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### 🚀 Modules Team 🚀
_10th-12th October 2022 - BCN_
This file: [https://hackmd.io/@nf-core/B1dlQPTGs/edit](https://hackmd.io/@nf-core/B1dlQPTGs/edit)
The Hackathon Oct 2022 [Project Board](https://github.com/orgs/nf-core/projects/38/views/7)
<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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# Modules Team
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# Tasks Ideas: Devs
- General development work
- New modules
- Fix modules tests
- Improve modules
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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/views/7)
- Post your progress here **daily**!
---
# Team Members
* 🤖 [Gisela Gabernet](https://github.com/ggabernet)
* 🤖 [Louisa Perelo](https://github.com/louperelo)
* 🤖 [Jose Espinosa-Carrasco](https://github.com/joseespinosa)
* [Nicolas Vannieuwkerke](https://github.com/nvnieuwk)
* [Jonathan Manning](https://github.com/pinin4fjords)
* [Martin Rippin](https://github.com/marrip)
* [Gertrude Lie-Nielsen](https://github.com/gertrudeln)
* [Christian Kniep](https://github.com/ChristianKniep)
---
# Team Members
* [Lynsey Kovar](https://github.com/lkov0)
* [Robert Petit](https://github.com/rpetit3)
* [Maulik Upadhyay](https://github.com/BioInf2305)
* [Alan Hoyle](https://github.com/alanhoyle/)
* [Roger Olivella](https://github.com/proteomicsunitcrg)
* [Emeline Favreaui](https://github.com/EmelineFavreau)
* [Chris Wyatt](https://github.com/chriswyatt1)
* [Toni Hermoso Pulido](https://github.com/toniher)
---
# Team members
* [Baptiste Imbert](https://github.com/baptisteImbert)
* [Sreeram Peela](https://github.com/sreerampeela)
* [Paweł Ciurka](https://github.com/pawelciurkaardigen)
* [Juan A. Cordero Varela](https://github.com/jacorvar)
* 👾 [Anan Ibrahim](https://github.com/Darcy220606)
* [Luca Cozzuto](https://github.com/lucacozzuto)
* [Solenne Correard](https://github.com/scorreard)
---
# Team members
* [Ilja Bezrukov](https://github.com/ibebio)
* [Saba Nafees](https://github.com/snafees) (airrflow)
* 👾 [Jasmin Frangenberg](https://github.com/jasmezz)
* [Laurence Kuhlburger](https://github.com/laurencekuhl)
* [Alison Meynert](https://github.com/ameynert)
* [Matthias De Smet](https://github.com/matthdsm)
---
# DAY THREE
## Module contributions of the last 3 days
---
## General updates
- Alison reviewing PRs and triggering discussion of **task.ext.args**. Params should not be passed as value channels to modules unless they are needed in the script section (e.g. if/else statements.)
- Jennifer updated the documentation on that in the modules guidelines
---
## New modules
- Anan and Louisa continued on the **AMPcombi** module, writing tests now.
- Alan added the test RNA BAM files and has a working **ABRA2 module** locally [#2186](https://github.com/nf-core/modules/issues/2186). Pull request (#2288)[https://github.com/nf-core/modules/pull/2288] created.
---
## New modules
- Sreeram had to continue working on module **repeatscout** (creating subtools instead of one main tool).
- Ilja is working on the **repeatscout submodules**.
- Saba and Gisela worked on the **presto/filterseq** module. Getting tests to pass on CI.
- Maulik was working on **fulcrumgenomics/fqgrep** [#1941](https://github.com/nf-core/modules/issues/1941); the tool search for user-defined refernce and alternative sequence in the paired-end fastq file https://github.com/BioInf2305/fqgrep-in-progress
---
## Module fixes
- Drop endedness check for **Fastqc** - https://github.com/nf-core/modules/issues/2278
& https://github.com/nf-core/modules/pull/2282
- Luca and Matthias updated **FastQC** and **Falco**. The **meta.single_end** is now ignored, the tools will just check for the number of files.
- Robert fixed **smoove** container on Biocontainers
---
## Running docker on M1 chips
M1 `--platform=linux/amd64` uses VM which degrades performance (@ChristianKniep @snafees)
- most likely depending on the tool (simple python scripts might work just fine)
- of course: **running slow** is always better than **not running at all**
---
---
# DAY TWO
---
## General updates
- Christian sets up a mirror of the blast container which provides x86 and arm images. (lots of papercuts :) )
- ...
---
## Fixing tests
- Robert fixing more tests [#2252](https://github.com/nf-core/modules/pull/2252)
- Others fixing tests listed on [#2154](https://github.com/nf-core/modules/issues/2154): @Emiller88, @pawelciurkaardigen, @EmelineFavreau, @chriswyatt1, @joseespinosa
---
## New modules
- Louisa, Anan and Jasmin started to work on a new module: AMPcombi [#2183](https://github.com/nf-core/modules/pull/2234). AMPcombi is a Antimicorbial peptides parsing and functional classification tool.
- Luca is working on a new module: falco [#2204](https://github.com/nf-core/modules/pull/2204) (ready to merge once test runs). Falco is a C++ implementation of FastQC and can replace it being more efficient and fast. It is particularly useful for nanopore reads.
- Solenne is working on a new module: smoove [#2222](https://github.com/nf-core/modules/pull/2222). Smoove efficiently calls and genotypes SVs.
- Getrude and Martin are working on new Module: PretextMap [#1947](https://github.com/nf-core/modules/pull/1947). PretextMap converts SAM or pairs formatted read pairs into genome contact maps
- handled TODOs in module `main.nf` and `meta.yml`
- created mulled container for pretextmap/samtools
- struggeling to create test.yml
- Robert added new module: Biohansel [#2234](https://github.com/nf-core/modules/pull/2234). Biohansel genotypes clonal microbial whole-genome sequencing (WGS) data using SNV targeting k-mer genotyping schemes.
- Aria2 module for proteinfold merged [#2182](https://github.com/nf-core/modules/issues/2182). Aria2 is a lightweight multi-protocol & multi-source command-line download utility supporting several protocols.
- Alan continued to work on Abra2 [#2186](https://github.com/nf-core/modules/issues/2186). It now works on 1,2,3 samples but needs RNAseq BAMs added to the test suite for test completeness. RNA bams generated from the RNA fastqs. Abra2 is an assembly based realigner used to improve alignments and detect indels.
- Toniher finished working in kofamscan module (works with local data). Requested minimum test datasets to be uploaded [#652](https://github.com/nf-core/test-datasets/pull/652). The module will allow to perform KEGG Orthology Search
- Saba and Gisela working on adding nf-core module presto/filterseq [PR](https://github.com/nf-core/modules/pull/2231). GH actions taking time to run the tests. presto/filterseq filters sequences in FASTA/FASTQ files
- Roger still working on the proteomics module openms/idfilter [2205](https://github.com/nf-core/modules/issues/2205). openms/idfilter filters peptide and protein identifications.
- Lynsey continued work on Crispresso2 module - getting tests working [#2191](https://github.com/nf-core/modules/issues/2191). Crispresso2 analyzes outcomes from genome editing experiments.
- Jon addressed feedback on DESeq module, awaiting further feedback/ discussion/ approval [#2167](https://github.com/nf-core/modules/pull/2167).
- Sreeram added step two of RepeatScout module. Planning for testing tomorrow [#2187](https://github.com/nf-core/modules/issues/2187).
- Laurence did a bioconda recipe of CRISPRcleanR to be able to make it into a module with Robert's help.
- Maulik is still working on the module fulcrumgenomics/fqgrep [#1941](https://github.com/nf-core/modules/issues/1941)
---
## Modules updates
- Louisa's updates from yesterday were merged (#funcscan issue #134 and issue #123)
- ..
---
# DAY ONE
---
## General updates
- Christian is working on [#2188](https://github.com/nf-core/modules/issues/2188) to simplify the curation of ARM images (Apple M1/M2). First by fixing the `nextflow run blast-example -with-docker` example.
- Alan made a modules+tools pull request [to fix the URLs in the module tempate #1901](https://github.com/nf-core/tools/pull/1901) ,
---
## Fixing tests
Fixing module tests after nf-core/modules restructuring:
- Paweł works on fixing tests [#2154](https://github.com/nf-core/modules/issues/2154)
- Robert working on fixing broken tests
- Emeline and Chris started working on [#2154](https://github.com/nf-core/modules/issues/2154)
---
## New modules
- Getrude and Martin started working on issue [#1947](https://github.com/nf-core/modules/issues/1947), (new module pretext/map) created PR and read up on what to do
- Toniher contributing new kofamscan module [#2189](https://github.com/nf-core/modules/issues/2189)
- Roger Olivella working on adapting to nf-core this proteomics local module openms/idfilter [#2205](https://github.com/nf-core/modules/issues/2205)
- Baptiste started working on an OrthoFinder module [#2196](https://github.com/nf-core/modules/issues/2196)
- Sreeram started working on Repeatscout module (new)[#2187](https://github.com/nf-core/modules/issues/2187)
- Maulik started working on fulcrumgenomics/fqgrep [#1941](https://github.com/nf-core/modules/issues/1941)
- Lynsey started working on a new Crispresso2 module [#2191](https://github.com/nf-core/modules/issues/2191)
- Laurence has been working on mageck modules (debugging and test-data files) [#2138](https://github.com/nf-core/modules/pull/2138) and updated her PRs.
- Jon has been working on a [DESeq differential wrapper](https://github.com/nf-core/modules/pull/2167), alongside discussion with other team members around the general approach to differential abundance.
- Alan is working on [#2186](https://github.com/nf-core/modules/issues/2186). He has a version of the abra2 module to work locally on single bam inputs and is working on accepting multiple inputs....
- Sreeram has been working on creating the first part (build lmer table) of the repeatscout module [2187](https://github.com/nf-core/modules/issues/2187). As per the authors, the full workflow takes lots of memory. As this command is similar to finding the most frequent kmers, I am planning to use other kmer-counting modules from nfcore as an alternative.
- Ilja is working on the other repeatscout submodules [2187](https://github.com/nf-core/modules/issues/2187)
---
## Module updates
- Louisa updated the usage.md for funcscan issue #134 regarding the database download of the module DEEPBGC_DOWNLOAD.
---
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