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🚀 Pipelines Team 🚀

27th-29th March 2023

The Hackathon March 2023 Project Board
Slack #hackathon-march-2023-pipelines

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@nf-core /
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@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)

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
  • Assign yourself on issues on the project board
  • 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 Åslin (@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 Valtueña (@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)
  • Björn Langer (@bjlang)

Team Members IV

  • Bożena Mika-Gospodorz (@bozmik)
  • Błażej Szczerba (@blazejszczerba)
  • Piotr Faba (@piotr-faba-ardigen)
  • Mauro Saporita (@mauro-saporita)
  • Olha Petryk (@opetryk)
  • Paweł Kościelny (@pkoscielnybio)
  • Paweł Ciurka (@pawelciurkaardigen)
  • Michał 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

Person A Person B
Maxime Rike
James Rike
Lili Sofia
Jasmin Louisa
Person A Person B
Simon Matilda
Danilo Emelie
Jon

Day One

eager (day 1)

Goal: DSL2 conversion!

👨‍👩‍👦‍👦: Selina, Aida, Judi, Merlin, Ian, Thiseas, James

  • ✅ #949 - Selina - Add Falco as FASTQC alternative
  • 👀 #948 - Judi, Thiseas - Add PreSeq
  • 👀 #955 - Judi - Add MTNucRatio
  • 🚧 #952 - James - Multiplexed mapping support

eager (day 1) (cont.)

  • 🚧 #957 - Thiseas - aDNA damage manipulation
  • 🚧 #816 - Thiseas - Update TSVs for eager test-datasets
  • 👀 #954 - Selina - Adding BWA-MEM
  • 🚧 #959 - Selina - Adding Bowtie 2
  • ✅ Aida - Fixed bug in endorspy
  • 👀 #3134 Aida - Updated nf-core/module for endorspy

eager (day 1) (cont. 2)

  • 🚧 #922 - Aida - working on adding endorspy
  • 🚧 #923 - Aida - working on adding Host Removal
  • 🚧 #923 - Merlin - Added bbduk step, working on synchronization with Ian (Princeseq step)
  • 🚧 #923 - Ian - Added prinseqplusplus step, working to finish synchronization for fork in pipeline. opened pull request
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sarek (day 1)

Goal: Fix issues

👨‍👩‍👦‍👦: Friederike, Maxime, Matilda, Susanne

  • 🚧 #950 - Samplesheet validation (Matilda)
  • 🚧 #808 - ControlFREEC ploidy (Rike)
  • 🚧 #702 - Updating bioconda recipe for ascat + creating new mulled container (SusiJo)

proteinfold (day 1)

Goal: Add new software and functionalities!

👨‍👩‍👦‍👦: Athanasios

  • 🚧 #86 - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows

taxprofiler (day 1)

Goal: Issues for 1.1.0

👨‍👩‍👦‍👦: Sofia, Lili, James

  • 🚧 #257- Sofia-Substitute samtools/bam2fq module with samtools/fastq module.
  • 👀 #247- Lili - Add a new module metaphlan/makedb to create a latest metaphlan database.
  • 🚧 #210 - Sofia, James - Add KMCP modules

differentialabundance (day 1)

Goal: Issues for #100, #102 nf-core Hackathon March 2023

👨‍👩‍👦‍👦: Oskar Wacker, Jonathan Manning, Erika

  • #100 - Erika - Add plot differentially expressed genes by Biotype
  • #102 - Oskar - Add multiple sets of gene signatures

pangenome (day 1)

Goal: Reimplement the pangenome pipeline following proper nf-core guidelines.

👨‍👩‍👦‍👦: Simon

  • ✅ Add graph visualization quality control subworkflow using ODGI modules.
  • ✅ Only run WFMASH.
  • 🚧 Parallelize WFMASH across nodes.

DualRNA-Seq (day 1)

Goal: DSL2 conversion!

👨‍👩‍👦‍👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota

  • ✅ #43 - Update Cutadapt process to DSL-2
  • 🚧 #42 - create test dataset for DSL2 pipeline
  • 🚧 #44 - Update tximport_host process from DSL1 process to DSL2 module
  • ✅ #45 - Update salmon index and salmon quantification process from DSL1 process to DSL2 module
  • 🚧 #46 - Create COMBINE_QUANTIFICATION_RESULTS modules

funcscan (day 1)

Goal: Solve all the issues!

👨‍👩‍👦‍👦: Jasmin, Louisa

  • ✅ #247 Update error messages
  • ✅ #244 Add Bakta annotation to CI tests
  • 👀 #173 Update RGI to latest version
  • Cleaned up issues

hgtseq (day 1)

Goal: Bug fixing

👨‍👩‍👦‍👦: Simone

lightsheetrecon (day 1)

Goal: finish the full pipeline workflow using completed subworkflows for running Spark

👨‍👩‍👦‍👦: Konrad

magmap (day 1)

Goal: minimal working pipeline

👨‍👩‍👦‍👦: Danilo, Emelie, Daniel Lundin

  • ✅ Template update
  • ✅ Pre-mapping-processing of reads
  • ✅ Decide approach to add reference

crisprseq (day 1)

Goal: minimal working pipeline

👨‍👩‍👦‍👦: Laurence, Júlia

  • 👀 PR Documentation update
  • 👀 PR Test datasets for a new module
  • 🚧 Add new module (crisprclean-r)

atacseq (day 1)

Goal: metro-map

👨‍👩‍👦‍👦: Björn

  • 👀 PR v2

new pipeline proposal

bamtofastq (day 1)

Goal: DSL2 conversion!

👨‍👩‍👦‍👦: SusiJo, Friederike, matrulda

  • 🚧 Adding tests
  • 👀 Started reviewing (a lot of changed files)

spinningjenny (day 1)

Goal: First draft

👨‍👩‍👦‍👦: Luca

ensembl sequence pipeline (day 1)

👨‍👩‍👦‍👦: Disha Lodha, Zahra Waheed, Ahmad Zyoud

  • 👀 Understand the Ensembl sequence pipeline
  • ✔️ Test the Ensembl sequence pipeline

ensembl genome_prepare pipeline (day 1)

🚧: #16
👨‍👩‍👦‍👦: Disha Lodha, Jorge Alvarez, Lahcen Campbell

  • 👀 Understand the Ensembl \BRC4 genome prepare pipeline
  • Started the migration of the different python modules
  • ✔️ Test initial stages of manifest and json file prep: Ensembl genome prepare pipeline

COSMIC CMC pipeline (day 1)

👨‍👩‍👦‍👦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Balasz, Helen
🚧: - 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 (day 1)

👨‍👩‍👦‍👦: Eerik

  • wrote a script for retrieving full taxonomic lineage for FCS-GX results based on the taxIDs of the FCS-GX results

PhuEgo (day 1)

👨‍👩‍👦‍👦: 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 (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

  • Bug fix release (1.1.1)

👨‍👩‍👦‍👦: 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)

Goal: DSL2 conversion!

👨‍👩‍👦‍👦: Selina, Aida, Judi, Merlin, Ian, Thiseas, James

  • ✅ #954 - Selina - Adding BWA-MEM
  • 🚧 #959 - Selina - Adding Bowtie 2
  • 🚧 #923 Ian creating metagenomics screening local subworkflow
  • 🚧 #957 - Thiseas - aDNA damage manipulation
  • ✅ #948 - Judith - Adding Preseq
  • 🚧 #958 - Judith - Adding MtNucRatio
  • ✅ #3134 Aida - Updated nf-core/module for endorspy
  • 🚧 #961 Aida - Adding endorspy
  • 🚧 #923 - Aida - working on adding Host Removal
  • 🚧 #923 - Merlin - Metagenomics Complexity Subworkflow ready for review

DualRNA-Seq (day 2)

Goal: DSL2 conversion!

👨‍👩‍👦‍👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota

  • ✅ #42 - create test dataset for DSL2 pipeline
  • 🚧 #44 - Update tximport_host process from DSL1 process to DSL2 module
  • ✅ #46 - Create COMBINE_QUANTIFICATION_RESULTS modules
  • 🚧 #48 - A new module to combine the host ambig and unique counts
  • ✅ #53 - Update star indexing and star alignment processes from DSL1 processes to DSL2 modules
  • 🚧 #54 - Update extract_annotations_* to DSL2
  • 🚧 #56 - Update tximport_host process from DSL1 process to DSL2 module
  • 🚧 #57 - Combine host annotations with quantification results
  • ✅ #60 - Update salmon split table process to DSL2
  • ✅ #58 - salmon quantification is not executed for all samplessalmon quantification is not executed for all samples

pangenome (day 2)

👨‍👩‍👦‍👦: Simon

Goal: Reimplement the pangenome pipeline following proper nf-core guidelines.

  • ✅ Optional PAF input starting from SEQWISH.
  • ✅ Parallelize WFMASH across nodes.
  • ✅ Option to skip SMOOTHXG.
  • 🚧 Add VG_DECONSTRUCT as a local module.

viralintegration (day 2)

Goal: Finalize first release and work on enhancements.

👨‍👩‍👦: Alyssa

  • 🚧 #2 - add metaphlan3 module
  • 🚧 #52 - get final review for first release
  • 🚧 #58 - organize into subworkflows

variantcatalogue (night 1?)

Goal: Starting the migration of the variant catalogue pipeline to nf-core

👨‍👩‍👦‍👦: Solenne

  • ✅ Created the mapping suubworkflow
  • ✅ Good progress on the ReADME / CITATIONS.md and other doc
  • 🚧 SNV subworkflow

Magmap (day 2)

Goal: add sourmash subworkflow + add some downstream modules

👨‍👩‍👦‍👦: Emelie, Danilo and Daniel

  • ✅ #11 - Danilo and Emelie - Adding Subworkflow bbmap Index
  • ✅ #5 - Danilo and Emelie - Adding test-database
  • ✅ #12 - Danilo and Emelie - new subworkflow concatenate gff + indexing
  • ✅ #14 - Danilo and Emelie - cleaning output directory
  • ✅ SOURMASH Sketch/gather subworkflow - Danilo and Emelie - Add subworkflow for SOURMASH SKETCH and GATHER
  • ✅ #15 - Danilo and Emelie - add bbmap_align module to the main workflow.

ensembl genome_prepare pipeline (day 2)

🚧: #16
👨‍👩‍👦‍👦: Disha Lodha, Jorge Alvarez, Lahcen Campbell

  • 👀 Understand the Ensembl \BRC4 genome prepare pipeline
  • First modules and backbone pipeline developed
  • ✔️ Test genome.json channel handling, downloading genomic data

sammyseq (day 2)

👨‍👩‍👦‍👦: Margherita

  • ✅ Update template to latest tool version
  • 🚧 Add test data

spinningjenny (day 2)

  • ✅ Embedded the code inside the nf-core template
  • 🚧 Adding the input data to test-dataset (waiting for review)
  • 🚧 Adding the recipe to bioconda (waiting for review)

sarek (day 2)

👨‍👩‍👦‍👦: Friederike, Maxime, Matilda, Michael, Susanne, Alison

  • ✅ #950 Samplesheet validation (Matilda)
  • More samplesheet validation (Michael)
  • 🚧 #808 ControlFREEC ploidy (Rike)
  • 🚧 #702 Updating bioconda recipe for ascat + creating new mulled container (SusiJo) - Help Wanted!
  • 👀 #981 Documentation on how to generate resource files for ASCAT (Alison)

taxprofiler (day 2)

Goal: Continue working on issues for 1.0.0

👨‍👩‍👦‍👦: Sofia, Lili, James

  • ✅ #247- Lili-Add a new module metaphlan/makedb to create a latest metaphlan database.
  • 🚧 #273 Lili- Add a new profiler: MetaPhlAn4.
  • 🚧 #210 - Sofia, James - Add KMCP modules

nanoseq (day 2)

👨‍👩‍👦‍👦: Chris & Yuk Kei

Goal: Move local to nf-core modules and simplify complex mapping

  • 🚧 Good progress moving local to nf-core
  • 🚧 Some progress on mapping

hgtseq (day 2)

Goal: bug fixing

👨‍👩‍👦‍👦: Simone

  • 🚧 #28 - Resolving conflicts to update template
  • 🚧 #30 - New local module

differentialabundance (day 2)

Goal: add-pre differential matrix subsetting, new plot and more input

👨‍👩‍👦‍👦: Jon, Oskar, Erika

  • ✅ #11 - Jon - Update differential module interface, add pre-contrast subsetting options
  • 🚧 Erika - Add biotype plot to report
  • 🚧 Oskar - Enable multiple GTFs for GSEA

proteinfold (day 2)

Goal: Add new software and functionalities!

👨‍👩‍👦‍👦: Athanasios, Leila

  • 🚧 #86 - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows
  • 🚧 85 - Leila - Update ColabFold version

funcscan (day 2)

Goal: Solve new issues!

👨‍👩‍👦‍👦: Jasmin

  • 🚧 #251 PR out: Implement new pyrodigal module into pipeline
  • 🚧 Implement changes of prodigal update

ampliseq (day 2)

👨‍👩‍👦‍👦: Daniel & Daniel

  • ✅ #563 - Renamed DADA2 taxonomic classification files to include the chosen reference taxonomy abbreviation.
  • 🚧 #564 - Added phylogenetic placement.

bamtofastq (day 2)

Goal: DSL2 conversion!

👨‍👩‍👦‍👦: SusiJo, Friederike, matrulda

  • 🚧 Adding tests
  • 👀 Still reviewing the huge PR

PhuEgo (day 2)

👨‍👩‍👦‍👦: Haoqi Chen

  • Modified scripts to have a minimal testable version, for faster testing. Initiate a nf-core pipeline.
  • Prepared testing dataset.

Nextflow-VEP (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

via GIPHY

Summary today:

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    8 New pipelines (without first release)
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    3 non nf-core pipelines
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    10 existing pipelines
    • 2 DSL2 conversion

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New pipelines

via GIPHY

pangenome (day 3)

Goal: Reimplement the pangenome pipeline following proper nf-core guidelines.

👨‍👩‍👦‍👦: Simon

  • ✅ Add VG_DECONSTRUCT as a local module.
  • ✅ Update tests.
  • 🚧 Community subworkflow.
  • 🚧 Squeeze subworkflow.

variantcatalogue (night 2)

Goal: Coding the Variant catalogue pipeline up to nf-core

👨‍👩‍👦‍👦: Solenne

  • ✅ Code ready for review
  • 🚧 Improve documentation

viralintegration (day 3)

Goal: Finalize first release and work on enhancements.

👨‍👩‍👦: Alyssa

  • 🚧 #2 - add metaphlan3 module
  • 👀 #52 - get final review for first release (being reviewed by @keslingmj)
  • 🚧 #58 - organize into subworkflows (done but waiting on first release to open PR for review!)

metapep (day 3)

👨‍👩‍👦‍👦: Till & Sabrina

  • ✅ Unforked nf-core/metapep repository
  • ✅ #56,#61 - Improved documentation about data model
  • ✅ #55 Updated framework of epitopeprediction to epytope 3.3.0
  • ✅ #58 Made various ids deterministic to ensure reproducibility
  • ✅ #62 Updated the nf-core module prodigal to the latest version

spinningjenny (day 3)

We have the first non bionformatics pipeline in nf-core! Models in Economics!

👨‍👩‍👦‍👦: Luca

  • ✅ Added the input data to test-dataset
  • ✅ Written the small test for ci
  • ✅ Transferred the pipeline in nf-core
  • 🚧 Adding the recipe of NetLogo to bioconda (waiting for review)

lightsheetrecon (day 3)

Goal: finish the full pipeline with Spark

👨‍👩‍👦‍👦: Konrad

  • ✅ Completed end-to-end pipeline workflow
  • ✅ Fixed Nextflow bug leaving orphan Spark processes after cancelling pipeline (nextflow#3606)
  • ✅ Wa new #microscopy channel discussing microscopy-related pipelines
  • 🚧 Add tests_full & Add test (with stubs)

bamtofastq (day 3)

Goal: DSL2 conversion & adding to nf-core!

👨‍👩‍👦‍👦: SusiJo, Friederike, matrulda

  • ✅ Transferred to nf-core
  • 🚧 Adding metro map
  • 👀 Reviewing DSL2 conversion

magmap (day 3)

Goal: fix some bugs and add more statistics output

👨‍👩‍👦‍👦:

  • ✅ #17 - Emelie and Danilo - Adding featurecounts and some associated modules
  • ✅ #16 - Danilo, Daniel and Emelie - update readme and bug fix!
  • 🚧 - Emelie and Danilo - Adding more statistics
    output
  • ✅ #22 - Emelie and Danilo - Adding new input index to feed sourmash
  • ✅ Danilo, Emelie and Daniel: minimal working pipeline!
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sammyseq (day3)

👨‍👩‍👦‍👦: Margherita

  • 🚧 #832 Preparing test data following the standards

PhuEgo (day 3)

👨‍👩‍👦‍👦: Haoqi Chen

  • Break apart python codes into individual nextflow process. Overall designed the pipeline.

Nextflow-VEP (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

via GIPHY

ensembl sequence pipeline (day 3)

👨‍👩‍👦‍👦: Disha Lodha, Zahra Waheed, Ahmad Zyoud - 👀 Modified manifest_stats python script to remove internal Ensembl dependencies - 💻 Created a nextflow module and ran a functional nextflow pipeline! 🎉🎉🎉

Aquatic Symbiosis Cobiont Check pipeline (day 2)

👨‍👩‍👦‍👦: 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 (day 3)

👨‍👩‍👦‍👦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Helen
🚧: - 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

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Bug fixes & features for existing pipelines

via GIPHY

DSL2 conversion

DualRNA-Seq (day 3)

Goal: DSL2 conversion!

👨‍👩‍👦‍👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota

  • 🚧 #44 - Update tximport_host process from DSL1 process to DSL2 module
  • 🚧 #48 - A new module to combine the host ambig and unique counts
  • ✅ #54 - Update extract_annotations_* to DSL2
  • ✅ #56 - Create subworkflow to create combined host/path transcriptome file
  • 🚧 #57 - Combine host annotations with quantification results
  • ✅ #62 - Add salmon quantification to salmon_alignment_base subworkflow
  • 🚧 #64 - create a module for generating bacterial transcriptome fasta file
  • 🚧 #66 - Add a module for count_total_reads and count_total_read_pairs processes
  • ✅ #69 - Add module extract processed reads to the pipeline
  • 🚧 #70 - 'Parent' is hard-coded in the replace_attribute_host_genome_gff_star_salmon process
  • 🚧 #73 - rethink check_replicates process for DSL2

Aquatic Symbiosis Cobiont Check pipeline (day 3)

👨‍👩‍👦‍👦: 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)

People: Selina, Aida Judi, Ian, Thiseas, James

  • 👀 #964 - Selina - Adding Bowtie 2
  • 🚧 #3210 - Selina - new angsd contamination subworkflow
  • 👀 - Thiseas - aDNA Damage Manipulation
  • 👀 - Judith - Adding MtNucRatio #958
  • 🚧 - Judith - Starting with DamageProfiler #966
  • 👀 - Ian - Finished initial implementation of metagenomics profiling 967

sarek (day 3)

Goal: Make it more awesome!

👨‍👩‍👦: Friederike, Maxime, Matilda, Michael, Susanne, Alison

  • ✅ #981 Documentation on how to generate resource files for ASCAT (Alison)
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    982 Avoid using exit statements (Rike)
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    #808 ControlFREEC ploidy (Rike)
  • 🚧 #702 Making ASCAT output reproducible: Bioconda recipe for ascat merged ✅, intergration in progress (SusiJo) + new mulled container ✅ + update module - currently testing

viralrecon (day 3)

Goal: Implement & test the freyja subworkflow for wastewater variant analysis within viralrecon

👨‍👩‍👦: Joon

  • 🚧 #299 Implement & test the freyja subworkflow

taxprofiler (day 3)

Goal: Continue working on issues for 1.0.0

👨‍👩‍👦‍👦: Sofia, Lili, James

  • 🚧 #273 Lili- Add a new profiler: MetaPhlAn4.
  • 👀 #210 - Sofia, James - Add KMCP modules
  • 👀 #257- Sofia-Substitute samtools/bam2fq module with samtools/fastq module.

proteinfold (day 3)

Goal: Add new software and functionalities!

👨‍👩‍👦‍👦: Athanasios, Leila

  • 🚧 #86 - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows
  • 🚧 #85 - Leila - Update ColabFold version
  • 🚧 #84 - Leila - Update AlphaFold2 version

ampliseq (day 3)

👨‍👩‍👦‍👦: Daniel & Daniel

  • ✅ #564 - Added phylogenetic placement.
  • 🚧 - Integrate phylogenetic placement into downstream analysis

funcscan (day 3)

👨‍👩‍👦‍👦: Jasmin

  • ✅ #251: Implement new pyrodigal module into pipeline
  • 🚧 #253 ready for review: Implement changes of prodigal update
  • 🚧 #173 Implement RGI update – more database stuff
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  • 🚧 #3217 Compress pyrodigal output files

atacseq (day 3)

👨‍👩‍👦‍👦: Björn

  • 👀 #259 Add support for optional control data

rnaseq (day 3)

👨‍👩‍👦‍👦: Harshil?

Just released nf-core/rnaseq v3.11.0

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treeval (day 3)

👨‍👩‍👦‍👦: Will Eagles

  • Updated longread_coverage workflow with all modules now included.
  • Began conversion of hic_mapping snakemake workflow into nf-core.

ensembl genome_prepare pipeline (day 3)

🚧: #16
👨‍👩‍👦‍👦: Disha Lodha, Jorge Alvarez, Lahcen Campbell

  • 👀 Understand the Ensembl \BRC4 genome prepare pipeline
  • 80% of the modules of the pipeline completed!
  • ✔️ Test genome.json channel handling, downloading genomic data

COSMIC CMC pipeline (day 3)

👨‍👩‍👦‍👦: Thomas, Avirup, Sumodh, Siew-Yit, Manpreet, Ian, Helen
🚧: - 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.

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)

“good job guys, let’s do it again”

- Friederike Hanssen (March 2023)

"its good that I am doing the wrap up and quoting myself"

- Friederike Hanssen (March 2023)

❤️ from James

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