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🚀 Pipeline Progress 🚀
27th-29th October 2021
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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
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:
- 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
mag/bacass - Achievements
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
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
Day One
- @ggabernet: Added cellranger mkref module #894
Day Two
- @ggabernet: finally merged cellranger module
- @ggabernet: working on template update for scRNAseq
- @emiller:
cellranger countandcellranger mkgtf#979
Day Three
cageseq - Achievements
Day One
- @mashehu+group: added paraclu module to nf-core/modules
#903
Day Two
- <Person>: <Achievement> <#Issue>
Day Three
- <Person>: <Achievement> <#Issue>
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
idrmodule (peakFilesadded to test-datasets).
Day Three
-
Refactor
genrichmodule, getting rid ofparams -
Add IDR to the pipeline (pending)
-
Implement
params.alignerin the pipeline (pending):- Implement
bowtie2as aligner (module ready) - Implement
CHROMAPas aligner (module ready)
- Implement
epitopeprediction - Achievements
Day One
- Distribution of the tasks:
- Initation of converting the
params.inputto 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
- Initation of converting the
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
- Luis Kuhn Cuellar: started command wrapper for guided grad-cam method for input feature importance visualization #1
General Modules - Achievements
Day One
- Robert Petit
- Michael Cipriano & Sateesh Peri
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.
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
🚀 Pipeline Progress 🚀 27th-29th October 2021 @nf-core / @nf-core
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