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# 🚀 Pipeline Progress 🚀
_27th-29th October 2021_
<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
---
# Pipeline Team
- Write modules
- Convert DSL1 to DSL2 template
---
# Team Members
- The Golden Delicious:
- Susanne Jodoin
- Jasmin Frangenberg
- Jun-Hoe Lee
- Gokce Oguz
- Laurence Kuhlburger
- Jonas Scheid
- Daniel Straub
- Gisela Gabernet
- The Pigeon Apples:
- Adam Taylor
- Lasse Folkersen
- Ilya Pletenev
- Gwenna Breton
- Sima Rahimi
- Maxime Garcia
- Encore:
- Christina Vasilopoulou
- Mei Wu
- Yuk Kei Wan
- Antonia Schuster
- Matthias Zepper
- Fyan:
- Emelie Nillsson
- Nicolas Rapin
- Adaikalavan Ramasamy
- Zhaowei Yang
- Francesco Lescai
- Spartans:
- Edmund Miller
- Bernardo Aguzzoli Heberle
- Bruno Grande
- Krishna Choudhary
- Saba Nafees
- Pippin
- Friederike Hanssen
- Dale Bridges
- Simeon Hebrew
- Jitao David Zhang
- Bhargava Reddy Morampalli
- Ashmead's Kernel
- James Fellows Yates
- Anan Ibrahim
- Alexandre Gilardet
- Louisa Perelo
- Ephifania Geza
- Ian Light
- Lobo
- Robert Petit
- Sateesh Peri
- Michael Cipriano
---
# EAGER - Achievements
[TODOs](https://github.com/orgs/nf-core/projects/20)
**Day Three**
- James: did a couple of reviews
- Anan: going through the review of MapDamage2
- Alex: 🆘 [Issue with conda-build](https://nfcore.slack.com/archives/CJRH30T6V/p1635510115305100): " Placeholder of length '80' too short in package"
- Louisa: completed `mtnucratio`! [#840](https://github.com/nf-core/modules/issues/849)
- Ian:
- waiting for krakenuniq biocontainer update,
- 90% done with MultiVCFAnalyzer tests
- need GATK 3.5 unified genotyper [#844](https://github.com/nf-core/modules/issues/844), but conda issue picking up old version!?
- Ephie: continued adapteremovalfixprefix
**Day Two**
- James: Completed DeDup [#840](https://github.com/nf-core/modules/issues/840), did some reviews (for mag)
- Alex G: PMDTools Module ready for review! [#847](https://github.com/nf-core/modules/issues/847)
- Louisa:
- Completed samtools/depth [#850](https://github.com/nf-core/modules/issues/850)
- Started mtnucratio [#840](https://github.com/nf-core/modules/issues/849)
- Ian: fighting (the) kraken(uniq) module [#911](https://github.com/nf-core/modules/issues/911)
- Anan: continued mapDamage2 (fixed unknown meta error: nextflow doesn't like numbers in channel names!)
- Alex P: started work on circular mapper [#842](https://github.com/nf-core/modules/issues/842)
**Day One**
- James: got DeDup module for review [#840](https://github.com/nf-core/modules/issues/840)
- Anan: Halfway through mapDamage module [#854](https://github.com/nf-core/modules/issues/854)
- Alex: working on PMDtools module [#847](https://github.com/nf-core/modules/issues/847)
- Louisa: Almost finished samtools/depth [#850](https://github.com/nf-core/modules/issues/850)
- Ephie: started adapterremovalfixprefix module [#837](https://github.com/nf-core/modules/issues/837)
- Ian: mostly done with krakenuniq module [#911](https://github.com/nf-core/modules/issues/911)
---
# mag/bacass - Achievements
[TODOs](https://github.com/orgs/nf-core/projects/20)
**Day One**
- Maxime: Metabat2 module [#875](https://github.com/nf-core/modules/pull/875), and CMSeq/polymut module [#918](https://github.com/nf-core/modules/pull/918)
- James: Maxbin2 module [#895](https://github.com/nf-core/modules/pull/895)
- Golden Delicious team: Porechop module [#914](https://github.com/nf-core/modules/pull/914)
- Encore: Nanopolish module [#917](https://github.com/nf-core/modules/pull/917)
- Daniel: Filtlong module [#919](https://github.com/nf-core/modules/pull/919)
- Mjakobs: Krona module [#928](https://github.com/nf-core/modules/pull/928)
- Fyle, Racon, Prodigal modules are worked on
**Day Two**
- Antonia: Add prodigal module to nf-core/mag [#240](https://github.com/nf-core/mag/pull/240)
- Andries van Tonder: Hopefully fixed test-data issues for miniasm [#825](https://github.com/nf-core/modules/issues/825) and racon [#949](https://github.com/nf-core/modules/pull/949). PRs submitted for both modules awaiting review
- Júlia Mir Pedrol: Fighting with test-data for flye [#830](https://github.com/nf-core/modules/issues/830)
- Encore: Optimising Nanopolish module [#917](https://github.com/nf-core/modules/pull/917)
- Mjakobs: Finishing up Krona module [#928](https://github.com/nf-core/modules/pull/928)
- Daniel: Update ampliseq full test sample sheet [#375](https://github.com/nf-core/test-datasets/pull/375), update summary figure [#342](https://github.com/nf-core/ampliseq/pull/342), prep release [#343](https://github.com/nf-core/ampliseq/pull/343), 2.1.1 release PR [#344](https://github.com/nf-core/ampliseq/pull/344), nf-core/ampliseq release 2.1.1
**Day Three**
- Júlia Mir Pedrol: Finishing Flye PR [#982](https://github.com/nf-core/modules/pull/982)
- Maria Jakobs: Krona module finished [#928](https://github.com/nf-core/modules/pull/928), Krona_db module PR [#995](https://github.com/nf-core/modules/pull/995)
- Antonia: Finished prodigal module addition to nf-core/mag [#240](https://github.com/nf-core/mag/pull/240), added --skip_prodigal [#241](https://github.com/nf-core/mag/pull/241), adding Prokka module to mag
- Andries van Tonder: Final changes to PRs for modules miniasm [#962](https://github.com/nf-core/modules/pull/962), Racon module finished [#949](https://github.com/nf-core/modules/pull/949), Medaka module finished [#992](https://github.com/nf-core/modules/pull/992)
- Daniel: After-release PR to bump version for ampliseq [#345](https://github.com/nf-core/ampliseq/pull/345), update preprint info in mag [#244](https://github.com/nf-core/mag/pull/244)
---
# sarek - Achievements
[TODOs](https://github.com/nf-core/modules/milestone/2)
**Day One**
- The Pigeon Apples: Manta [#906](https://github.com/nf-core/modules/issues/906)
- Francesco: FGBIO/FastqToBam [#916](https://github.com/nf-core/modules/issues/916)
- The Pippin Apples: Manta Somatic [#912](https://github.com/nf-core/modules/issues/912)
- Rike: Strelka BP module [#913](https://github.com/nf-core/modules/issues/913)
**Day Two**
- Francesco: FGBIO/GroupReadsByUMI [#952](https://github.com/nf-core/modules/issues/952)
- Francesco: samblaster [#954](https://github.com/nf-core/modules/issues/954)
- Francesco: samtools/bam2fq [#958](https://github.com/nf-core/modules/issues/958) (check needed on failing yaml tests)
- Rike: Close sarek [#429](https://github.com/nf-core/sarek/issues/429): Allow to skip BQSR
- Rike: GATK4/EstimateLibaryComplexity [#910](https://github.com/nf-core/modules/issues/910)
- Discussion: Human Test data workarounds for mutect2 and downstream tools
(Gavin,Harshil,Maxime,Jose,Rike)
**Day Three**
- Rike: Update a bunch of nf-core/modules to also handle CRAM [#976](https://github.com/nf-core/modules/issues/976):
- Samtools/{view/merge/stats}
- GATK4/{ApplyBQSR,BasequalityRecalibrator,HaplotypeCaller}
- Manta & Strelka (rename: bam -> input)
- Gavin: Updated mutect2:
- mutect2 now has a dedicated mitochondria mode, which will also help with rare diseases
- updated tests to confirm cram inputs work
- changed tumor_normal test to increase sensitivity as a workaround to current human test data issue
- Rike: Update freebayes/germline and add freebayes/somatic [#990](https://github.com/nf-core/modules/issues/990)
- Francesco:
- fixed samblaster names convension (thanks Harshil) [#954](https://github.com/nf-core/modules/issues/954)
- testing simulator for sarek test data, aimed at fixing issues for tumor/normal, mutect single sample and other modules (so far, promising )
- Maxime: Trying to update modules and versions in Sarek [#440](https://github.com/nf-core/sarek/pull/440)
- Gavin: updated createsomaticpanelofnormals with new streamlined test.
- just waiting on test to finish and merge.
- Gavin: New module genomicsdbimport almost added.
- just need to fix test.yml due to review changes.
- Gavin: Started work on create somatic panel of normals subworkflow:
- will be developed in nf-core modules then ported to sareks subworkflow/nf-core when finished.
- This should make it easier to keep modules up to date until finished.
---
# scRNASeq - Achievements
[TODOs](https://github.com/orgs/nf-core/projects/20)
**Day One**
- @ggabernet: Added cellranger mkref module [#894](https://github.com/nf-core/modules/issues/894)
**Day Two**
- @ggabernet: finally merged cellranger module
- @ggabernet: working on template update for scRNAseq
- @emiller: `cellranger count` and `cellranger mkgtf` [#979](https://github.com/nf-core/modules/pull/979)
**Day Three**
- @emiller: Started spaceranger modules [#994](https://github.com/nf-core/modules/pull/994)
- @ggabernet: Template update and PR [#73](https://github.com/nf-core/scrnaseq/pull/73)
---
# cageseq - Achievements
**Day One**
- @mashehu+group: added paraclu module to nf-core/modules :sleuth_or_spy: [#903](https://github.com/nf-core/modules/issues/903)
**Day Two**
- <Person>: <Achievement> <#Issue>
**Day Three**
- <Person>: <Achievement> <#Issue>
---
# atacseq - Achievements
**Day One**
- Ilya Pletenev: working on ataqv module [#904](https://github.com/nf-core/modules/issues/904)
**Day Two**
- <Person>: <Achievement> <#Issue>
**Day Three**
- Ilya Pletenev: finished main file of ataqv module [#904](https://github.com/nf-core/modules/issues/904). Now writing tests.
---
# chipseq - Achievements
**Day One**
- Jose Espinosa: Added missing mulled container to biocontainers (waiting for approval).
- Jose Espinosa, Harshil Patel: Migration of the current DSL1 released implementation to DSL2.
**Day Two**
- Jose Espinosa, Harshil Patel: Draft implementation of the `idr` module (`peakFiles` added to test-datasets).
**Day Three**
- Refactor `genrich` module, getting rid of `params`
- Add IDR to the pipeline (pending)
- Implement `params.aligner` in the pipeline (pending):
- Implement `bowtie2` as aligner (module ready)
- Implement `CHROMAP` as aligner (module ready)
---
# epitopeprediction - Achievements
**Day One**
- Distribution of the tasks:
- Initation of converting the `params.input` to a sheet [#102](https://github.com/nf-core/epitopeprediction/issues/102)
- Started with the template conversion [#100](https://github.com/nf-core/epitopeprediction/issues/100)
- Started with conversion local module - check_requested_models [#92](https://github.com/nf-core/epitopeprediction/issues/92)
- Started with conversion local modules - csvtk_split and snpsift_split [#93](https://github.com/nf-core/epitopeprediction/issues/93)
- Started with conversion local module - get_peptides [#94](https://github.com/nf-core/epitopeprediction/issues/94)
- Started creating a nfcore module - csvtk_split [#105](https://github.com/nf-core/epitopeprediction/issues/105)
**Day Two**
- Updating the template, PR has been accepted [#100](https://github.com/nf-core/epitopeprediction/issues/100)
- Worked on the cvstk split module [#105](https://github.com/nf-core/epitopeprediction/issues/105)
- Added sample sheets to the test datasets [#103](https://github.com/nf-core/epitopeprediction/issues/103)
- Updated the BioContainers/multi-package-containers > waiting on mulled container [#91](https://github.com/nf-core/epitopeprediction/issues/91)
- Adjusting the sample sheet validation and beloning scripts [#102](https://github.com/nf-core/epitopeprediction/issues/102)
- Started creating local module - peptidePrediction [#96](https://github.com/nf-core/epitopeprediction/issues/96)
**Day Three**
- Started creating new nf-core/module/snpsift [#104](https://github.com/nf-core/epitopeprediction/issues/104)
- Created local nf-core/test-datasets/data/generic/csv file for testing csvtk/split module
- Implemented sample sheet validation
- Worked on multiple other local modules
**Participants**
[@christopher-mohr](https://github.com/christopher-mohr), [@marissaDubbelaar](https://github.com/marissaDubbelaar), [@jonasscheid](https://github.com/jonasscheid), and [@SusiJo](https://github.com/SusiJo)
---
# metatdenovo - Achievements
**Day One**
- Daniel Lundin: added QC and trimming to main workflow
- Emelie Nilsson: started a module for interleaving reads
**Day Two**
- Emelie Nilsson: finished module for interleaving results
- Daniel Lundin: added the megahit module to the pipeline
**Day Three**
- Daniel Lundin: New module khmer/normalizebymedian that can be used to resolve [#1](https://github.com/LNUc-EEMiS/metatdenovo/issues/1)
- Emelie Nilsson: working on installing prokka in the workflow to resolve [#6](https://github.com/LNUc-EEMiS/metatdenovo/issues/6)
---
# raredisease - Achievements
**Day One**
- Gwenna Breton: started module bcftools/sort [#915](https://github.com/nf-core/modules/issues/915)
**Day Two**
- <Person>: <Achievement> <#Issue>
**Day Three**
- <Person>: <Achievement> <#Issue>
---
# liverctanalysis - Achievements
**Day One**
- Luis Kuhn Cuellar: re-tested uncertainty of prediction and interpretability scripts for prediction package [#1](https://github.com/nf-core/liverctanalysis/issues/1)
**Day Two**
- Luis Kuhn Cuellar: wrapped the monte-carlo dropout procedure (uncertainty) as a package command [#1](https://github.com/nf-core/liverctanalysis/issues/1)
**Day Three**
- Luis Kuhn Cuellar: started command wrapper for [guided grad-cam method](https://arxiv.org/abs/1610.02391) for input feature importance visualization [#1](https://github.com/nf-core/liverctanalysis/issues/1)
---
# General Modules - Achievements
**Day One**
- Robert Petit
- _Ready for Review_
- ectyper ([#948](https://github.com/nf-core/modules/pull/948))
- fastq-scan ([#935](https://github.com/nf-core/modules/pull/935))
- hicap (minor fix) ([#937](https://github.com/nf-core/modules/pull/937))
- SpaTyper (minor fix) ([#938](https://github.com/nf-core/modules/pull/938))
- TBProfiler ([#947](https://github.com/nf-core/modules/pull/947))
- _Started_
- SeqSero2 ([#943](https://github.com/nf-core/modules/issues/943))
- Michael Cipriano & Sateesh Peri
- Ready For Review
- added MUMMER module ([#940](https://github.com/nf-core/modules/pull/940
))
- added NUCmer module ([#945](https://github.com/nf-core/modules/pull/945))
**Day Two**
- Alex P
- Fixed tests for OptiType Module together with Jose Espinosa for future hlatyping pipeline
- Lasse F
- More work on [#883](https://github.com/nf-core/modules/issues/883) - imputeme module (now battling with $config.args)
- Michael Cipriano & Sateesh Peri
- Assembly Scan ([#969](https://github.com/nf-core/modules/pull/969))
- Robert P.
- AgrVATE (update version for fixes) ([#970](https://github.com/nf-core/modules/pull/970))
- ClonalFrameML ([#974](https://github.com/nf-core/modules/pull/974))
- ncbi-genome-download ([#980](https://github.com/nf-core/modules/pull/980))
**Day Three**
- [Subworkflow implementation chat](https://github.com/nf-core/modules/pull/933#issuecomment-954718326)
- James FY, Jasmin F, Anan I
- Setup of FuncScan repo (new pipeline)
- First module (almost?) finished
- More modules are also tackled by Moritz B and Louisa P!
- Simon Pearce
- Made a module for samtools fixmate
- Started on a module for hmmcopy readCounter, towards implementing ichorCNA
- Simeon Hebrew
- Made a module for gatk addorreplacereadgroups
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