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<a href="https://www.nf-co.re"><img src="https://i.imgur.com/hEDjpCs.png" width="65%"><img></a>
### 🚀 Pipelines Team 🚀
_10th-12th October 2022 - BCN_
This file: [https://hackmd.io/@nf-core/BJ5sszsGj/edit](https://hackmd.io/@nf-core/BJ5sszsGj/edit)
The Hackathon Oct 2022 [Project Board](https://github.com/orgs/nf-core/projects/38/views/10)
[<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 Leads
- Team Leads
- Friederike, James, Maxime, Luis
- Tasks
- Orientating new people
- Progress update reminders
- Presenting progress updates
---
# Tasks Ideas: Devs
- General development work
- DSL2 transition
- Bug fixes/functionality extensions
- New pipelines
- Buddy system!
- Buddy with someone for rapid reciprocal PR reviews!
- See table!
---
# Tasks Ideas: Volunteers
- Ask existing devs
- Help with bug fixes (review issues)
- Help with implementing new functionality
- Help with reviews
---
# Remember
- Add yourself to Team Members slide
- Assign yourself on issues on the [project board](https://github.com/orgs/nf-core/projects/38/views/10)
- Post your progress here **daily**! One slide per pipeline
- Sign up for a reviewing buddy (see slide)!
---
# Reviewing Buddy List
| Person A | Person B |
|----------|----------|
| Maxime | Rike |
| James | Rike |
| Alex | Rob |
| Luis | Hanka |
| Alison | Oliver |
| Aaron | Luis |
---
# Pipelines - Part I
- [eager](https://github.com/nf-core/eager)
- [sarek](https://github.com/nf-core/sarek)
- [liverctanalysis](https://github.com/nf-core/liverctanalysis)
- [funcscan](https://github.com/nf-core/funcscan)
- [airrflow](https://github.com/nf-core/airrflow)
- [smrnaseq](https://github.com/nf-core/smrnaseq)
- [tautyping](https://github.com/hseabolt/tautyping-nf)
- [hgtseq](https://github.com/nf-core/hgtseq)
---
# Pipelines - Part II
- [proteinfold](https://github.com/nf-core/proteinfold)
- [taxprofiler](https://github.com/nf-core/taxprofiler)
- [differentialabundance (currently rnadeseq)](https://github.com/qbic-pipelines/rnadeseq)
- [viralintegration](https://github.com/nf-osi/viralintegration)
- [nascent](https://github.com/nf-core/nascent)
---
# Team Members I
* 👩🏽💻 [James Fellows Yates](https://github.com/jfy133) (eager, funcscan, taxprofiler)
* 👩🏽💻 [Friederike Hanssen](https://github.com/FriederikeHanssen) (sarek)
* 💻 [Luis Kuhn](https://github.com/luiskuhn) (liverctanalysis)
* 🤖 [Maxime Garcia](https://github.com/maxulysse) (sarek)
* 👾 [Jasmin Frangenberg](https://github.com/jasmezz) (funcscan)
* 👩🏽💻 [Sofia Stamouli](https://github.com/sofstam) (taxprofiler)
* [Alison Meynert](https://github.com/ameynert) (scrnaseq)
* 👩🏽💻 [Susanne Jodoin](https://github.com/SusiJo) (sarek)
* 🤖 [Alexander Peltzer](https://github.com/apeltzer) (smrnaseq, scrnaseq)
---
# Team Members II
* 👩🏽💻 [Anders Sune Pedersen](https://github.com/asp8200) (sarek)
* 👩🏽💻 [Konrad Rokicki](https://github.com/krokicki/) (lightsheetrecon)
* 👩🏽💻 [Vladimir Mikryukov](https://github.com/vmikk/) (taxprofiler)
* [Joshua Forstedt](https://github.com/jforstedt) (tautyping)
* [Hunter Seabolt](https://github.com/hseabolt) (tautyping)
* [Arun Boddapati](https://github.com/arunbodd) (tautyping)
* [Sam Rusher](https://github.com/srusher) (tautyping)
* [Hanka Medová](https://github.com/medulka)
* [Simone Carpanzano](https://github.com/carpanz) (hgtseq)
---
# Team Members III
* [Wei-An Chen](https://github.com/Vivian-chen16) (scrnaseq)
* [Oliver Gibson](https://github.com/ogibson) (scrnaseq)
* [Jack Tierney](https://github.com/JackCurragh) (eager)
* 👩🏽💻 [Athanasios Baltzis](https://github.com/athbaltzis) (proteinfold)
* [Leila Mansouri](https://github.com/l-mansouri) (proteinfold)
* [Rob Syme](https://github.com/robsyme) (smrnaseq)
* [Susanna Marquez](https://github.com/ssnn-airr) (airrflow)
* [Saba Nafees](https://github.com/snafees) (airrflow)
* [Oskar Wacker](https://github.com/WackerO) (differentialabundance)
---
# Team Members IV
* [Alyssa Briggs](https://github.com/alyssa-ab) (viralintegration)
* [Aaron Riedling](https://github.com/) (liverctanalysis)
* [Edmund Miller](https://github.com/emiller88)
---
# Day Three
---
## Stats
---
## Stats(ish)
- Team members: 30
- Pipelines worked on: 16
- Brand new pipelines: 5
- PRs (merged or opened):
- Day 1: ~21
- Day 2: ~23
- Day 3: ~22
---
## Brand new pipelines
---
## New pipelines
- differentialabundance
- lightsheetrecon
- sammyseq
- tautyping
- viralintegration
---
## differentialabundance
_Pipeline for differential expression analysis (and pathway analysis?) of RNASeq data_
Oskar
- Modified the workflow diagram
- Started with the actual pipeline creation, now trying out Jonathan's module
- repository is now created
---
## lightsheetrecon
_Pipeline for lightsheet microscopy image reconstruction with Spark-based image stitching_
- Added subworkflows for transient Spark clusters and image stitching
- (in progress) Working on adjusting parameters to use nf-core conventions
---
## sammyseq
_Pipeline to analyze 'Sequential Analysis of MacroMolecules accessibilitY sequencing data'_
- [Margherita] (in progress) installing the first module and drafting initial workflow
---
## tautyping
_Identification of genes/genomic segments with genome-wide phylogenetic signal of an organism using the Kendall Tau rank correlation statistic._
- [Hunter, Arun, Josh, Sam] Currently working on finishing initial workflow described in workflow diagram and reference from this [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8105021/)
- ⏺️ Bug fix for input params
- ⏺️ Open Issues for remaining modulesa and subworkflow development
---
## viralintegration
_Finds viral integration sites within the human genome. Currently based on ctat-VIF using STAR alignment._
- [Alyssa] Planning fix for ExtractChimericGenomicTargets module not passing fasta index files [#33](https://github.com/nf-osi/viralintegration/issues/33) (still WIP)
- [Alyssa] Planning changes for wiki documentation
---
## DSL2 conversion
---
## eager
_Pipeline for best-practise genomic and metagenomic analyses of ancient DNA data_
* [Jack] Samtools/calmd module PR [#2254](https://github.com/nf-core/modules/pull/2254)
---
# Development
---
## sarek
_Germline & somatic variantcalling pipeline_
* [Rike] :trophy: Won the PR race with Maxime, Fix small issues (publishing, ...)
* [Susanne] Implementing msisensor2 for tumoronly + ✅ fixed typo in msisensor2 PR [#2268](https://github.com/nf-core/modules/pull/2268)
* [Anders] Concatenating vcfs [#792](https://github.com/nf-core/sarek/pull/792)
---
## liverctanalysis
_Quantitative image analysis of abdominal CT scans from hepatocellular carcinoma patients, using deterministic deep-learning_
- [Aaron] Reading DICOM input functionality ([#10](https://github.com/nf-core/liverctanalysis/pull/10))
- [Luis] Template sync ([#10](https://github.com/nf-core/liverctanalysis/pull/10))
- [Aaron, Luis] Disscussion on general pipline structure/next steps, and to-do lists
- [Hanka] Review of PR with integrated functionality
---
## funcscan
_Screening for antimicrobial resistance genes, antimicrobial peptides and biosynthetic gene clusters_
Getting ready for first release!
---
## funcscan
_Screening for antimicrobial resistance genes, antimicrobial peptides and biosynthetic gene clusters_
- [Jasmin] ⏺️ Only [#64](https://github.com/nf-core/funcscan/issues/64) Summarizing BGC workflow (module comBGC) needs to be completed!
- [Anan] ✅ PR [#140](https://github.com/nf-core/funcscan/pull/140) Adding GBK format to prodigal + cleaning up its results channels.
- [Louisa, Anan, Jasmin] ⏺️ Aaaalmost having AMPcombi in! Summarizing AMP workflow.
---
## smrnaseq
_miRNA / smRNA seq analysis pipeline_
- ✅ [#195](https://github.com/nf-core/smrnaseq/pull/195) - FastA known adapter sequence file added to improve auto-detection of adapters even further (Rob + Alex)
- Lots of testing with real data on that (~2500 samples)
---
## taxprofiler
_Parallelised taxonomic profiling across multiple classifiers/databases for shotgun metagenomics_
- [Vladimir] started new modules `taxonomy annotate` and `taxonomy metagenome`
- [Sofia] ✅ Started working on documentation [README.md](https://github.com/genomic-medicine-sweden/taxprofiler/edit/dev/README.md)
- [Sofia] Started to update [usage.md](https://github.com/nf-core/taxprofiler/blob/dev/docs/usage.md) to include database creation tutorials
- [James, Moritz, Sofia] Discussion to include falco as an alternative to FastQC [#144](https://github.com/nf-core/taxprofiler/issues/144)
---
## scrnaseq
_A single-cell RNAseq pipeline for 10X genomics data_
- [Pol/Kristian] Merged [#163](https://github.com/nf-core/scrnaseq/pull/163) to autocancel previous tests when pushing new changes.
- [Pol/Kristian] Pushed [#160](https://github.com/nf-core/scrnaseq/pull/160) which adds 10x counts as output format. Makes scflow compatible with scrnaseq ([#66](https://github.com/nf-core/scrnaseq/issues/66)) and solves [#159](https://github.com/nf-core/scrnaseq/issues/159).
- PR for adding expected cells and sequencing centre created, waiting for final tests [#150](https://github.com/nf-core/scrnaseq/pull/150)
---
## hgtseq
_Pipeline built to investigate horizontal gene transfer from NGS data._
- Closed [#14](https://github.com/nf-core/hgtseq/pull/14) and [#15](https://github.com/nf-core/hgtseq/pull/15), updated pipeline documentation
- Preparing the PR to master (work in progress)
---
## proteinfold
_Pipeline for protein structure prediction_
- Preparing the PRs for the following issues:
[Athanasios] #37 - Bug fix when manually providing the AlphaFold2 or ColabFold databases and params
[Leila] #24 - Add module version reporting
[Leila] #36 - CRG institutional config file
---
## airrflow
_Pipeline for b & t cell sequence analysis_
- debugging issues with mulled containers
---
## nascent
_Pipeline for nascent transcript identification analysis_
- [Merged PINTS support for TSS identification](https://github.com/nf-core/nascent/pull/58)
---
_fin_
---
# Day Two
---
# New pipelines
- differentialabundance
- lightsheetrecon
- sammyseq
- tautyping
- viralintegration
---
## differentialabundance
_Pipeline for differential expression analysis (and pathway analysis?) of RNASeq data_
- [Oskar] Working on a draft of the workflow diagram on paper -->now digitizing it in [hackmd](https://hackmd.io/pZlsU-u2RT-bgvZG0olXEQ?view)
---
## lightsheetrecon
_Pipeline for lightsheet microscopy image reconstruction with Spark-based image stitching_
- [Konrad] Created a [new pipeline](https://github.com/krokicki/nf-core-lightsheetrecon) from the template using nf-core tools
- [Konrad] Finished creating some local Biocontainers for Spark modules
- [Konrad] Working on subworkflows for Spark
---
## sammyseq
*Pipeline to analyze Sequential Analysis of MacroMolecules accessibilitY sequencing data*
- [Margherita] Created the [new pipeline repository](https://github.com/daisymut/sammyseq) from the template using `nf-core create`
- Writing down the workflow of the existing bash pipeline to design the module implementation
---
## tautyping
*Identification of genes/genomic segments with genome-wide phylogenetic signal of an organism using the Kendall Tau rank correlation statistic.*
- [Hunter, Arun, Josh, Sam] Currently working on finishing initial workflow described in workflow diagram and reference from this [paper](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8105021/)
- TODO: Bug fix for input params, update config files
---
## viralintegration
_Finds viral integration sites within the human genome. Currently based on ctat-VIF using STAR alignment._
- [Alyssa] Currently finishing up building the initial workflow referenced from [ctat-VIF](https://github.com/broadinstitute/CTAT-VirusIntegrationFinder/wiki)
- [Alyssa] Work on bug fix for ExtractChimericGenomicTargets module not passing fasta index files [#33](https://github.com/nf-osi/viralintegration/issues/33)
---
# DSL2 conversion
---
## eager
_Pipeline for best-practise genomic and metagenomic analyses of ancient DNA data_
- ⏺️ [James] Started adding fastp/adapterremoval (i.e., copy-pasting from taxprofiler, yay for past-James!)
- ⏺️ [Jack] Samtools calmd module [PR #2254](https://github.com/nf-core/modules/pull/2254)
---
# Development
---
## sarek
_Germline & somatic variantcalling pipeline_
- ✅ [Susanne] Update docu`bcftools stats` [PR #788](https://github.com/nf-core/sarek/pull/788)
- ✅ [Susanne] Fixed tests for mutect2 [PR #790](https://github.com/nf-core/sarek/pulls)
- ⏺️ [Anders] Merge vcfs of different callers (https://github.com/nf-core/sarek/issues/738)
- ⏺️ [Rike] Make MD return CRAM directly
- ⏺️ [Maxime] Update all subworkflows with new nf-core/subworkflows naming scheme and refactor everything
---
## liverctanalysis
_Quantitative image analysis of abdominal CT scans from hepatocellular carcinoma patients using deterministic deep-learning_
- [Aaron] Work on functionality to read DICOM input (PR)
- [Luis] Initial transfer of working codebase, and rough clean-up ([PR #10](https://github.com/nf-core/liverctanalysis/pull/10))
- [Aaron, Luis] Work on tomogram/label re-stacking tool
---
## funcscan
_Screening for antimicrobial resistance genes, antimicrobial peptides and biosynthetic gene clusters_
- [Jasmin] ⏺️ More work on [#64](https://github.com/nf-core/funcscan/issues/64) (Add BGC summary table)
- [Louisa] ✅ Add test data to the funcscan repo (for upcoming module AMPcombi 🙌)
---
## smrnaseq
_miRNA / smRNA seq analysis pipeline_
- [Rob/Alex] ✅ - [#188](https://github.com/nf-core/smrnaseq/pull/188) - Merged the FASTP adapter detection & handling
- [Rob] ✅ - [#193](https://github.com/nf-core/smrnaseq/pull/193) - More flexible samplesheet handling
- [Rob/Alex] ⏺️ - [#192](https://github.com/nf-core/smrnaseq/pull/192) - Debugging smaller issues to prepare for 2.1.0 release
- [Rob/Alex] ⏺️ - [#194](https://github.com/nf-core/smrnaseq/issues/194) - Working on support for default miRNA adapters to be checked in fastp
---
## taxprofiler
_Parallelised taxonomic profiling across multiple classifiers/databases for shotgun metagenomics_
- [James] ✅ Fix KrakenUniq bioconda recipe
- [Sofia] ⏺️ Started working on documentation [README.md](https://github.com/genomic-medicine-sweden/taxprofiler/edit/dev/README.md)
- [Sofia] ✅ Add kaiju to taxpasta [#26](https://github.com/taxprofiler/taxpasta/pull/26)
- [James] ✅ [#140](https://github.com/nf-core/taxprofiler/issues/140) Removed a patch for minimap2 module
- [Vladimir] ⏺️ [#2250](https://github.com/nf-core/modules/pull/2250) Prepared `sourmash/gather` module
---
## scrnaseq I
_A single-cell RNAseq pipeline for 10X genomics data_
- [Alison] [#150](https://github.com/nf-core/scrnaseq/issues/150) Adding expected cell count and sequencing centre optional parameter columns to samplesheet.csv
<!-- - Related PR in test-datasets - add new columns to samplesheet for tests (https://github.com/nf-core/test-datasets/pull/642)
- Closed related PR in modules - add expected cell parameter to cellranger/counts (https://github.com/nf-core/modules/pull/2251)-->
- [Oliver] ⏺️ implement tests with pytest-workflow ([#91](https://github.com/nf-core/scrnaseq/issues/91))
- [Pol/Kristian] ⏺️ add annotations to exported matrix files ([#159](https://github.com/nf-core/scrnaseq/issues/159))
- [Vivian] ✅ [#134](https://github.com/nf-core/scrnaseq/issues/134), has been fixed in v2.1.0
---
## scrnaseq II
_A single-cell RNAseq pipeline for 10X genomics data_
- [Oliver/Alex] ✅ [#137](https://github.com/nf-core/scrnaseq/issues/137), single nuclei already supported with Kallisto.
- [Oliver/Alex] ✅ [#116](https://github.com/nf-core/scrnaseq/issues/116), issue resolved.
---
## hgtseq
_Pipeline built to investigate horizontal gene transfer from NGS data._
- [Simone] Closed [#12](https://github.com/nf-core/hgtseq/pull/12), introduced taxID param and bamtools/stats module
- [Simone] Closed [#13](https://github.com/nf-core/hgtseq/pull/13), small changes to Documentation
- [Simone] Now working on R local module
---
## proteinfold
_Pipeline for protein structure prediction_
- [Athanasios] Reviewed [#34](https://github.com/nf-core/proteinfold/pull/34) - Update and reconstruct modules
- Preparing the PRs for the following issues:
- [Athanasios] [#37](https://github.com/nf-core/proteinfold/issues/37) - Bug fix when manually providing the AlphaFold2 or ColabFold databases and params
- [Leila] [#24](https://github.com/nf-core/proteinfold/issues/24) - Add module version reporting
---
## airrflow
_Pipeline for b & t cell sequence analysis_
Susanna, Saba, Gisela
- [Saba/Gisela] Working on adding nf-core module presto/filterseq [PR](https://github.com/nf-core/modules/pull/2231) & getting tests to pass (waiting on GH CI)
- working on mulled containers
---
# Day One
---
## eager
James, Jack
- [#778](https://github.com/nf-core/eager/issues/778) Convert to DSL2 😱
- ✅ reference indexing (single reference)
- reference indexing (multiple references)
- SAMTOOLS/CALM module
---
## sarek
Rike, Maxime, Susanne, Anders,
- WIP: [#2159](https://github.com/nf-core/modules/issues/2159) Make subworkflows
- WIP: [#738](https://github.com/nf-core/modules/issues/738) Merge vcf-files (Anders)
- Make AWS full size tests smoother:
- ✔️ [#777](https://github.com/nf-core/sarek/pull/777) : Fix full size AWS tests output path names (Rike)
- [#782](https://github.com/nf-core/sarek/pull/782) Reduce scatter/gather on AWS (Rike)
- [#783](https://github.com/nf-core/sarek/pull/783) Add chromosome length file for controlfreec to work out out-of-the-box (Rike)
- WIP: Fix BCFTools stats empty depth plot that includes a fix to MultiQC first (Susanne):
- ✔️ [#1777](https://github.com/ewels/MultiQC/pull/1777) Add PR to MultiQC
- WIP: [#784](https://github.com/nf-core/sarek/pull/784) Rename all subworkflows
---
## liverctanalysis
Luis, Aaron
- Review of pipline and modules
- Prepared clean-up PR
- Work on tomogram re-stacking tool
---
## funcscan
Anan, Louisa, Jasmin
- [#64](https://github.com/nf-core/funcscan/issues/64) Add BGC summary table
- AMPcombi: get docker + singularity images online
---
## smrnaseq
Alex, Rob
- [#188](https://github.com/nf-core/smrnaseq/pull/188) Add FASTP + Adapter Detection mode to pipeline (@robsyme / @apeltzer) - big size tests are running (2x 488 samples)
- ✔️ [#189](https://github.com/nf-core/smrnaseq/pull/189) Merge Template 2.6. to smrnaseq (@apeltzer, @3FgPhTJKS2mcFD0gPp8UiA)
- ✔️ [#190](https://github.com/nf-core/smrnaseq/pull/190) Document PE behaviour properly (@robsyme)
---
## taxprofiler
Sofia, James, Vladimir
- [#26](https://github.com/taxprofiler/taxpasta/pull/26) Add kaiju profiler in taxpasta
- [#21](https://github.com/taxprofiler/taxpasta/pull/21) Add metaphlan3 profiler in taxpasta
- [#18](https://github.com/nf-core/taxprofiler/issues/18) Write documentation
- Tried (and failed) fixing KrakenUniq bioconda recipe (with @RobertPetitIII)
- Tried (and failed for today) adding CLARK-S (issue [#122](https://github.com/nf-core/taxprofiler/issues/122))
- Discussed metaxa2 inclusion (issue [#139](https://github.com/nf-core/taxprofiler/issues/139))
---
## scrnaseq
Alison, Alex, Wei-An, Oliver
- issue cleanup (issues fixed in merged PRs)
- [#86](https://github.com/nf-core/scrnaseq/issues/86) iGenomes
- [#119](https://github.com/nf-core/scrnaseq/issues/119) Invalid segment with kallisto aligner
- [#150](https://github.com/nf-core/scrnaseq/issues/150) Adding expected cell count and sequencing centre optional parameter columns to samplesheet.csv
---
## tautyping
Joshua, Hunter, Arun, Sam
- new pipeline developement
- Under discussion on #new-pipe
- De novo assembly portion under construction
---
## hgtseq
Simone
- trying to fix linting issue with Julia Mir and Francesco Lescai, not finished yet
- next step: prepare first release
---
## proteinfold
Athanasios, Leila
- bug fixes and enhancements
- [#37](https://github.com/nf-core/proteinfold/issues/37) - Bug fix when manually providing the AlphaFold2 databases and params
- [#24](https://github.com/nf-core/proteinfold/issues/24) - Add module version reporting
---
# airrflow
Susanna, Saba, Gisela
- Upgrade conda versions: [#188](https://github.com/nf-core/airrflow/issues/188) @ssnn
- Working on fixing docker profile to run on M1 chips @snafees
- Working on structuring code using subworkflows @Nh3_dlomTSazslbF_cWJJg
---
## differentialabundance
(currently rnadeseq)
Oskar, Gisela
- meeting with Oskar Wacker Gisela Gabernet, Alex Peltzer and Jonathan Manning to discuss
----
- rnadeseq will be ported to nf-core (i.e. a new pipeline will be created, current plan is to rename it to differentialabundance)
- will use [Jonathan's module](https://github.com/nf-core/modules/pull/2167) as core for DESeq2 analysis, some changes might be necessary
- WIP/plans are documented [here](https://hackmd.io/pZlsU-u2RT-bgvZG0olXEQ?view)
---
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