 Shiny-Seq - https://bmcresnotes.biomedcentral.com/articles/10.1186/s13104-019-4471-1
https://github.com/nf-core/rnaseq
NGS-pipe - https://github.com/cbg-ethz/NGS-pipe/wiki

Metrics for comparing pipelines for RNA-seq analysis

  • Input
    • size of the input that needs to be provided
    • type: Accessions - repositories / Fastq files
    • automated inferences: type of sample preparation, adaptors
    • custom genomes and annotations possible?
  • Output
    • sample quality metrics
      • complexity
      • mapping rate
      • duplication level
      • saturation level
      • RNA integrity
    • bam files
    • quantification
      • gene level
      • isoform level
      • annotation categories
      • proportion structural RNAs
      • includes multi-mappers
    • inference
      • novel isoforms: splicing/polyadenylation
      • SNPs/mutations
  • Workflow engine
    • Modern (CWL, WDL, Snakemake, Galaxy, Nextflow)
    • Legacy (anything else that's not homegrown)
    • Custom
  • User interface
    • Browser app
    • Desktop app
    • Mobile app
    • Command line interface (programmable)
    • HTTP/"REST" API available (programmable)
  • Supported platforms
    • Cloud (AWS, GCP, Azure, ...)
    • Kubernetes / OpenShift
    • HPC (Slurm, SGE/OGE/UGA, ...)
    • Desktop/laptop
  • Installation
    • Type
      • VM
      • Containerized
      • Virtual env cross-language (conda)
      • Virtual env single language (e.g., virtualenv)
      • Package manager without virtualization (e.g., pip, Bioconductor)
      • Manual install
    • Instructions & auxiliary scripts available for supported platforms
  • Openness
    • License
    • Open source development encouraged?
    • Contribution instructions available?
    • Contact options
      • Issue tracker
      • Q/A forum (e.g., Biostars)
      • Chat (e.g., Slack or Gitter channel)
      • Email
  • Maintenance
    • Actively developed?
      • number of contributors
      • last update
      • frequency of commits
    • Tests available
    • Test code coverage published?
  • Usability
    • Clean, well-documented, programmable, easy-to-use, intuitive API for input and outputs?
    • Workflow can be started quickly for one sample (incl. preparation of configs)
    • Workflow can be started quickly for multiple samples (incl. preparation of configs)
    • Supports local data
    • Supports uploading data
    • Supports cloud data (e.g., Amazon S3)
    • Interfacing with SRA and/or other relevant data repos
    • Interfacing with Ensembl and/or other genome resource repos
    • Tooling available to filter genome resources or compile custom ones?

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