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🚀 Subworkflows Team 🚀

27th-29th March 2023

The Hackathon March 2023 Project Board
The Group Discussion Channel #hackathon-march-2023-subworkflows

@nf-core / @nf-core


Subworkflows Team


Team Leads

  • General advice, pointers, co-ordination etc.
    • Maxime Garcia (@maxulysse)
    • Matthias De Smet (@matthdsm)
    • Harshil Patel (@drpatelh)
    • Edmund Miller (@emiller)

But always ask first in: #hackathon-march-2023-subworkflows!


Tasks Ideas

  • General development work
    • New Subworkflows
    • Fix Subworkflows tests
    • Improve Subworkflows

Remember

  • Add yourself to Team Members slide
  • Assign yourself on issues on the project board
  • Post your progress here daily!
  • Sign up for a reviewing buddy (see slide)!

Team Members


Reviewing Buddy

Person A Person B
Maxime Rike
Matthias Rike

Day One

  • #2994 - Update all gatk subworkflows
    • PR: #3125 - gatk tumor only (JP)
  • #2982 - Remove parameter dependencies in subworkflows
  • #3102 - UMI subworkflow update
    • PR #3104 (Francesco @lescai)
  • NGScheckmate subworkflow
  • #3002 - Creating the freyja subworkflow #ready4Review (@Joon-Klaps)
  • #371 - adding viralrecon subworkflows to nf-core
    • PR: #3130 - Bam_trim_primers_ivar (@Joon-Klaps)
    • PR: 3146 - Fastq_trim_fastp_fastqc (@Joon-Klaps)

Day Two

  • #2978 - Update index handling in bam subworkflows (NV)
  • #3102 UMI subworkflow update
    • PR #3104 merged (Francesco @lescai)
    • feature: fgbio best practices implemented
    • feature: now handles duplex UMIs

Day Three

  • #3191 - CI to facilitate piecemeal migration to nf-test(@emiller)
  • #217 - Cellranger-arc subworkflow for scrnaseq (@heylf)
  • #175 - Cellranger-atac subworkflow for scrnaseq (@heylf)
  • #2978 - Update index handling in bam subworkflows - fix (NV)
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