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🚀 Pipeline Progress 🚀

27th-29th October 2021

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@nf-core /
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@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

Day Three

  • James: did a couple of reviews
  • Anan: going through the review of MapDamage2
  • Alex: 🆘 Issue with conda-build: " Placeholder of length '80' too short in package"
  • Louisa: completed mtnucratio! #840
  • Ian:
    • waiting for krakenuniq biocontainer update,
    • 90% done with MultiVCFAnalyzer tests
    • need GATK 3.5 unified genotyper #844, but conda issue picking up old version!?
  • Ephie: continued adapteremovalfixprefix

Day Two

  • James: Completed DeDup #840, did some reviews (for mag)
  • Alex G: PMDTools Module ready for review! #847
  • Louisa:
    • Completed samtools/depth #850
    • Started mtnucratio #840
  • Ian: fighting (the) kraken(uniq) module #911
  • Anan: continued mapDamage2 (fixed unknown meta error: nextflow doesn't like numbers in channel names!)
  • Alex P: started work on circular mapper #842

Day One

  • James: got DeDup module for review #840
  • Anan: Halfway through mapDamage module #854
  • Alex: working on PMDtools module #847
  • Louisa: Almost finished samtools/depth #850
  • Ephie: started adapterremovalfixprefix module #837
  • Ian: mostly done with krakenuniq module #911

mag/bacass - Achievements

TODOs

Day One

  • Maxime: Metabat2 module #875, and CMSeq/polymut module #918
  • James: Maxbin2 module #895
  • Golden Delicious team: Porechop module #914
  • Encore: Nanopolish module #917
  • Daniel: Filtlong module #919
  • Mjakobs: Krona module #928
  • Fyle, Racon, Prodigal modules are worked on

Day Two

  • Antonia: Add prodigal module to nf-core/mag #240
  • Andries van Tonder: Hopefully fixed test-data issues for miniasm #825 and racon #949. PRs submitted for both modules awaiting review
  • Júlia Mir Pedrol: Fighting with test-data for flye #830
  • Encore: Optimising Nanopolish module #917
  • Mjakobs: Finishing up Krona module #928
  • Daniel: Update ampliseq full test sample sheet #375, update summary figure #342, prep release #343, 2.1.1 release PR #344, nf-core/ampliseq release 2.1.1

Day Three

  • Júlia Mir Pedrol: Finishing Flye PR #982
  • Maria Jakobs: Krona module finished #928, Krona_db module PR #995
  • Antonia: Finished prodigal module addition to nf-core/mag #240, added –skip_prodigal #241, adding Prokka module to mag
  • Andries van Tonder: Final changes to PRs for modules miniasm #962, Racon module finished #949, Medaka module finished #992
  • Daniel: After-release PR to bump version for ampliseq #345, update preprint info in mag #244

sarek - Achievements

TODOs

Day One

  • The Pigeon Apples: Manta #906
  • Francesco: FGBIO/FastqToBam #916
  • The Pippin Apples: Manta Somatic #912
  • Rike: Strelka BP module #913

Day Two

  • Francesco: FGBIO/GroupReadsByUMI #952
  • Francesco: samblaster #954
  • Francesco: samtools/bam2fq #958 (check needed on failing yaml tests)
  • Rike: Close sarek #429: Allow to skip BQSR
  • Rike: GATK4/EstimateLibaryComplexity #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:
    • 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
  • Francesco:
    • fixed samblaster names convension (thanks Harshil) #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
  • 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

Day One

  • @ggabernet: Added cellranger mkref module #894

Day Two

  • @ggabernet: finally merged cellranger module
  • @ggabernet: working on template update for scRNAseq
  • @emiller: cellranger count and cellranger mkgtf #979

Day Three

  • @emiller: Started spaceranger modules #994
  • @ggabernet: Template update and PR #73

cageseq - Achievements

Day One

  • @mashehu+group: added paraclu module to nf-core/modules
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    #903

Day Two

  • <Person>: <Achievement> <#Issue>

Day Three

  • <Person>: <Achievement> <#Issue>

atacseq - Achievements

Day One

  • Ilya Pletenev: working on ataqv module #904

Day Two

  • <Person>: <Achievement> <#Issue>

Day Three

  • Ilya Pletenev: finished main file of ataqv module #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
    • Started with the template conversion #100
    • Started with conversion local module - check_requested_models #92
    • Started with conversion local modules - csvtk_split and snpsift_split #93
    • Started with conversion local module - get_peptides #94
    • Started creating a nfcore module - csvtk_split #105

Day Two

  • Updating the template, PR has been accepted #100
  • Worked on the cvstk split module #105
  • Added sample sheets to the test datasets #103
  • Updated the BioContainers/multi-package-containers > waiting on mulled container #91
  • Adjusting the sample sheet validation and beloning scripts #102
  • Started creating local module - peptidePrediction #96

Day Three

  • Started creating new nf-core/module/snpsift #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, @marissaDubbelaar, @jonasscheid, and @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
  • Emelie Nilsson: working on installing prokka in the workflow to resolve #6

raredisease - Achievements

Day One

  • Gwenna Breton: started module bcftools/sort #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

Day Two

  • Luis Kuhn Cuellar: wrapped the monte-carlo dropout procedure (uncertainty) as a package command #1

Day Three

General Modules - Achievements

Day One

  • Robert Petit
    • Ready for Review
      • ectyper (#948)
      • fastq-scan (#935)
      • hicap (minor fix) (#937)
      • SpaTyper (minor fix) (#938)
      • TBProfiler (#947)
    • Started
  • Michael Cipriano & Sateesh Peri
    • Ready For Review
      • added MUMMER module (#940)
      • added NUCmer module (#945)

Day Two

  • Alex P

    • Fixed tests for OptiType Module together with Jose Espinosa for future hlatyping pipeline

  • Lasse F

    • More work on #883 - imputeme module (now battling with $config.args)

  • Michael Cipriano & Sateesh Peri

    • Assembly Scan (#969)

  • Robert P.

    • AgrVATE (update version for fixes) (#970)
    • ClonalFrameML (#974)
    • ncbi-genome-download (#980)

Day Three

  • Subworkflow implementation chat
  • 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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