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### 🚀 Subworkflows Team 🚀
_27th-29th March 2023_
The Hackathon March 2023 [Project Board](https://github.com/orgs/nf-core/projects/38)
The Group Discussion Channel `#hackathon-march-2023-subworkflows`
[<img src="https://openmoji.org/data/color/svg/E040.svg" width=50>](https://twitter.com/nf_core) @nf-core / [<img src="https://openmoji.org/data/color/svg/E045.svg" width=50>](https://github.com/nf-core) @nf-core
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# Subworkflows Team
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# 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`!_
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# Tasks Ideas
- General development work
- New Subworkflows
- Fix Subworkflows tests
- Improve Subworkflows
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# Remember
- Add yourself to Team Members slide
- Assign yourself on issues on the [project board](https://github.com/orgs/nf-core/projects/38)
- Post your progress here **daily**!
- Sign up for a reviewing buddy (see slide)!
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# Team Members
- [Maxime Garcia](@maxulysse)
- [Jelena Pejovic Simeunovic](@JPejovicApis)
- [Nevena Vucinic](@nevenavucinic)
- [Francesco Lescai](@lescai)
- [Simon Pearce](@SPPearce)
- [Joon Klaps](@Joon-Klaps)
- [Florian Heyl](@heylf)
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# Reviewing Buddy
| Person A | Person B |
|-------------|----------|
| Maxime | Rike |
| Matthias | Rike |
---
# Day One
<small>
- [#2994](https://github.com/nf-core/modules/issues/2994) - Update all gatk subworkflows
- PR: [#3125](https://github.com/nf-core/modules/issues/3125) - gatk tumor only (JP)
- [#2982](https://github.com/nf-core/modules/issues/2982) - Remove parameter dependencies in subworkflows
- PR: [#3137](https://github.com/nf-core/modules/pull/3137)
- [#3102](https://github.com/nf-core/modules/issues/3102) - UMI subworkflow update
- PR [#3104](https://github.com/nf-core/modules/pull/3104) (Francesco @lescai)
- NGScheckmate subworkflow
- PR: [#3094](https://github.com/nf-core/modules/pull/3094) (@SPPearce)
- [#3002](https://github.com/nf-core/modules/issues/3002) - Creating the freyja subworkflow #ready4Review (@Joon-Klaps)
- PR: [#3003](https://github.com/nf-core/modules/pull/3003)
- [#371](https://github.com/nf-core/viralrecon/issues/371) - adding viralrecon subworkflows to nf-core
- PR: [#3130](https://github.com/nf-core/modules/pull/3130) - Bam_trim_primers_ivar (@Joon-Klaps)
- PR: [3146](https://github.com/nf-core/modules/pull/3146) - Fastq_trim_fastp_fastqc (@Joon-Klaps)
---
# Day Two
- [#2978](https://github.com/nf-core/modules/issues/2978) - Update index handling in bam subworkflows (NV)
- [#3102](https://github.com/nf-core/modules/issues/3102) UMI subworkflow update
- PR [#3104](https://github.com/nf-core/modules/pull/3104) **merged** (Francesco @lescai)
- feature: *fgbio* best practices implemented
- feature: now handles duplex UMIs
---
# Day Three
- [#3191](https://github.com/nf-core/modules/pull/3191) - CI to facilitate piecemeal migration to nf-test(@emiller)
- [#217](https://github.com/nf-core/scrnaseq/pull/217) - Cellranger-arc subworkflow for scrnaseq (@heylf)
- [#175](https://github.com/nf-core/scrnaseq/pull/175) - Cellranger-atac subworkflow for scrnaseq (@heylf)
- [#2978](https://github.com/nf-core/modules/issues/2978) - Update index handling in bam subworkflows - fix (NV)
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