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<a href="https://www.nf-co.re"><img src="https://i.imgur.com/hEDjpCs.png" width="65%"><img></a>
### π Pipelines Team π
_27th-29th March 2023_
The Hackathon March 2023 [Project Board](https://github.com/orgs/nf-core/projects/38/views/10)
Slack `#hackathon-march-2023-pipelines`
[<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
---
# Pipelines Team
---
# Team Purpose
**For people:**
- Maintaining existing nf-core pipelines
- Starting new nf-core pipelines
- Working on own pipelines (using nf-core infrastructure)
<iframe src="https://giphy.com/embed/U4de7cZbtg8XmJbxho" width="240" height="135" frameBorder="0" class="giphy-embed" allowFullScreen></iframe>
---
# Team Leads
- General advice, pointers, co-ordination etc.
- Friederike Hanssen (@FriederikeHanssen)
- James Fellows Yates (@jfy133)
- Susanne Jodoin (@SusiJo)
_But always ask first in: `#hackathon-march-2023-pipelines`!_
---
# Tasks: Devs
- General development work
- DSL2 transition
- Bug fixes/functionality extensions
- New pipelines (make sure to get approval on #new-pipelines first!)
- Review Buddy system!
- Buddy with someone for rapid reciprocal PR reviews!
- See table!
---
# Tasks: Volunteers
- For those who want to help a _specific_ pipeline
- Ask existing devs! Ideas:
- **Beginner**: Help review and extend docs
- **Novice**: Making new #modules
- **Intermediate**: Help with small bug fixes (review issues)
- **Advanced**: Help with implementing new functionality
---
# Remember
- Add yourself to Team Members slide (next slide)
- Add your issues to the [project board](https://github.com/orgs/nf-core/projects/38)
- Assign yourself on issues on the [project board](https://github.com/orgs/nf-core/projects/38)
- Post your progress here **daily**! One slide per pipeline per day
- Sign up for a reviewing buddy (see slide)!
---
# Team Members I
- Friederike Hanssen (@FriederikeHanssen)
- James Fellows Yates (@jfy133)
- Susanne Jodoin (@SusiJo)
- Matilda Γ
slin (@matrulda)
- Lili (@Lili Li)
- Sofia Stamouli (@sofstam)
- Luca Cozzuto (@lucacozzuto)
- Silvia Shen (@shensilv)
- Jasmin Frangenberg (@jasmezz)
---
# Team Members II
- Louisa Perelo (@louperelo)
- Simon Heumos (@subwaystation)
- Simone Carpanzano (@carpanz)
- Laurence Kuhlburger (@LaurenceKuhl)
- Konrad Rokicki (@krokicki)
- Athanasios Baltzis (@athbaltzis)
- Danilo di Leo (@danilodileo)
- Daniel Lundin (@erikrikarddaniel)
- Emelie Nilsson (@emnilsson)
- Daniel Straub (@d4straub)
---
# Team Members III
- Aida Andrades ValtueΓ±a (@aidaanva)
- Thiseas C. Lamnidis (@TCLamnidis)
- Judith Ballesteros (@jbv2)
- Merlin Szymanski (@merszym)
- Selina Carlhoff (@scarlhoff)
- Ian Light-Maka (@ilight1542)
- Alyssa Briggs (@alyssa-ab)
- Solenne Correard (@scorreard)
- BjΓΆrn Langer (@bjlang)
---
# Team Members IV
- BoΕΌena Mika-Gospodorz (@bozmik)
- BΕaΕΌej Szczerba (@blazejszczerba)
- Piotr Faba (@piotr-faba-ardigen)
- Mauro Saporita (@mauro-saporita)
- Olha Petryk (@opetryk)
- PaweΕ KoΕcielny (@pkoscielnybio)
- PaweΕ Ciurka (@pawelciurkaardigen)
- MichaΕ Stachowiak (@MichalStachowiakArdigen)
- Dorota Pikul (@DorotaPikulArdigen)
- Jonathan Manning (@pinin4fjords)
---
# Team Members V
- Margherita Mutarelli (@daisymut)
- Leila Mansouri (@l-mansouri)
- Till Englert (@tillenglert)
- Sabrina Krakau (@skrakau)
---
# Team Members VI
- Haoqi Chen (@haoqichen20)
---
# Team Members VII
- Disha Lodha (@Dishalodha)
- Lahcen Campbell (@ens-LCampbell)
- Jorge Alvarez-Jarreta (@JAlvarezJarreta)
---
# Team Members VIII
- Nuno Agostinho (@nuno-agostinho)
- Likhitha Surapaneni (@likhitha-surapaneni)
---
# Reviewing Buddy List
<div class="multi-column">
<div>
| Person A | Person B |
|----------|----------|
| Maxime | Rike |
| James | Rike |
| Lili | Sofia |
| Jasmin | Louisa |
</div>
<div>
| Person A | Person B |
|----------|----------|
| Simon | Matilda |
| Danilo | Emelie |
| Jon | |
</div>
</div>
---
# Day One
---
# [eager](https://nf-co.re/eager) (day 1)
> **Goal**: DSL2 conversion!
π¨βπ©βπ¦βπ¦: Selina, Aida, Judi, Merlin, Ian, Thiseas, James
- β
[#949](https://github.com/nf-core/eager/pull/949) - Selina - Add Falco as FASTQC alternative
- π [#948](https://github.com/nf-core/eager/pull/948) - Judi, Thiseas - Add PreSeq
- π [#955](https://github.com/nf-core/eager/pull/955) - Judi - Add MTNucRatio
- π§ [#952](https://github.com/nf-core/eager/pull/952) - James - Multiplexed mapping support
---
# [eager](https://nf-co.re/eager) (day 1) (cont.)
- π§ [#957](https://github.com/nf-core/eager/pull/957) - Thiseas - aDNA damage manipulation
- π§ [#816](https://github.com/nf-core/test-datasets/pull/816) - Thiseas - Update TSVs for eager test-datasets
- π [#954](https://github.com/nf-core/eager/pull/954) - Selina - Adding BWA-MEM
- π§ [#959](https://github.com/nf-core/eager/issues/959) - Selina - Adding Bowtie 2
- β
Aida - Fixed bug in endorspy
- π [#3134](https://github.com/nf-core/modules/pull/3134) Aida - Updated nf-core/module for endorspy
---
# [eager](https://nf-co.re/eager) (day 1) (cont. 2)
- π§ [#922](https://github.com/nf-core/eager/issues/922) - Aida - working on adding endorspy
- π§ [#923](https://github.com/nf-core/eager/issues/923) - Aida - working on adding Host Removal
- π§ [#923](https://github.com/nf-core/eager/issues/923) - Merlin - Added bbduk step, working on synchronization with Ian (Princeseq step)
- π§ [#923](https://github.com/nf-core/eager/issues/923) - Ian - Added prinseqplusplus step, working to finish synchronization for fork in pipeline. opened pull request :smile_cat:
---
# [sarek](https://nf-co.re/sarek) (day 1)
> **Goal**: Fix issues
π¨βπ©βπ¦βπ¦: Friederike, Maxime, Matilda, Susanne
- π§ [#950](https://github.com/nf-core/sarek/issues/950) - Samplesheet validation (Matilda)
- π§ [#808](https://github.com/nf-core/sarek/issues/808) - ControlFREEC ploidy (Rike)
- π§ [#702](https://github.com/nf-core/sarek/issues/702) - Updating bioconda recipe for ascat + creating new mulled container (SusiJo)
---
# [proteinfold](https://nf-co.re/proteinfold) (day 1)
> **Goal**: Add new software and functionalities!
π¨βπ©βπ¦βπ¦: Athanasios
- π§ [#86](https://github.com/nf-core/proteinfold/issues/86) - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows
---
# [taxprofiler](https://github.com/nf-core/taxprofiler) (day 1)
> **Goal**: Issues for 1.1.0
π¨βπ©βπ¦βπ¦: Sofia, Lili, James
- π§ [#257](https://github.com/nf-core/taxprofiler/issues/257)- Sofia-Substitute samtools/bam2fq module with samtools/fastq module.
- π [#247](https://github.com/nf-core/taxprofiler/issues/247)- Lili - Add a new module metaphlan/makedb to create a latest metaphlan database.
- π§ [#210](https://github.com/nf-core/taxprofiler/issues/210) - Sofia, James - Add KMCP modules
---
# [differentialabundance](https://github.com/nf-core/differentialabundance) (day 1)
> **Goal**: Issues for #100, #102 [nf-core Hackathon March 2023](https://github.com/orgs/nf-core/projects/38/views/16?sortedBy%5Bdirection%5D=asc&sortedBy%5BcolumnId%5D=Repository&filterQuery=)
π¨βπ©βπ¦βπ¦: Oskar Wacker, Jonathan Manning, Erika
- [#100](https://github.com/nf-core/differentialabundance/issues/100) - Erika - Add plot differentially expressed genes by Biotype
- [#102](https://github.com/nf-core/differentialabundance/issues/102) - Oskar - Add multiple sets of gene signatures
---
# [pangenome](https://github.com/nf-core/pangenome) (day 1)
> **Goal**: Reimplement the pangenome pipeline following proper nf-core guidelines.
π¨βπ©βπ¦βπ¦: Simon
- β
Add graph visualization quality control subworkflow using ODGI modules.
<!-- - [x] ODGI 1D
- [x] ODGI_VIZ_COLOR
- [x] ODGI_VIZ_POS
- [x] ODGI_VIZ_DEPTH
- [x] ODGI_VIZ_INV
- [x] ODGI_VIZ_COMPR
- [x] ODGI_VIZ_UNCALLED -->
<!-- - [x] ODGI 2D
- [x] ODGI_LAYOUT
- [x] ODGI_DRAW -->
<!-- - [ ] Optional PAF input starting from SEQWISH. -->
- β
Only run WFMASH.
- π§ Parallelize WFMASH across nodes.
<!-- - [x] WFMASH_MAP
- [ ] SPLIT_APPROX_MAPPINGS_IN_CHUNKS
- [ ] WFMASH_ALIGN -->
<!-- - [ ] Option to skip SMOOTHXG.
- [ ] Add VG_DECONSTRUCT as a local module. -->
---
# [DualRNA-Seq](https://github.com/piotr-faba-ardigen/dualrnaseq) (day 1)
> **Goal**: DSL2 conversion!
π¨βπ©βπ¦βπ¦: BoΕΌena, BΕaΕΌej, Mauro, MichaΕ, PaweΕ, PaweΕ, Olha, Piotr, Dorota
- β
[#43](https://github.com/nf-core/dualrnaseq/issues/43) - Update Cutadapt process to DSL-2
- π§ [#42](https://github.com/nf-core/dualrnaseq/issues/42) - create test dataset for DSL2 pipeline
- π§ [#44](https://github.com/nf-core/dualrnaseq/issues/44) - Update tximport_host process from DSL1 process to DSL2 module
- β
[#45](https://github.com/nf-core/dualrnaseq/issues/45) - Update salmon index and salmon quantification process from DSL1 process to DSL2 module
- π§ [#46](https://github.com/nf-core/dualrnaseq/issues/46) - Create COMBINE_QUANTIFICATION_RESULTS modules
---
# [funcscan](https://github.com/nf-core/funcscan) (day 1)
> **Goal**: Solve all the issues!
π¨βπ©βπ¦βπ¦: Jasmin, Louisa
- β
[#247](https://github.com/nf-core/funcscan/issues/247) Update error messages <!-- -> β
[#248](https://github.com/nf-core/funcscan/pull/248) -->
- β
[#244](https://github.com/nf-core/funcscan/issues/244) Add Bakta annotation to CI tests <!-- -> β
[#249](https://github.com/nf-core/funcscan/pull/249) -->
- π [#173](https://github.com/nf-core/funcscan/issues/173) Update RGI to latest version
- Cleaned up issues
---
# [hgtseq](https://github.com/nf-core/hgtseq) (day 1)
> **Goal**: Bug fixing
π¨βπ©βπ¦βπ¦: Simone
---
# [lightsheetrecon](https://github.com/krokicki/nf-lightsheetrecon) (day 1)
> **Goal**: finish the full pipeline workflow using completed subworkflows for running Spark
π¨βπ©βπ¦βπ¦: Konrad
---
# [magmap](https://github.com/LNUc-EEMiS/magmap) (day 1)
> **Goal**: minimal working pipeline
π¨βπ©βπ¦βπ¦: Danilo, Emelie, Daniel Lundin
- β
Template update
- β
Pre-mapping-processing of reads
- β
Decide approach to add reference
<!-- - [ ] Sourmash index module
- [ ] Sourmash subworkflow
- [ ] BBMap index
- [ ] BBMap map
- [ ] featureCounts -->
---
# [crisprseq](https://github.com/nf-core/crisprseq) (day 1)
> **Goal**: minimal working pipeline
π¨βπ©βπ¦βπ¦: Laurence, JΓΊlia
- π PR Documentation update
- π PR Test datasets for a new module
- π§ Add new module (crisprclean-r)
---
# [atacseq](https://github.com/nf-core/atacseq) (day 1)
> **Goal**: metro-map
π¨βπ©βπ¦βπ¦: BjΓΆrn
- π PR v2
---
# new pipeline proposal
---
# [bamtofastq](https://github.com/qbic-pipelines/bamtofastq) (day 1)
> **Goal**: DSL2 conversion!
π¨βπ©βπ¦βπ¦: SusiJo, Friederike, matrulda
- π§ Adding tests
- π Started reviewing (a lot of changed files)
---
# [spinningjenny](https://github.com/lucacozzuto/nf-core-spinningjenny) (day 1)
> **Goal**: First draft
π¨βπ©βπ¦βπ¦: Luca
---
# [ensembl sequence pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/22) (day 1)
π¨βπ©βπ¦βπ¦: Disha Lodha, Zahra Waheed, Ahmad Zyoud
- π Understand the Ensembl sequence pipeline
- βοΈ Test the Ensembl sequence pipeline
# [ensembl genome_prepare pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16) (day 1)
π§: [#16](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16)
π¨βπ©βπ¦βπ¦: Disha Lodha, Jorge Alvarez, Lahcen Campbell
- π Understand the Ensembl \BRC4 genome prepare pipeline
- Started the migration of the different python modules
- βοΈ Test initial stages of manifest and json file prep: Ensembl genome prepare pipeline
---
# [COSMIC CMC pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/8#issuecomment-1485328883) (day 1)
π¨βπ©βπ¦βπ¦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Balasz, Helen
π§: - one group looked at using Docker/Singularity with Nexflow. Working to wrap up our environment inside a container
- Another group worked on how we can use nexflow with the LSF farm
- Another group started creating the nexflow pipeline and wrapping up our first steps.
---
# [Aquatic Symbiosis Cobiont Check pipeline](https://github.com/sanger-tol/cobiontcheck) (day 1)
π¨βπ©βπ¦βπ¦: Eerik
- wrote a script for retrieving full taxonomic lineage for FCS-GX results based on the taxIDs of the FCS-GX results
---
# [PhuEgo](https://github.com/haoqichen20/PhuEgo) (day 1)
π¨βπ©βπ¦βπ¦: Haoqi Chen
- Set up conda environment for pipeline running (pipeline is originally developed by collagues, and based on python only)
- Successful test run scripts.
# [Nextflow-VEP](https://github.com/Ensembl/ensembl-vep/tree/release/109/nextflow) (day 1)
Nuno Agostinho and Likhitha Surapaneni
* Support multiple files ( usecase: multiple variant sets, pangenomes, species )
* give directory as an input
* change mergeVCF to merge files by each input file
* support multiple VEP config files
# pipeline release
# [quantms](https://github.com/nf-core/quantms)
- Bug fix release (1.1.1)
π¨βπ©βπ¦βπ¦: Yasset Perez-Riverol, Julianus Pfeuffer, Sam Minot, Fabian
---
# Day Two
- 16 pipelines worked on:
- DSL2 conversion (2)
- New pipelines (6)
- Fixing issues (8)
---
# eager (day 2)
<small>
> **Goal**: DSL2 conversion!
π¨βπ©βπ¦βπ¦: Selina, Aida, Judi, Merlin, Ian, Thiseas, James
- β
[#954](https://github.com/nf-core/eager/pull/954) - Selina - Adding BWA-MEM
- π§ [#959](https://github.com/nf-core/eager/issues/959) - Selina - Adding Bowtie 2
- π§ [#923](https://github.com/nf-core/eager/issues/923) Ian creating metagenomics screening local subworkflow
- π§ [#957](https://github.com/nf-core/eager/pull/957) - Thiseas - aDNA damage manipulation
- β
[#948](https://github.com/nf-core/eager/pull/948) - Judith - Adding Preseq
- π§ [#958](https://github.com/nf-core/eager/pull/958) - Judith - Adding MtNucRatio
- β
[#3134](https://github.com/nf-core/modules/pull/3134) Aida - Updated nf-core/module for endorspy
- π§ [#961](https://github.com/nf-core/eager/pull/961) Aida - Adding endorspy
- π§ [#923](https://github.com/nf-core/eager/issues/923) - Aida - working on adding Host Removal
- π§ [#923](https://github.com/nf-core/eager/issues/923) - Merlin - Metagenomics Complexity Subworkflow ready for review
</small>
---
# [DualRNA-Seq](https://github.com/piotr-faba-ardigen/dualrnaseq) (day 2)
<small>
> **Goal**: DSL2 conversion!
π¨βπ©βπ¦βπ¦: BoΕΌena, BΕaΕΌej, Mauro, MichaΕ, PaweΕ, PaweΕ, Olha, Piotr, Dorota
- β
[#42](https://github.com/nf-core/dualrnaseq/issues/42) - create test dataset for DSL2 pipeline
- π§ [#44](https://github.com/nf-core/dualrnaseq/issues/44) - Update tximport_host process from DSL1 process to DSL2 module
- β
[#46](https://github.com/nf-core/dualrnaseq/issues/46) - Create COMBINE_QUANTIFICATION_RESULTS modules
- π§ [#48](https://github.com/nf-core/dualrnaseq/issues/48) - A new module to combine the host ambig and unique counts
- β
[#53](https://github.com/nf-core/dualrnaseq/issues/53) - Update star indexing and star alignment processes from DSL1 processes to DSL2 modules
- π§ [#54](https://github.com/nf-core/dualrnaseq/issues/54) - Update extract_annotations_* to DSL2
- π§ [#56](https://github.com/nf-core/dualrnaseq/issues/56) - Update tximport_host process from DSL1 process to DSL2 module
- π§ [#57](https://github.com/nf-core/dualrnaseq/issues/57) - Combine host annotations with quantification results
- β
[#60](https://github.com/nf-core/dualrnaseq/issues/60) - Update salmon split table process to DSL2
- β
[#58](https://github.com/nf-core/dualrnaseq/issues/58) - salmon quantification is not executed for all samplessalmon quantification is not executed for all samples
</small>
---
# [pangenome](https://github.com/nf-core/pangenome) (day 2)
<small>
π¨βπ©βπ¦βπ¦: Simon
> **Goal**: Reimplement the pangenome pipeline following proper nf-core guidelines.
- β
Optional PAF input starting from SEQWISH.
- β
Parallelize WFMASH across nodes.
- β
Option to skip SMOOTHXG.
- π§ Add VG_DECONSTRUCT as a local module.
</small>
---
# [viralintegration](https://github.com/nf-core/viralintegration) (day 2)
<small>
> **Goal**: Finalize first release and work on enhancements.
π¨βπ©βπ¦: Alyssa
- π§ [#2](https://github.com/nf-core/viralintegration/issues/2) - add metaphlan3 module
- π§ [#52](https://github.com/nf-core/viralintegration/pull/52) - get final review for first release
- π§ [#58](https://github.com/nf-core/viralintegration/issues/58) - organize into subworkflows
</small>
---
# [variantcatalogue](https://github.com/scorreard/nfcore-variantcatalogue/tree/master) (night 1?)
<small>
> **Goal**: Starting the migration of the variant catalogue pipeline to nf-core
π¨βπ©βπ¦βπ¦: Solenne
- β
Created the mapping suubworkflow
- β
Good progress on the ReADME / CITATIONS.md and other doc
- π§ SNV subworkflow
</small>
---
# [Magmap](https://github.com/LNUc-EEMiS/magmap) (day 2)
<small>
> **Goal**: add sourmash subworkflow + add some downstream modules
π¨βπ©βπ¦βπ¦: Emelie, Danilo and Daniel
- β
[#11](https://github.com/LNUc-EEMiS/magmap/pull/11) - Danilo and Emelie - Adding Subworkflow bbmap Index
- β
[#5](https://github.com/LNUc-EEMiS/magmap/pull/5) - Danilo and Emelie - Adding test-database
- β
[#12](https://github.com/LNUc-EEMiS/magmap/pull/12) - Danilo and Emelie - new subworkflow concatenate gff + indexing
- β
[#14](https://github.com/LNUc-EEMiS/magmap/pull/14) - Danilo and Emelie - cleaning output directory
- β
SOURMASH Sketch/gather subworkflow - Danilo and Emelie - Add subworkflow for SOURMASH SKETCH and GATHER
- β
[#15](https://github.com/LNUc-EEMiS/magmap/pull/15) - Danilo and Emelie - add bbmap_align module to the main workflow.
</small>
---
# [ensembl genome_prepare pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16) (day 2)
π§: [#16](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16)
π¨βπ©βπ¦βπ¦: Disha Lodha, Jorge Alvarez, Lahcen Campbell
- π Understand the Ensembl \BRC4 genome prepare pipeline
- First modules and backbone pipeline developed
- βοΈ Test genome.json channel handling, downloading genomic data
---
# [sammyseq](https://github.com/daisymut/sammyseq) (day 2)
π¨βπ©βπ¦βπ¦: Margherita
- β
Update template to latest tool version
- π§ Add test data
---
# [spinningjenny](https://github.com/lucacozzuto/nf-core-spinningjenny) (day 2)
- β
Embedded the code inside the nf-core template
- π§ Adding the input data to test-dataset (waiting for review)
- π§ Adding the recipe to bioconda (waiting for review)
---
# sarek (day 2)
<small>
π¨βπ©βπ¦βπ¦: Friederike, Maxime, Matilda, Michael, Susanne, Alison
- β
[#950](https://github.com/nf-core/sarek/issues/950) Samplesheet validation (Matilda)
- More samplesheet validation (Michael)
- π§ [#808](https://github.com/nf-core/sarek/issues/808) ControlFREEC ploidy (Rike)
- π§ [#702](https://github.com/nf-core/sarek/issues/702) Updating bioconda recipe for ascat + creating new mulled container (SusiJo) - Help Wanted!
- π [#981](https://github.com/nf-core/sarek/pull/981) Documentation on how to generate resource files for ASCAT (Alison)
</small>
---
# [taxprofiler](https://github.com/nf-core/taxprofiler) (day 2)
<small>
> **Goal**: Continue working on issues for 1.0.0
π¨βπ©βπ¦βπ¦: Sofia, Lili, James
- β
[#247](https://github.com/nf-core/taxprofiler/issues/247)- Lili-Add a new module metaphlan/makedb to create a latest metaphlan database.
- π§ [#273](https://github.com/nf-core/taxprofiler/issues/273) Lili- Add a new profiler: MetaPhlAn4.
- π§ [#210](https://github.com/nf-core/taxprofiler/issues/210) - Sofia, James - Add KMCP modules
</small>
---
# [nanoseq](https://github.com/nf-core/nanoseq/tree/update_3_1_dev) (day 2)
<small>
π¨βπ©βπ¦βπ¦: Chris & Yuk Kei
> **Goal**: Move local to nf-core modules and simplify complex mapping
- π§ Good progress moving local to nf-core
- π§ Some progress on mapping
</small>
---
# [hgtseq](https://github.com/nf-core/hgtseq) (day 2)
<small>
> **Goal**: bug fixing
π¨βπ©βπ¦βπ¦: Simone
- π§ [#28](https://github.com/nf-core/hgtseq/pull/28) - Resolving conflicts to update template
- π§ [#30](https://github.com/nf-core/hgtseq/pull/30) - New local module
</small>
---
# [differentialabundance](https://github.com/nf-core/differentialabundance) (day 2)
<small>
> **Goal**: add-pre differential matrix subsetting, new plot and more input
π¨βπ©βπ¦βπ¦: Jon, Oskar, Erika
- β
[#11](https://github.com/nf-core/differentialabundance/pull/103) - Jon - Update differential module interface, add pre-contrast subsetting options
- π§ Erika - Add biotype plot to report
- π§ Oskar - Enable multiple GTFs for GSEA
</small>
---
# [proteinfold](https://nf-co.re/proteinfold) (day 2)
> **Goal**: Add new software and functionalities!
π¨βπ©βπ¦βπ¦: Athanasios, Leila
- π§ [#86](https://github.com/nf-core/proteinfold/issues/86) - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows
- π§ [85](https://github.com/nf-core/proteinfold/issues/85) - Leila - Update ColabFold version
---
# [funcscan](https://github.com/nf-core/funcscan) (day 2)
> **Goal**: Solve new issues!
π¨βπ©βπ¦βπ¦: Jasmin
- π§ [#251](https://github.com/nf-core/funcscan/pull/251) PR out: Implement new pyrodigal module into pipeline
- π§ Implement changes of prodigal update
---
# [ampliseq](https://github.com/nf-core/ampliseq) (day 2)
π¨βπ©βπ¦βπ¦: Daniel & Daniel
- β
[#563](https://github.com/nf-core/ampliseq/pull/563) - Renamed DADA2 taxonomic classification files to include the chosen reference taxonomy abbreviation.
- π§ [#564](https://github.com/nf-core/ampliseq/pull/564) - Added phylogenetic placement.
---
# [bamtofastq](https://github.com/qbic-pipelines/bamtofastq) (day 2)
> **Goal**: DSL2 conversion!
π¨βπ©βπ¦βπ¦: SusiJo, Friederike, matrulda
- π§ Adding tests
- π Still reviewing the huge PR
-
---
# [PhuEgo](https://github.com/haoqichen20/PhuEgo) (day 2)
π¨βπ©βπ¦βπ¦: Haoqi Chen
- Modified scripts to have a minimal testable version, for faster testing. Initiate a nf-core pipeline.
- Prepared testing dataset.
---
# [Nextflow-VEP](https://github.com/Ensembl/ensembl-vep/tree/release/109/nextflow) (day 2)
Nuno Agostinho and Likhitha Surapaneni
* Chunking by variants
* Encapsulate in Nextflow tower
* Support error reporting and visualization
* Nextflow trace insufficient, compare with NF tower
# Day Three
<iframe src="https://giphy.com/embed/TuDaPP6VwTObsqzG4p" width="480" height="478" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/marchmadness-TuDaPP6VwTObsqzG4p">via GIPHY</a></p>
---
Summary today:
- :sparkles: 8 New pipelines (without first release)
- :alien: 3 non nf-core pipelines
- :older_adult: 10 existing pipelines
- 2 DSL2 conversion
---
# :sparkles: New pipelines
<iframe src="https://giphy.com/embed/LQ3cfzLDUQnfEWChJx" width="480" height="270" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/true-and-the-rainbow-kingdom-true-and-the-rainbow-kingdom-bartleby-LQ3cfzLDUQnfEWChJx">via GIPHY</a></p>
---
# [pangenome](https://github.com/nf-core/pangenome) (day 3)
<small>
> **Goal**: Reimplement the pangenome pipeline following proper nf-core guidelines.
π¨βπ©βπ¦βπ¦: Simon
- β
Add VG_DECONSTRUCT as a local module.
- β
Update tests.
- π§ Community subworkflow.
- π§ Squeeze subworkflow.
</small>
---
# [variantcatalogue](https://github.com/scorreard/nfcore-variantcatalogue/tree/master) (night 2)
<small>
> **Goal**: Coding the Variant catalogue pipeline up to nf-core
π¨βπ©βπ¦βπ¦: Solenne
- β
Code ready for review
- π§ Improve documentation
</small>
---
# [viralintegration](https://github.com/nf-core/viralintegration) (day 3)
<small>
> **Goal**: Finalize first release and work on enhancements.
π¨βπ©βπ¦: Alyssa
- π§ [#2](https://github.com/nf-core/viralintegration/issues/2) - add metaphlan3 module
- π [#52](https://github.com/nf-core/viralintegration/pull/52) - get final review for first release (being reviewed by @keslingmj)
- π§ [#58](https://github.com/nf-core/viralintegration/issues/58) - organize into subworkflows (done but waiting on first release to open PR for review!)
</small>
---
# [metapep](https://github.com/nf-core/metapep) (day 3)
π¨βπ©βπ¦βπ¦: Till & Sabrina
- β
Unforked nf-core/metapep repository
- β
[#56](https://github.com/nf-core/metapep/pull/56),[#61](https://github.com/nf-core/metapep/pull/61) - Improved documentation about data model
- β
[#55](https://github.com/nf-core/metapep/pull/55) Updated framework of epitopeprediction to epytope 3.3.0
- β
[#58](https://github.com/nf-core/metapep/pull/58) Made various ids deterministic to ensure reproducibility
- β
[#62](https://github.com/nf-core/metapep/pull/62) Updated the nf-core module prodigal to the latest version
---
# [spinningjenny](https://github.com/nf-core/spinningjenny) (day 3)
> We have the first non bionformatics pipeline in nf-core! **Models in Economics!**
π¨βπ©βπ¦βπ¦: Luca
- β
Added the input data to `test-dataset`
- β
Written the small test for ci
- β
Transferred the pipeline in nf-core
- π§ Adding the recipe of NetLogo to bioconda (waiting for review)
---
# [lightsheetrecon](https://github.com/krokicki/nf-lightsheetrecon) (day 3)
> **Goal**: finish the full pipeline with Spark
π¨βπ©βπ¦βπ¦: Konrad
- β
Completed end-to-end pipeline workflow
- β
Fixed Nextflow bug leaving orphan Spark processes after cancelling pipeline ([nextflow#3606](https://github.com/nextflow-io/nextflow/issues/3606))
- β
Wa new #microscopy channel discussing microscopy-related pipelines
- π§ Add tests_full & Add test (with stubs)
---
# [bamtofastq](https://github.com/qbic-pipelines/bamtofastq) (day 3)
> **Goal**: DSL2 conversion & adding to nf-core!
π¨βπ©βπ¦βπ¦: SusiJo, Friederike, matrulda
- β
Transferred to nf-core
- π§ Adding metro map
- π Reviewing DSL2 conversion
---
# [magmap](https://github.com/LNUc-EEMiS/magmap) (day 3)
<small>
> **Goal**: fix some bugs and add more statistics output
π¨βπ©βπ¦βπ¦:
- β
[#17](https://github.com/LNUc-EEMiS/magmap/pull/17) - Emelie and Danilo - Adding featurecounts and some associated modules
- β
[#16](https://github.com/LNUc-EEMiS/magmap/pull/16) - Danilo, Daniel and Emelie - update readme and bug fix!
- π§ []() - Emelie and Danilo - Adding more statistics
output
- β
[#22](https://github.com/LNUc-EEMiS/magmap/pull/22) - Emelie and Danilo - Adding new input index to feed sourmash
- β
Danilo, Emelie and Daniel: minimal working pipeline! :tada:
</small>
---
---
# [sammyseq](https://github.com/daisymut/sammyseq) (day3)
π¨βπ©βπ¦βπ¦: Margherita
- π§ [#832](https://github.com/nf-core/test-datasets/issues/832) Preparing test data following the standards
---
# [PhuEgo](https://github.com/haoqichen20/PhuEgo) (day 3)
π¨βπ©βπ¦βπ¦: Haoqi Chen
- Break apart python codes into individual nextflow process. Overall designed the pipeline.
---
# [Nextflow-VEP](https://github.com/Ensembl/ensembl-vep/tree/release/109/nextflow) (day 3)
Nuno Agostinho and Likhitha Surapaneni
* Clean temporary files
* Support relative paths
* Speed optimizations
* Support input not bgzipped or tabixed
# new non nf-core pipelines
<iframe src="https://giphy.com/embed/P1OUwUpTlLzEGAUHpN" width="480" height="270" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/Avatar-avatar-james-cameron-the-way-of-water-P1OUwUpTlLzEGAUHpN">via GIPHY</a></p>
---
# [ensembl sequence pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/22) (day 3)
<small>
π¨βπ©βπ¦βπ¦: Disha Lodha, Zahra Waheed, Ahmad Zyoud
- π Modified manifest_stats python script to remove internal Ensembl dependencies
- π» Created a nextflow module and ran a functional nextflow pipeline! πππ
</small>
---
# [Aquatic Symbiosis Cobiont Check pipeline](https://github.com/sanger-tol/cobiontcheck) (day 2)
π¨βπ©βπ¦βπ¦: Eerik
- wrote a script for combining FCS-GX results and Tiara results to get a list of contigs/scaffolds that can be automatically removed from the assembly as contaminants
---
# [COSMIC CMC pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/8#issuecomment-1487091898) (day 3)
<small>
π¨βπ©βπ¦βπ¦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Helen
π§: - one group looked at using Docker/Singularity with Nexflow. Working to wrap up our environment inside a container. Progress on containers, nextflow and sqlplus now setup
- Another group worked on how we can use nexflow with the LSF farm. Progress, now can submit and monitor jobs from Nextflow
- Another group started creating the nexflow pipeline and wrapping up our first steps.
- Implemented two Nexflow pipeline:
- Dump chromosome steps done
- Frequency tables generation done
- DN/DS step in progress
</small>
---
# :older_adult: Bug fixes & features for existing pipelines
<iframe src="https://giphy.com/embed/8A2jEyKYXS2IZVBo0d" width="480" height="360" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/8A2jEyKYXS2IZVBo0d">via GIPHY</a></p>
---
# DSL2 conversion
---
# [DualRNA-Seq](https://github.com/piotr-faba-ardigen/dualrnaseq) (day 3)
<small>
> **Goal**: DSL2 conversion!
π¨βπ©βπ¦βπ¦: BoΕΌena, BΕaΕΌej, Mauro, MichaΕ, PaweΕ, PaweΕ, Olha, Piotr, Dorota
- π§ [#44](https://github.com/nf-core/dualrnaseq/issues/44) - Update tximport_host process from DSL1 process to DSL2 module
- π§ [#48](https://github.com/nf-core/dualrnaseq/issues/48) - A new module to combine the host ambig and unique counts
- β
[#54](https://github.com/nf-core/dualrnaseq/issues/54) - Update extract_annotations_* to DSL2
- β
[#56](https://github.com/nf-core/dualrnaseq/issues/56) - Create subworkflow to create combined host/path transcriptome file
- π§ [#57](https://github.com/nf-core/dualrnaseq/issues/57) - Combine host annotations with quantification results
- β
[#62](https://github.com/nf-core/dualrnaseq/issues/62) - Add salmon quantification to salmon_alignment_base subworkflow
- π§ [#64](https://github.com/nf-core/dualrnaseq/issues/64) - create a module for generating bacterial transcriptome fasta file
- π§ [#66](https://github.com/nf-core/dualrnaseq/issues/66) - Add a module for count_total_reads and count_total_read_pairs processes
- β
[#69](https://github.com/nf-core/dualrnaseq/issues/69) - Add module extract processed reads to the pipeline
- π§ [#70](https://github.com/nf-core/dualrnaseq/issues/70) - 'Parent' is hard-coded in the replace_attribute_host_genome_gff_star_salmon process
- π§ [#73](https://github.com/nf-core/dualrnaseq/issues/73) - rethink check_replicates process for DSL2
</small>
---
# [Aquatic Symbiosis Cobiont Check pipeline](https://github.com/sanger-tol/cobiontcheck) (day 3)
π¨βπ©βπ¦βπ¦: Eerik
- Connected the script for removing contaminant scaffolds from the assembly (based on FCS-GX and Tiara results) to the master scripts of the pipeline, so that it can be run as a part of the pipeline
---
# eager (day 3)
<small>
People: Selina, Aida Judi, Ian, Thiseas, James
- π [#964](https://github.com/nf-core/eager/pull/964) - Selina - Adding Bowtie 2
- π§ [#3210](https://github.com/nf-core/modules/issues/3210) - Selina - new angsd contamination subworkflow
- π - Thiseas - aDNA Damage Manipulation
- π - Judith - Adding MtNucRatio [#958](https://github.com/nf-core/eager/pull/958)
- π§ - Judith - Starting with DamageProfiler [#966](https://github.com/nf-core/eager/issues/966)
- π - Ian - Finished initial implementation of metagenomics profiling [967](https://github.com/nf-core/eager/pull/967)
</small>
---
# sarek (day 3)
<small>
> **Goal**: Make it more awesome!
π¨βπ©βπ¦: Friederike, Maxime, Matilda, Michael, Susanne, Alison
- β
[#981](https://github.com/nf-core/sarek/pull/981) Documentation on how to generate resource files for ASCAT (Alison)
- :eyes: [982](https://github.com/nf-core/sarek/pull/982) Avoid using `exit` statements (Rike)
- :eyes: [#808](https://github.com/nf-core/sarek/issues/808) ControlFREEC ploidy (Rike)
- π§ [#702](https://github.com/nf-core/sarek/issues/702) Making ASCAT output reproducible: Bioconda recipe for ascat merged β
, intergration in progress (SusiJo) + new mulled container β
+ update module - currently testing
</small>
---
# [viralrecon](https://github.com/nf-core/viralrecon) (day 3)
<small>
> **Goal**: Implement & test the freyja subworkflow for wastewater variant analysis within viralrecon
π¨βπ©βπ¦: Joon
- π§ [#299](https://github.com/nf-core/viralrecon/issues/299) Implement & test the freyja subworkflow
</small>
---
# [taxprofiler](https://github.com/nf-core/taxprofiler) (day 3)
<small>
> **Goal**: Continue working on issues for 1.0.0
π¨βπ©βπ¦βπ¦: Sofia, Lili, James
- π§ [#273](https://github.com/nf-core/taxprofiler/issues/273) Lili- Add a new profiler: MetaPhlAn4.
- π [#210](https://github.com/nf-core/taxprofiler/issues/210) - Sofia, James - Add KMCP modules
- π [#257](https://github.com/nf-core/taxprofiler/issues/257)- Sofia-Substitute samtools/bam2fq module with samtools/fastq module.
</small>
---
# [proteinfold](https://nf-co.re/proteinfold) (day 3)
<small>
> **Goal**: Add new software and functionalities!
π¨βπ©βπ¦βπ¦: Athanasios, Leila
- π§ [#86](https://github.com/nf-core/proteinfold/issues/86) - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows
- π§ [#85](https://github.com/nf-core/proteinfold/issues/85) - Leila - Update ColabFold version
- π§ [#84](https://github.com/nf-core/proteinfold/issues/84) - Leila - Update AlphaFold2 version
</small>
---
# [ampliseq](https://github.com/nf-core/ampliseq) (day 3)
<small>
π¨βπ©βπ¦βπ¦: Daniel & Daniel
- β
[#564](https://github.com/nf-core/ampliseq/pull/564) - Added phylogenetic placement.
- π§ []() - Integrate phylogenetic placement into downstream analysis
</small>
---
# [funcscan](https://github.com/nf-core/funcscan) (day 3)
<small>
π¨βπ©βπ¦βπ¦: Jasmin
- β
[#251](https://github.com/nf-core/funcscan/pull/251): Implement new pyrodigal module into pipeline
- π§ [#253](https://github.com/nf-core/funcscan/pull/253) ready for review: Implement changes of prodigal update
- π§ [#173](https://github.com/nf-core/funcscan/issues/173) Implement RGI update β more database stuff :raised_hands:
- π§ [#3217](https://github.com/nf-core/modules/issues/3217) Compress pyrodigal output files
</small>
---
# [atacseq](https://github.com/nf-core/atacseq) (day 3)
<small>
π¨βπ©βπ¦βπ¦: BjΓΆrn
- π [#259](https://github.com/nf-core/atacseq/pull/259) Add support for optional control data
</small>
---
# [rnaseq](https://github.com/nf-core/rnaseq) (day 3)
<small>
π¨βπ©βπ¦βπ¦: Harshil?
Just released nf-core/rnaseq v3.11.0 :tada:
</small>
---
# [treeval](https://github.com/sanger-tol/treeval) (day 3)
<small>
π¨βπ©βπ¦βπ¦: Will Eagles
- Updated longread_coverage workflow with all modules now included.
- Began conversion of hic_mapping snakemake workflow into nf-core.
</small>
---
# [ensembl genome_prepare pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16) (day 3)
π§: [#16](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16)
π¨βπ©βπ¦βπ¦: Disha Lodha, Jorge Alvarez, Lahcen Campbell
- π Understand the Ensembl \BRC4 genome prepare pipeline
- 80% of the modules of the pipeline completed!
- βοΈ Test genome.json channel handling, downloading genomic data
---
# [COSMIC CMC pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/8#issuecomment-1488831043) (day 3)
<small>
π¨βπ©βπ¦βπ¦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Helen
π§: - More improvement on the Docker container, progress on the singularity container. Investigation integration with Nextflow
- part of Clinvar part of pipeline done in Nextflow, Nextflow can submit some of the processes as LSF jobs.
- Setup of Nexflow Tower almost done
- Part of DN/DS part of the pipeline created in Nextflow
- part of VEP part of the pipeline created in Nexflow, running with LSF for one chromosome. converting a wrapper script into nextflow code.
</small>
---
# Summary
- 42 team members (at least)
- 25 pipelines worked on (19, 20, 22)
- 2 new pipelines started
- 3 non nf-core pipelines
- 2 releases (quantms, rnaseq)
- 31 completed issues (6 RfR, 33 in progress)
---
> βgood job guys, letβs do it againβ
\- Friederike Hanssen (March 2023)
<small>
> "its good that I am doing the wrap up and quoting myself"
\- Friederike Hanssen (March 2023)
</small>
<p style="font-size:20%"> β€οΈ from James
</p>
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