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### 🚀 Subworkflows Team 🚀
_10th-12th October 2022 - BCN_
This file: [https://hackmd.io/@nf-core/B1gKO8afj/edit](https://hackmd.io/@nf-core/B1gKO8afj/edit)
The Hackathon Oct 2022 [Project Board](https://github.com/orgs/nf-core/projects/38/views/8)
<img src="https://openmoji.org/data/color/svg/E040.svg" width=50> @nf-core / <img src="https://openmoji.org/data/color/svg/E045.svg" width=50> @nf-core
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# Subworkflows Team
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# Team Members
* 🤖 [Maxime Garcia](https://github.com/maxulysse) (sarek)
* [Matthias De Smet](https://github.com/matthdsm)
* [Francesco Lescai](https://github.com/lescai)
* [Edmund Miller](https://github.com/emiller88)
* [David Marron](https://github.com/dmarron)
* [Priyanka Surana](https://github.com/priyanka-surana)
* [Quentin Clayssen](https://github.com/qclayssen)
* [Kamil Malisz](https://github.com/KamilMaliszArdigen)
* [Solenne Correard](https://github.com/scorreard) (sarek)
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# Day One
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## [Naming conventions](https://starwarsintrocreator.kassellabs.io/#!/DNE1b9E-zP1saQwPcLqz)
[Gist](https://gist.github.com/Emiller88/414aa38d1da5714023976ffb6bec1ffe)
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## Sarek
- Converting sarek meta to generic before creating nf-core/subworkflows
- WIP: [#784](https://github.com/nf-core/sarek/pull/784) Rename all subworkflows
- Also moving all nf-core proposed modules from sarek to local
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## [Integrate pytest-workflow into template](https://github.com/nf-core/tools/issues/1900)
- [Original PR from Dec 2020](https://github.com/nf-core/rnaseq/pull/546)
- Integrated into Sarek already
- Test default always
- Check for changes on PRs to dev and run associated tests
- Workflow, Subworkflow, and Module level
- Same concept as pytest-workflow in modules
- Test every tag requested in CI on a release
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## FGBIO CreateUMIconsensus
- Francesco L.
- check all fgbio modules
- listed changes needed to update [fgbio subworkflow](https://github.com/nf-core/modules/issues/2185) and sync them with [fgbio best practices](https://github.com/fulcrumgenomics/fgbio/blob/main/docs/best-practice-consensus-pipeline.md)
- new nf-core modules needed:
- fgbio/zipperbams
- fgbio/callduplexconsensusreads
- fgbio/collectduplexseqmetrics
- PR on fgbio/zipperbams
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## BCL demultiplexing :heavy_check_mark:
- @matthdsm
- issue: https://github.com/nf-core/modules/issues/1515
- PR: https://github.com/nf-core/modules/pull/2198
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## Fastq align - WIP
- @matthdsm
- issue: https://github.com/nf-core/modules/issues/2161
- PR: https://github.com/nf-core/modules/pull/2201
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## new subworkflow bam_markduplicates_picard - WIP
- @dmarron
- issue: https://github.com/nf-core/modules/issues/2168
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## rnaseq subworkflow bedgraph_bedclip_bedgraphtobigwig migration - WIP
- @KamilMalisz
- https://github.com/nf-core/modules/issues/2194
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# Day Two
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### FGBIO CreateUMIconsensus
- Francesco L.
- identified new [test data](https://www.ncbi.nlm.nih.gov/bioproject/PRJNA451009)
- implemented UMI structure described in [paper](https://academic.oup.com/nar/article/47/15/e87/5498633)
- test data added: [PR 644](https://github.com/nf-core/test-datasets/pull/644) merged
- new module fgbio/zipperbams [PR #2240](https://github.com/nf-core/modules/pull/2240) under review
- new module fgbio/callduplexconsensusreads [PR #2243](https://github.com/nf-core/modules/pull/2243) under review
- new module fgbio/filterconsensusreads [PR #2248](https://github.com/nf-core/modules/pull/2248) submitted
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## Fastq align :heavy_check_mark:
- @matthdsm
- issue: https://github.com/nf-core/modules/issues/2161
- PR: https://github.com/nf-core/modules/pull/2201
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## rnaseq subworkflow bedgraph_bedclip_bedgraphtobigwig :heavy_check_mark:
- @KamilMalisz
- issue: https://github.com/nf-core/modules/issues/2194
- PR: https://github.com/nf-core/modules/pull/2216/
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## Rename bam_sort_samtools to bam_sort_stats_samtools to follow convention - Blocked
- @KamilMalisz
- issue: https://github.com/nf-core/modules/issues/2230
- PR: https://github.com/nf-core/modules/pull/2232/
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## New subworkflow bam_dedup_stats_samtools_umitools - waits for CI
- @KamilMalisz
- issue: https://github.com/nf-core/modules/issues/2224
- PR: https://github.com/nf-core/modules/pull/2247/
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## New subworkflow fastq_fastqc_trimgalore - WIP
- @KamilMalisz
- issue: https://github.com/nf-core/modules/issues/2253
- PR: -
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## new subworkflow bam_markduplicates_picard - WIP
- @dmarron
- issue: https://github.com/nf-core/modules/issues/2168
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## update picard markduplicates module to handle cram input
- @dmarron
- issue: https://github.com/nf-core/modules/issues/2245
- PR: https://github.com/nf-core/modules/pull/2256
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## update bowtie2_align to fastq_align_bowtie2 subworkflow and tests - WIP
- @qclayssen
- issue: https://github.com/nf-core/modules/issues/2195
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## [Migrate CI tests to Pytest workflow](https://github.com/nf-core/rnaseq/pull/883)
- @emiller
- [X] Only test the changes
- [X] Run all the tests on Release
- [X] Only run on PRs
- [X] md5sum on default test profile
- [X] Testing of local subworkflows
- [ ] Latest CI run
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# Day Three
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### FGBIO CreateUMIconsensus
- Francesco L.
- new module fgbio/zipperbams [PR #2240](https://github.com/nf-core/modules/pull/2240) merged :beers:
- implemented some comments from reviews [PR #2243](https://github.com/nf-core/modules/pull/2243) and [PR #2248](https://github.com/nf-core/modules/pull/2248)
- PRs stuck on a more general conversation :see_no_evil:
- updated sub-workflow to be drafted once new modules are merged :eyes:
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## Finish update bowtie2_align to fastq_align_bowtie2 subworkflow and tests
- @qclayssen @emiller
- Merged : https://github.com/nf-core/modules/pull/2265
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## update picard markduplicates module to handle cram input :heavy_check_mark:
- @dmarron
- issue: https://github.com/nf-core/modules/issues/2245
## new subworkflow bam_markduplicates_picard :heavy_check_mark:
- @dmarron
- issue: https://github.com/nf-core/modules/issues/2168
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## Rename bam_sort_samtools to bam_sort_stats_samtools to follow convention :heavy_check_mark:
- @KamilMalisz
- issue: https://github.com/nf-core/modules/issues/2230
## New subworkflow bam_dedup_stats_samtools_umitools :heavy_check_mark:
- @KamilMalisz
- issue: https://github.com/nf-core/modules/issues/2224
## New subworkflow fastq_fastqc_trimgalore :heavy_check_mark:
- @KamilMalisz
- issue: https://github.com/nf-core/modules/issues/2253
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## New subworkflow bam_rseqc :heavy_check_mark:
- @HarshilPatel
- issue: https://github.com/nf-core/modules/pull/2281
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## [Add a "New subworkflow" issue template](https://github.com/nf-core/modules/pull/2275)
- @emiller
- Submit your subworkflow requests!
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## [nf-core/rnaseq Migrate CI tests to Pytest workflow](https://github.com/nf-core/rnaseq/pull/883)
- @emiller
- Works!
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## SHINY NEW COMMANDS!!
- @Julia @mashehu
- `nf-core subworkflows create` :heavy_check_mark:
- `nf-core subworkflows create-test-yml` :heavy_check_mark:
- `nf-core subworkflows install` :heavy_check_mark:
- `nf-core subworkflows list` :heavy_check_mark:
- `nf-core subworkflows info` :heavy_check_mark:
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## Install subworkflows into nf-core/rnaseq :hourglass_flowing_sand:
- @emiller
- `nf-core subworkflows install` FTW!!!! :tada:
- https://github.com/nf-core/rnaseq/pull/886
---
---
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