---
title: Modules Team - nf-core Hackathon March 2023
tags: march-2023,nf-core,hackathon,progress
description: View the slide with "Slide Mode".
---

<!-- .slide: data-background="https://raw.githubusercontent.com/maxulysse/maxulysse.github.io/main/assets/img/svg/green_white_bg.svg" -->

<a href="https://www.nf-co.re"><img src="https://i.imgur.com/hEDjpCs.png" width="65%"><img></a>

### 🚀 Modules 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-modules`

<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

---

# Modules Team

---

# Team Leads

- General advice, pointers, co-ordination etc.
- Maxime Garcia (@maxulysse)
- Matthias De Smet (@matthdsm)
- Harshil Patel (@drpatelh)
- Jonathan Manning (@pinin4fjords)
- Nicolas Vannieuwkerke (@nvnieuwk)

---

- Highly-multiplexed imaging subgroup
- Adam Taylor (@adamjtaylor)
- Florian Wuennemann (@FloWuenne)

_But always ask first in: `#hackathon-march-2023-modules`!_

---

# Tasks Ideas

- General development work
- New modules
- Fix modules tests
- Improve modules

---

- Highly-multiplexed imaging / Spatial Omics
- Add new modules geared at this type of data analsysis, starting with porting core modules of [MCMICRO](https://mcmicro.org/)
- Please label issues `imaging` in Github
- [Imaging specific project board view](https://github.com/orgs/nf-core/projects/38/views/7?filterQuery=repo%3A%22nf-core%2Fmodules%22+label%3A%22new+module%22++label%3Aimaging)

---

# 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)!

---

# Team Members

<div class="multi-column">
<div>

- [Maxime Garcia](@maxulysse)
- [Verena Kutschera](@verku)
- [Adrien Coulier](@Aratz)
- [Bojan Balic](@boleodole)
- [Darko Cucin](@darko-cucin)
- [Remi-Andre Olsen](@remiolsen)
- [Sandro Carollo](@sandrocarollo)

</div>
<div>

- [Georgios Fotakis](@abyssum)
- [Valentin Marteau](@vjmarteau)
- [Marie Lataretu](@MarieLataretu)
- [Fynn Freyer](@FynnFreyer)
- [Toni Hermoso Pulido](@toniher)
- [Paul Wolk](@paulwolk)
- [Roger Olivella](@rolivellla)
- [Maulik Upadhyay](@BioInf2305)

</div>
</div>

---

<div class="multi-column">
<div>

- [Lili Andersson-Li](@Lili)
- [Joan Gaztelu](@LlaneroHiboreo)
- [Narci](@kubranarci)
- [Aleksandra Vitkovac](@alexiandra97)
- [Anabella Trigila](@atrigila)
- [Mariangela Santorsola](@msantorsola)
- [Florian Heyl](@heylf)

</div>
<div>

- [Milena Amidzic](@milenaamidzic)
- [Gordon Draskic](@gordondraskic)
- [Vojislav Lukic](@VojislavLukic)
- [Alfred Kedhammar](@kedhammar)
- [Louisa Perelo](@louperelo)
- [Ferriol Calvet](@ferriolcalvet)
- [Federica Brando](@FedericaBrando)

</div>
</div>

---

## Highly-multiplexed imaging subgroup

<div class="multi-column">
<div>

- [Florian Wuennemann](@FloWuenne)
- [Adam Taylor](@adamjtaylor)
- [Margot Chazotte](@MargotCh)
- [Jose Nimo](@josenimo)
- [Chiara Schiller](@chiarasch)
- [Kresimir Bestak](@kbestak)

</div>
<div>

- [Aroj Hada](@ArozHada)
- [Miguel A. Ibarra-Arellano](@migueLib)
- [Victor Perez](@VictorDidier)
- [Wouter-Michiel Vierdag](@melonora)
- [Luis Kuhn Cuellar](@luiskuhn)
- [Carolin Schwitalla ](@CaroAMN)
- [Dominik Molitor](@DojakM)
- [Jelena Pejovic Simeunovic](@JPejovicApis)
- [Svetozar Nesic](@snesic)
- [Emilio Palumbo](@emi80)

</div>
</div>

---

# Reviewing Buddy List

<div class="multi-column">
<div>

| Person A | Person B |
|-------------|----------|
| Bojan | Darko |
| Kresimir | Chiara |
| Aroj | Margot |
| Jose | Florian |
| Gordon | Vojislav |
| Vojislav | Gordon |

</div>
<div>

| Person A | Person B |
|-------------|----------|
| Fynn | Paul |
| Marie | Fynn |
| Paul | Marie |
| Verena | Alfred |
| Louisa | Jasmin |

</div>
</div>

---

# Day One - Imaging I/IV

<small>

- 🧡 [#3090 - Background subtraction](https://github.com/nf-core/modules/issues/3090) (KB)
- [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
- [EOD] figuring out passing optional inputs such as px size
- [Tuesday AM] Working from nf-core but test dataset does not have the right metadata.
- Small tonsil test data should work
- Need to add columns to it
- 🧡 [#3089 - BaSicPy](https://github.com/nf-core/modules/issues/3089) (VP)
- [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
- [EOD] looking at passing optional inputs. Issues with docker container working
- [Tuesday AM]
- 🧡 [#3076 - Deepcell/Mesmer](https://github.com/nf-core/modules/issues/3076) (CS, MI)
- [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
- [EOD] Passes testing with local data
- Detail work for optional inputs ongoing
- [Tuesday AM] Need image with membrane and nuclear marker
(does this work? https://github.com/nf-core/test-datasets/pull/821)

</small>

---

# Day One - Imaging II/IV

<small>

- 🧡 [#3065 - Coreograph](https://github.com/nf-core/modules/issues/3065) (AH, MC)
- [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
- [EOD] Need to make bioconda package. Asking for help on this. (Really nice to have bioconda even if not strictly required)
- To make seperate HackMD for technical details at this stage. Can skip bioconda tests manually
- [Tuesday AM] Agree to skip bioconda for now with exceptions in test file,. Submit just DAPI from exemplar-001 as test-dataset
- 🧡 [#3044 - Mcquant](https://github.com/nf-core/modules/issues/3044) (FW)
- [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
- Waiting on a suitable test-dataset from AT
- [EOD] As above. Works on real data!
- [Tuesday AM] Can test once test data is merged

</small>

---

# Day One - Imaging III/IV

<small>

- 💜 [#2864 - Ilastik/pixelclassification](https://github.com/nf-core/modules/issues/2864) (FW)
- [Monday, 3.30 CET] Assigned and ready for review
- PR [#2875](https://github.com/nf-core/modules/pull/2875) approved by Nicolas Vannieuwkerke
- 16.10 CET Merged!
- [EOD] Conda tests skipped as has its own coda channel
- 💜 [#2865 - Ilastik/Multicut](https://github.com/nf-core/modules/issues/2865) (FW)
- [Monday, 3.30 CET] Assigned and ready for review
- PR [#2894](https://github.com/nf-core/modules/pull/2894) approved by Nicolas Vannieuwkerke, waiting for review by Maxime Garcia => Failing CI tests
- [EOD] prettier lint failing. Request out on how to solve
- 11.35 CET -> Merged

</small>

---

# Day One - Imaging IV/IV

<small>

- 🧡 [#2477 - Mindagap/Mindagap](https://github.com/nf-core/modules/issues/2477) (FW)
- [Monday, 3.30 CET] Assigned and ready for review
- PR [#2477](https://github.com/nf-core/modules/issues/2477)
- Three reviewers assigned
- Fails nf-core linting
- [EOD] stub test needed
- [Tuesday AM] Refactoring to add mandatory args
- 🧡 [#3095 - SpatialData/MCMICRO](https://github.com/nf-core/modules/issues/3095) (WM, FW)
- [Monday, 3.30 CET] Assigned and in progress but no linked branch/PR CET
- [EOD] Docker image being built for this. Figuring out right output structure. Draft working
- [Tues AM] Creating CLI tool. Looking for valid output directories.
- 💚 [#3100 - Scimap/MCMICRO](https://github.com/nf-core/modules/issues/3100) (LKC, DM, CS)
- [Monday, 16:00 CET] Worked on general structure
- [EOD] First module attempt 🚀. Have basic structure but not working yet. Need to confirm right test data.
- [Tues AM] Have positive results with test data. wiring parameters together. Used quantification test data.

</small>

---

# Day One - New Modules I

<small>

- [#2571 - MitoHiFi/findMitoReference](https://github.com/nf-core/modules/issues/2571) (@verku)
- [#3103 - interproscan](https://github.com/nf-core/modules/issues/3103) (@toniher)
- [#14 - RNA Velocity](https://github.com/nf-core/scrnaseq/issues/14)
- [#3109 - chopper](https://github.com/nf-core/modules/issues/3109) (@FynnFreyer)
- [PR](https://github.com/nf-core/modules/pull/3174) waiting for review
- [#3105 - thermorawfileparser](https://github.com/nf-core/modules/issues/3105) (@rolivella)
- [#3113 - SURVIVOR/FILTER](https://github.com/nf-core/modules/issues/3113) (@LlaneroHiboreo)
- [#2572 - HyPo](https://github.com/nf-core/modules/issues/2572) (@remiolsen)
- [#2937 - purecn/intervalfile](https://github.com/nf-core/modules/issues/2937) (@lbeltrame, @aldosr)
- [#2938 - purecn/coverage](https://github.com/nf-core/modules/issues/2938) (@lbeltrame, @aldosr)
- [#2939 - purecn/normaldb](https://github.com/nf-core/modules/issues/2939) (@lbeltrame, @aldosr)
- [#2940 - purecn/run](https://github.com/nf-core/modules/issues/2940) (@lbeltrame, @aldosr)
- [#3078 - sigprofilerextractor](https://github.com/nf-core/modules/issues/3078) (@ferriolcalvet)
- [#3147 - plink/indeppairwise](https://github.com/nf-core/modules/issues/3147) (@atrigila)

</small>

---

# Day One - New Modules II

<small>

- [#2940 - purecn/dx](https://github.com/nf-core/modules/issues/2941) (@lbeltrame, @aldosr)
- [#3087 - bioqc](https://github.com/nf-core/modules/issues/3087) (@boleodole)
- [#1869 - wisecondorx/convert](https://github.com/nf-core/modules/issues/1869) (@nvnieuwk)
- PR awaiting approval
- [#3133 - sambamba/flagstat](https://github.com/nf-core/modules/issues/3133) (@kubranarci)
- [#2957 - brackenbuild](https://github.com/nf-core/modules/issues/2957) (@darko-cucin)
- [#3110 - NanoComp](https://github.com/nf-core/modules/issues/3110) (@paulwolk)
- Monday: Getting familiar with nf-core modules and writing the base of the module
- Tuesday: Testing
- Wednesday: PR awaiting approval
- [#3112 - ART/art_illumina](https://github.com/nf-core/modules/issues/3112) (ML)
- PR awaiting approval
- [#3114 - Pyrodigal](https://github.com/nf-core/modules/issues/3114) (@louperelo)
- [#3108 - LoFreq3](https://github.com/nf-core/modules/issues/3108) (@gordondraskic, @vojislavlukic, @milenaamidzic, @alexiandra97)

</small>

---

# Day One - New Modules I

<small>

# Modules update

- [#3096 - Update limma for new module standards and sample subsetting](https://github.com/nf-core/modules/issues/3096) ([Jonathan Manning](https://github.com/pinin4fjords))
- [Monday, 15:00 BST] - Work complete, ready for review in PR [#3116]
- [#922 - Prodigal: zip output](https://github.com/nf-core/modules/issues/922) (@kedhammar)
- PR: [#3136](https://github.com/nf-core/modules/pull/3136/) made, waiting on CI-testing and/or review
- [#3143 - Allow decompression utilities to output files channels](https://github.com/nf-core/modules/issues/3143)
- [Monday, 19:20 BST] - Work complete, ready for review in PR [#3144]

</small>

---

# Day Two - New Modules

<small>

- [#3157 - FastQ-Screen ](https://github.com/nf-core/modules/issues/3157)(@JPejovicApis,@snesic):
- hackaton: create a module where the inputs are fastqs and config (which a user would provide), adding test files
- future: discuss how to generate config file
- [#2571 - MitoHiFi/findMitoReference](https://github.com/nf-core/modules/issues/2571) (@verku) cont.
- in review [#3135](https://github.com/nf-core/modules/pull/3135)
- [#3161 - Openvariant/groupby](https://github.com/nf-core/modules/issues/3161) (@FedericaBrando)
- [#3107 - svaba](https://github.com/nf-core/modules/issues/3107) (@kubranarci)
- in review
- [#3173 - gridss generatebedpe](https://github.com/nf-core/modules/issues/3173) (@kubranarci)
- [#3167 - gridss gridss_somatic_filter](https://github.com/nf-core/modules/issues/3167) (@kubranarci)
- [#2571 - MitoHiFi/mitohifi](https://github.com/nf-core/modules/issues/2571) (@verku)
- did not reach stage to create PR
- [#3165 - Pyrodigal](https://github.com/nf-core/modules/pull/3165) ✅ merged (@louperelo)
- [#214 - Auto rename fastq files for cellranger input](https://github.com/nf-core/scrnaseq/issues/214) (@sandrocarollo)
- [#3158 - epigen](https://github.com/nf-core/modules/issues/3158) (@msantorsola)
- [#3142 - IslandPath](https://github.com/nf-core/modules/issues/3142) (@jvfe)
- Ready for review in PR [#3145](https://github.com/nf-core/modules/pull/3145)
- [#3147 - plink/indeppairwise](https://github.com/nf-core/modules/issues/3147) (@atrigila)
- Ready for review in PR [#3150]
- [#1851 - picard/collectinsertsizemetrics](https://github.com/nf-core/modules/issues/1851) (@FerriolCalvet)
- Ready for review in PR [[#3179](https://https://github.com/nf-core/modules/pull/3179)]
- [#1792 - windowmasker/convert](https://github.com/nf-core/modules/issues/1792) (@alxndrdiaz)
- Ready for review in PR [[#3152](https://github.com/nf-core/modules/pull/3152)]

</small>

---

# Day Two - Module updates

<small>

- [#922 - Prodigal: zip output](https://github.com/nf-core/modules/issues/922) (@kedhammar)
- Merged
- [#3115 - update RGI to latest version 6.0.2](https://github.com/nf-core/modules/issues/3115)(@louperelo)
- Discussion and change of strategy on [#3143 - Allow decompression utilities to output files channels](https://github.com/nf-core/modules/issues/3143)
- [Tuesday, 14:40 BST] - Re-worked to separate modules, ready for review in PR [[#3144]](https://github.com/nf-core/modules/pull/3144)
- [thermorawfileparser test data PR](https://github.com/nf-core/test-datasets/pull/826) (@rolivella)
- [#2957 - modifying .nf and .yml files for brackenbuild, testing locally] (@darko-cucin)
- [#2572 - HyPo](https://github.com/nf-core/modules/issues/2572) (@remiolsen)
- PR made: [#3181](https://github.com/nf-core/modules/pull/3181)
- [#3103 - interproscan](https://github.com/nf-core/modules/issues/3103) (@toniher)
- PR made: [#3180](https://github.com/nf-core/modules/pull/3180)
- [#3161 - Openvariant/groupby](https://github.com/nf-core/modules/issues/3161) (@FedericaBrando)
- Testing locally
- [#3183 - panaroo/run](https://github.com/nf-core/modules/issues/3183) (@jvfe)
- PR made: [#3184](https://github.com/nf-core/modules/pull/3184)

</small>

---

# Day Two - Imaging Intro 1/6

<img src="https://raw.githubusercontent.com/labsyspharm/mcmicro/master/docs/assets/images/mcmicro-logo.svg" width="40%" height="30%"></img>
- Multiplexed tissue imaging techniques such as CyCIF, CODEX and MIBI require several processing steps including registration, segmentation and quantification to provide cell-by-feature arays for dowstream analysis
- MCMICRO is a nextflow pipeline for this, enabling scalable and robust analysis!
- Teams at HMS, U Heidleberg and Sage Bionetworks are working add key tools as nf-core modules with a view to adding as a nf-core module (next hackathon goals!)
- Join us in the #mcmicro channel or at mcmicro.org

---

# Day Two - Imaging 2/6

<small></small>
#### 🚀🎉 Merged!
- 💜 [#2864 - Ilastik/pixelclassification](https://github.com/nf-core/modules/issues/2864) (FW)
- 💜 [#2865 - Ilastik/Multicut](https://github.com/nf-core/modules/issues/2865) (FW)

</small>

---

# Day Two - Imaging 3/6

<small>

- 🧡 [#3090 - Background subtraction](https://github.com/nf-core/modules/issues/3090) (KB)
- [Tuesday AM] Working from nf-core but test dataset does not have the right metadata.
- Small tonsil test data should work
- Need to add columns channels (to open PR)
- 🧡 [#3089 - BaSicPy](https://github.com/nf-core/modules/issues/3089) (VP)
- 🧡 [#3076 - Deepcell/Mesmer](https://github.com/nf-core/modules/issues/3076) (CS, MI)
- [Tuesday AM] Need image with membrane and nuclear marker (can use tonsil test data (waiting on registered image))

</small>

---

# Day Two - Imaging 4/6

<small>

- 🧡 [#3065 - Coreograph](https://github.com/nf-core/modules/issues/3065) (AH, MC)
- [Tuesday AM] Agree to skip bioconda for now with exceptions in test file,. Submit just DAPI from exemplar-001 as test-dataset
- 🧡 [#3044 - Mcquant](https://github.com/nf-core/modules/issues/3044) (FW)
- [Tuesday AM] Passing. Can test once test data is merged

</small>

---

# Day Two - Imaging 5/6

<small>

- 🧡 [#2477 - Mindagap/Mindagap](https://github.com/nf-core/modules/issues/2477) (FW)
- [Tuesday AM] Refactoring to add mandatory args
- 🧡 [#3095 - SpatialData/MCMICRO](https://github.com/nf-core/modules/issues/3095) (WM, FW)
- [Tues AM] Creating CLI tool. Looking for valid output directories.
- 💚 [#3100 - Scimap/MCMICRO](https://github.com/nf-core/modules/issues/3100) (LKC, DM, CS)
- [Tues AM] Have positive results with test data. wiring parameters together. Used quantification test data.

</small>

---

# Day Two - Imaging test data 6/6

Preparing end-to-end test datasets for imaging modules

- [Rename spatialomics to imaging for modules branch #815](https://github.com/nf-core/test-datasets/issues/815)
- [Add test datasets for imaging modules](https://github.com/nf-core/test-datasets/issues/822)
- BASIC, exemplar-001 downsized, with downsized illumination profiles (VP)
- ASHLAR (PR open, AT/JM)
- Backsub (Uses registered image)
- Choreograph (DAPI only from -001)
- Registered image (AT)
- Labelled tiff mask output
- Quantification - csv

---

# Day Three Wrap Up: Modules

---

# Day Three Imaging Summary

<small>

- 🔬+🍏=❤️ Thank you for welcoming microscopists and image analysts into the nf-core community!
- 🚀 11 modules started with several merged/lined up. We almost have a draft workflow for multiplexed image processing using all `nf-core` modules in place
- 🤩 Huge shout out to Florian Wuennemann, Adam Taylor, Margot Chazotte, Jose Nimo, Chiara Schiller, Kresimir Bestak, Aroj Hada, Wouter-Michiel Vierdag, Luis Kuhn Cuellar, Carolin Schwitalla, Dominik Molitor, Jelena Pejovic Simeunovic, Svetozar Nesic and Emilio Palumbo
- 🥳 Thank you for those who have reviewed and advised us!
- 🔬 Join #microscopy on nf-core slack to bring more imaging to `nf-core` (MCMICRO+Janelia+EMBL-EBI+ more!)

</small>

---

## Imaging Agenda for Weds AM

<small>

- Todays goals
- Remaining modules into PR and merge (expect slow down in tests)
- Demo pipeline (from samplesheet, or revert to single file)

<div class="multi-column">
<div>

<br>

- Blockers
- BaSiCPy
- Docker container not working for nextflow
- Python script is parsing args in a odd way
- Reqriting to use argparse.
- This is for BaSicPy
- Module status
- Wrap up
- Issues
- Project board
- HackMD
- Planning Spreadsheet

</div>
<div>

<br>

- Follow up on Slack
- #microscopy (nf-core)
- #mcmicro (HMS)
- #mcmicro (nf-core)
- Follow up on MCMICRO community call
- Hackathon debrief
- GalaxyME
- Follow up on Bioconda environments
- 🎉

</div>
</div>
</small>

---

# Imaging Module Status

<small>

- 💚💜 [#3044 - Mcquant](https://github.com/nf-core/modules/issues/3044) (FW)
- [Wednesday AM] Passing tests with public test-datasets. PR opened: https://github.com/nf-core/modules/pull/3196
- [Wednesday 2:17 CET] Auto-merge enabled.
- 💚💜 [#2477 - Mindagap/Mindagap](https://github.com/nf-core/modules/issues/2477) (FW)
- [Wednesday AM] Passing tests with public test-datasets. PR opened:
https://github.com/nf-core/modules/pull/2860
- [Wednesday 2:17 CET] Auto-merge enabled.
- 🧡 [#3095 - SpatialData/MCMICRO](https://github.com/nf-core/modules/issues/3095) (WM)
- Figuring out options for storage, and compression
- Documentation for docker image completed
- Push to docker container
- Start module

</small>

---

<small>

- 💚 [#3100 - Scimap/MCMICRO](https://github.com/nf-core/modules/issues/3100) (LKC, DM, CS)
- Streamlined some of the process, working but now testing with new test data
- 🧡 [#3065 - Coreograph](https://github.com/nf-core/modules/issues/3065) (AH, MC)
- Minor issue with versions being worked on
- PR nearly ready
- ~~AT to add test dataset once shared -sent on slack
- 💚 [#3090 - Background subtraction](https://github.com/nf-core/modules/issues/3090) (KB)
- Previous issues fixed. Adding test-datasets
- Fixed versioning
- passing Docker and Singularity tests with public dataset
- PR ready for review

</small>

---

<small>

- 🧡 [#3089 - BaSicPy](https://github.com/nf-core/modules/issues/3089) (VP)
- See blockers above
- 🧡 [#3076 - Deepcell/Mesmer](https://github.com/nf-core/modules/issues/3076) (CS, MI)
- Failed for singularity
- Adding new test datasets
- 🧡 [#3111 cellpose](https://github.com/nf-core/modules/issues/3111)
- Passes initial tests, to add PR and test datasets

</small>

---

Merged!

<small>

- 💜 [#2864 - Ilastik/pixelclassification](https://github.com/nf-core/modules/issues/2864) (FW)
- 💜 [#2865 - Ilastik/Multicut](https://github.com/nf-core/modules/issues/2865) (FW)
- [Test nf-core pipeline repo](https://github.com/SchapiroLabor/mcmicro_nfcore_demo) (FW)

</small>

---

# Day Three - New Modules

<small>

- [#3193 - bamstats](https://github.com/nf-core/modules/issues/3193) (@emi80)
- [#3106 - Cellranger-arc modules](https://github.com/nf-core/modules/pull/3106)(@heylf)
- [#2450 - Cellranger-atac modules](https://github.com/nf-core/modules/pull/2450)(@heylf)
- [#3202 - vg/pack](https://github.com/nf-core/modules/pull/3202)(@WackerO) In progress, trying to get a GAM file for test runs
- [#2807 - svtyper](https://github.com/nf-core/modules/issues/2807) (@kubranarci)

</small>

---

<small>

- [#3213 - rgi/autoload](https://github.com/nf-core/modules/issues/3213) (@louperelo)
- [#3122 - WisecondorX/newref](https://github.com/nf-core/modules/issues/3122) (@nvnieuwk)
- [#3108 - LoFreq3](https://github.com/nf-core/modules/issues/3108) (@gordondraskic)
- [#3109 - chopper](https://github.com/nf-core/modules/issues/3109)
- [Pull Request](https://github.com/nf-core/modules/pull/3174) was reviewed, and is waiting for last round of checks to finish before merge

</small>

---

# Day Three - Module updates

<small>

- [#3143 - Allow decompression utilities to output files channels](https://github.com/nf-core/modules/issues/3143)
- [Tuesday, 12:00 BST] - Complete and merged [[#3144]](https://github.com/nf-core/modules/pull/3144)
- [#3115 - update RGI to latest version 6.0.2](https://github.com/nf-core/modules/issues/3115)(@louperelo)
- depends on #3213 new module: rgi/autoload
- [#3193 - new module: bamstats](https://github.com/nf-core/modules/issues/3193)
- module and tests completed
- containers URLs depend on [bioconda #40108](https://github.com/bioconda/bioconda-recipes/pull/40108)

</small>

---

<small>

- [#3157 - FastQ-Screen ](https://github.com/nf-core/modules/issues/3157)(@JPejovicApis,@snesic) continue work on a new module
- [#2572 - HyPo](https://github.com/nf-core/modules/issues/2572) (@remiolsen)
- PR under review: [#3181](https://github.com/nf-core/modules/pull/3181)
- [#3103 - interproscan](https://github.com/nf-core/modules/issues/3103) (@toniher)
- PR under review: [#3180](https://github.com/nf-core/modules/pull/3180)
- [#3108 - LoFreq3](https://github.com/nf-core/modules/tree/3108-new-module-lofreq3/modules/nf-core/lofreq3) (@gordondraskic, @VojislavLukic)
- processes for lofreq variant calling and pileup added
- dockerfile created and tested
- meta.yml files updated

</small>

---

<small>

- [#3218 - thermorawfileparser](https://github.com/nf-core/modules/pull/3218) (@rolivella)
- Adding extra input params.
- Adding a stub.
- Adding test_data.config
- [#3127 - purecn/intervalfile](https://github.com/nf-core/modules/pull/3127) (@lbeltrame, @aldosr)
- Module set up and tested locally
- Waiting for (https://github.com/bioconda/bioconda-recipes/pull/40076) to finish testing

</small>

---

<small>

- [#3132 - purecn/coverage](https://github.com/nf-core/modules/pull/3132) (@lbeltrame, @aldosr)
- Module set up
- Waiting (https://github.com/bioconda/bioconda-recipes/pull/40076) for testing
- [#3129 - purecn/normaldb](https://github.com/nf-core/modules/pull/3129) (@lbeltrame, @aldosr)
- Module set up
- Waiting (https://github.com/bioconda/bioconda-recipes/pull/40076) for testing
- [#3140 - purecn/run](https://github.com/nf-core/modules/pull/3140) (@lbeltrame, @aldosr)
- Module set up
- Waiting (https://github.com/bioconda/bioconda-recipes/pull/40076) for testing
- [#2957] - testing brackenbuild locally with docker and preparing for the commiting and pushing (@darko-cucin)
- [#3217 - pyrodigal](https://github.com/nf-core/modules/issues/3217) Compress pyrodigal output files (@jasmezz)
- [# 3206 - sambamba_sort](https://github.com/nf-core/modules/pull/3206) sorting bam file using sambamba sort (@BioInf2305)
- implementing changes after review

</small>

---

# 🥳
# Thank you to all who have worked on modules!

---

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