Pipelines Team - nf-core Hackathon March 2023

--- title: Pipelines Team - nf-core Hackathon March 2023 tags: march-2023,nf-core,hackathon,progress description: View the slide with "Slide Mode". ---  <a href="https://www.nf-co.re"><img src="https://i.imgur.com/hEDjpCs.png" width="65%"><img></a> ### 🚀 Pipelines Team 🚀 _27th-29th March 2023_ The Hackathon March 2023 [Project Board](https://github.com/orgs/nf-core/projects/38/views/10) Slack `#hackathon-march-2023-pipelines` [<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 Purpose **For people:** - Maintaining existing nf-core pipelines - Starting new nf-core pipelines - Working on own pipelines (using nf-core infrastructure) <iframe src="https://giphy.com/embed/U4de7cZbtg8XmJbxho" width="240" height="135" frameBorder="0" class="giphy-embed" allowFullScreen></iframe> --- # 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](https://github.com/orgs/nf-core/projects/38) - Assign yourself on issues on the [project board](https://github.com/orgs/nf-core/projects/38) - 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 <div class="multi-column"> <div> | Person A | Person B | |----------|----------| | Maxime | Rike | | James | Rike | | Lili | Sofia | | Jasmin | Louisa | </div> <div> | Person A | Person B | |----------|----------| | Simon | Matilda | | Danilo | Emelie | | Jon | | </div> </div> --- # Day One --- # [eager](https://nf-co.re/eager) (day 1) > **Goal**: DSL2 conversion! 👨‍👩‍👦‍👦: Selina, Aida, Judi, Merlin, Ian, Thiseas, James - ✅ [#949](https://github.com/nf-core/eager/pull/949) - Selina - Add Falco as FASTQC alternative - 👀 [#948](https://github.com/nf-core/eager/pull/948) - Judi, Thiseas - Add PreSeq - 👀 [#955](https://github.com/nf-core/eager/pull/955) - Judi - Add MTNucRatio - 🚧 [#952](https://github.com/nf-core/eager/pull/952) - James - Multiplexed mapping support --- # [eager](https://nf-co.re/eager) (day 1) (cont.) - 🚧 [#957](https://github.com/nf-core/eager/pull/957) - Thiseas - aDNA damage manipulation - 🚧 [#816](https://github.com/nf-core/test-datasets/pull/816) - Thiseas - Update TSVs for eager test-datasets - 👀 [#954](https://github.com/nf-core/eager/pull/954) - Selina - Adding BWA-MEM - 🚧 [#959](https://github.com/nf-core/eager/issues/959) - Selina - Adding Bowtie 2 - ✅ Aida - Fixed bug in endorspy - 👀 [#3134](https://github.com/nf-core/modules/pull/3134) Aida - Updated nf-core/module for endorspy --- # [eager](https://nf-co.re/eager) (day 1) (cont. 2) - 🚧 [#922](https://github.com/nf-core/eager/issues/922) - Aida - working on adding endorspy - 🚧 [#923](https://github.com/nf-core/eager/issues/923) - Aida - working on adding Host Removal - 🚧 [#923](https://github.com/nf-core/eager/issues/923) - Merlin - Added bbduk step, working on synchronization with Ian (Princeseq step) - 🚧 [#923](https://github.com/nf-core/eager/issues/923) - Ian - Added prinseqplusplus step, working to finish synchronization for fork in pipeline. opened pull request :smile_cat: --- # [sarek](https://nf-co.re/sarek) (day 1) > **Goal**: Fix issues 👨‍👩‍👦‍👦: Friederike, Maxime, Matilda, Susanne - 🚧 [#950](https://github.com/nf-core/sarek/issues/950) - Samplesheet validation (Matilda) - 🚧 [#808](https://github.com/nf-core/sarek/issues/808) - ControlFREEC ploidy (Rike) - 🚧 [#702](https://github.com/nf-core/sarek/issues/702) - Updating bioconda recipe for ascat + creating new mulled container (SusiJo) --- # [proteinfold](https://nf-co.re/proteinfold) (day 1) > **Goal**: Add new software and functionalities! 👨‍👩‍👦‍👦: Athanasios - 🚧 [#86](https://github.com/nf-core/proteinfold/issues/86) - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows --- # [taxprofiler](https://github.com/nf-core/taxprofiler) (day 1) > **Goal**: Issues for 1.1.0 👨‍👩‍👦‍👦: Sofia, Lili, James - 🚧 [#257](https://github.com/nf-core/taxprofiler/issues/257)- Sofia-Substitute samtools/bam2fq module with samtools/fastq module. - 👀 [#247](https://github.com/nf-core/taxprofiler/issues/247)- Lili - Add a new module metaphlan/makedb to create a latest metaphlan database. - 🚧 [#210](https://github.com/nf-core/taxprofiler/issues/210) - Sofia, James - Add KMCP modules --- # [differentialabundance](https://github.com/nf-core/differentialabundance) (day 1) > **Goal**: Issues for #100, #102 [nf-core Hackathon March 2023](https://github.com/orgs/nf-core/projects/38/views/16?sortedBy%5Bdirection%5D=asc&sortedBy%5BcolumnId%5D=Repository&filterQuery=) 👨‍👩‍👦‍👦: Oskar Wacker, Jonathan Manning, Erika - [#100](https://github.com/nf-core/differentialabundance/issues/100) - Erika - Add plot differentially expressed genes by Biotype - [#102](https://github.com/nf-core/differentialabundance/issues/102) - Oskar - Add multiple sets of gene signatures --- # [pangenome](https://github.com/nf-core/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](https://github.com/piotr-faba-ardigen/dualrnaseq) (day 1) > **Goal**: DSL2 conversion! 👨‍👩‍👦‍👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota - ✅ [#43](https://github.com/nf-core/dualrnaseq/issues/43) - Update Cutadapt process to DSL-2 - 🚧 [#42](https://github.com/nf-core/dualrnaseq/issues/42) - create test dataset for DSL2 pipeline - 🚧 [#44](https://github.com/nf-core/dualrnaseq/issues/44) - Update tximport_host process from DSL1 process to DSL2 module - ✅ [#45](https://github.com/nf-core/dualrnaseq/issues/45) - Update salmon index and salmon quantification process from DSL1 process to DSL2 module - 🚧 [#46](https://github.com/nf-core/dualrnaseq/issues/46) - Create COMBINE_QUANTIFICATION_RESULTS modules --- # [funcscan](https://github.com/nf-core/funcscan) (day 1) > **Goal**: Solve all the issues! 👨‍👩‍👦‍👦: Jasmin, Louisa - ✅ [#247](https://github.com/nf-core/funcscan/issues/247) Update error messages  - ✅ [#244](https://github.com/nf-core/funcscan/issues/244) Add Bakta annotation to CI tests  - 👀 [#173](https://github.com/nf-core/funcscan/issues/173) Update RGI to latest version - Cleaned up issues --- # [hgtseq](https://github.com/nf-core/hgtseq) (day 1) > **Goal**: Bug fixing 👨‍👩‍👦‍👦: Simone --- # [lightsheetrecon](https://github.com/krokicki/nf-lightsheetrecon) (day 1) > **Goal**: finish the full pipeline workflow using completed subworkflows for running Spark 👨‍👩‍👦‍👦: Konrad --- # [magmap](https://github.com/LNUc-EEMiS/magmap) (day 1) > **Goal**: minimal working pipeline 👨‍👩‍👦‍👦: Danilo, Emelie, Daniel Lundin - ✅ Template update - ✅ Pre-mapping-processing of reads - ✅ Decide approach to add reference  --- # [crisprseq](https://github.com/nf-core/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](https://github.com/nf-core/atacseq) (day 1) > **Goal**: metro-map 👨‍👩‍👦‍👦: Björn - 👀 PR v2 --- # new pipeline proposal ![](https://hackmd.io/_uploads/r16UqGk-3.gif) --- # [bamtofastq](https://github.com/qbic-pipelines/bamtofastq) (day 1) > **Goal**: DSL2 conversion! 👨‍👩‍👦‍👦: SusiJo, Friederike, matrulda - 🚧 Adding tests - 👀 Started reviewing (a lot of changed files) --- # [spinningjenny](https://github.com/lucacozzuto/nf-core-spinningjenny) (day 1) > **Goal**: First draft 👨‍👩‍👦‍👦: Luca --- # [ensembl sequence pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/22) (day 1) 👨‍👩‍👦‍👦: Disha Lodha, Zahra Waheed, Ahmad Zyoud - 👀 Understand the Ensembl sequence pipeline - ✔️ Test the Ensembl sequence pipeline # [ensembl genome_prepare pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16) (day 1) 🚧: [#16](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/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](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/8#issuecomment-1485328883) (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](https://github.com/sanger-tol/cobiontcheck) (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](https://github.com/haoqichen20/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](https://github.com/Ensembl/ensembl-vep/tree/release/109/nextflow) (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](https://github.com/nf-core/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) <small> > **Goal**: DSL2 conversion! 👨‍👩‍👦‍👦: Selina, Aida, Judi, Merlin, Ian, Thiseas, James - ✅ [#954](https://github.com/nf-core/eager/pull/954) - Selina - Adding BWA-MEM - 🚧 [#959](https://github.com/nf-core/eager/issues/959) - Selina - Adding Bowtie 2 - 🚧 [#923](https://github.com/nf-core/eager/issues/923) Ian creating metagenomics screening local subworkflow - 🚧 [#957](https://github.com/nf-core/eager/pull/957) - Thiseas - aDNA damage manipulation - ✅ [#948](https://github.com/nf-core/eager/pull/948) - Judith - Adding Preseq - 🚧 [#958](https://github.com/nf-core/eager/pull/958) - Judith - Adding MtNucRatio - ✅ [#3134](https://github.com/nf-core/modules/pull/3134) Aida - Updated nf-core/module for endorspy - 🚧 [#961](https://github.com/nf-core/eager/pull/961) Aida - Adding endorspy - 🚧 [#923](https://github.com/nf-core/eager/issues/923) - Aida - working on adding Host Removal - 🚧 [#923](https://github.com/nf-core/eager/issues/923) - Merlin - Metagenomics Complexity Subworkflow ready for review </small> --- # [DualRNA-Seq](https://github.com/piotr-faba-ardigen/dualrnaseq) (day 2) <small> > **Goal**: DSL2 conversion! 👨‍👩‍👦‍👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota - ✅ [#42](https://github.com/nf-core/dualrnaseq/issues/42) - create test dataset for DSL2 pipeline - 🚧 [#44](https://github.com/nf-core/dualrnaseq/issues/44) - Update tximport_host process from DSL1 process to DSL2 module - ✅ [#46](https://github.com/nf-core/dualrnaseq/issues/46) - Create COMBINE_QUANTIFICATION_RESULTS modules - 🚧 [#48](https://github.com/nf-core/dualrnaseq/issues/48) - A new module to combine the host ambig and unique counts - ✅ [#53](https://github.com/nf-core/dualrnaseq/issues/53) - Update star indexing and star alignment processes from DSL1 processes to DSL2 modules - 🚧 [#54](https://github.com/nf-core/dualrnaseq/issues/54) - Update extract_annotations_* to DSL2 - 🚧 [#56](https://github.com/nf-core/dualrnaseq/issues/56) - Update tximport_host process from DSL1 process to DSL2 module - 🚧 [#57](https://github.com/nf-core/dualrnaseq/issues/57) - Combine host annotations with quantification results - ✅ [#60](https://github.com/nf-core/dualrnaseq/issues/60) - Update salmon split table process to DSL2 - ✅ [#58](https://github.com/nf-core/dualrnaseq/issues/58) - salmon quantification is not executed for all samplessalmon quantification is not executed for all samples </small> --- # [pangenome](https://github.com/nf-core/pangenome) (day 2) <small> 👨‍👩‍👦‍👦: 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. </small> --- # [viralintegration](https://github.com/nf-core/viralintegration) (day 2) <small> > **Goal**: Finalize first release and work on enhancements. 👨‍👩‍👦: Alyssa - 🚧 [#2](https://github.com/nf-core/viralintegration/issues/2) - add metaphlan3 module - 🚧 [#52](https://github.com/nf-core/viralintegration/pull/52) - get final review for first release - 🚧 [#58](https://github.com/nf-core/viralintegration/issues/58) - organize into subworkflows </small> --- # [variantcatalogue](https://github.com/scorreard/nfcore-variantcatalogue/tree/master) (night 1?) <small> > **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 </small> --- # [Magmap](https://github.com/LNUc-EEMiS/magmap) (day 2) <small> > **Goal**: add sourmash subworkflow + add some downstream modules 👨‍👩‍👦‍👦: Emelie, Danilo and Daniel - ✅ [#11](https://github.com/LNUc-EEMiS/magmap/pull/11) - Danilo and Emelie - Adding Subworkflow bbmap Index - ✅ [#5](https://github.com/LNUc-EEMiS/magmap/pull/5) - Danilo and Emelie - Adding test-database - ✅ [#12](https://github.com/LNUc-EEMiS/magmap/pull/12) - Danilo and Emelie - new subworkflow concatenate gff + indexing - ✅ [#14](https://github.com/LNUc-EEMiS/magmap/pull/14) - Danilo and Emelie - cleaning output directory - ✅ SOURMASH Sketch/gather subworkflow - Danilo and Emelie - Add subworkflow for SOURMASH SKETCH and GATHER - ✅ [#15](https://github.com/LNUc-EEMiS/magmap/pull/15) - Danilo and Emelie - add bbmap_align module to the main workflow. </small> --- # [ensembl genome_prepare pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16) (day 2) 🚧: [#16](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/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](https://github.com/daisymut/sammyseq) (day 2) 👨‍👩‍👦‍👦: Margherita - ✅ Update template to latest tool version - 🚧 Add test data --- # [spinningjenny](https://github.com/lucacozzuto/nf-core-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) <small> 👨‍👩‍👦‍👦: Friederike, Maxime, Matilda, Michael, Susanne, Alison - ✅ [#950](https://github.com/nf-core/sarek/issues/950) Samplesheet validation (Matilda) - More samplesheet validation (Michael) - 🚧 [#808](https://github.com/nf-core/sarek/issues/808) ControlFREEC ploidy (Rike) - 🚧 [#702](https://github.com/nf-core/sarek/issues/702) Updating bioconda recipe for ascat + creating new mulled container (SusiJo) - Help Wanted! - 👀 [#981](https://github.com/nf-core/sarek/pull/981) Documentation on how to generate resource files for ASCAT (Alison) </small> --- # [taxprofiler](https://github.com/nf-core/taxprofiler) (day 2) <small> > **Goal**: Continue working on issues for 1.0.0 👨‍👩‍👦‍👦: Sofia, Lili, James - ✅ [#247](https://github.com/nf-core/taxprofiler/issues/247)- Lili-Add a new module metaphlan/makedb to create a latest metaphlan database. - 🚧 [#273](https://github.com/nf-core/taxprofiler/issues/273) Lili- Add a new profiler: MetaPhlAn4. - 🚧 [#210](https://github.com/nf-core/taxprofiler/issues/210) - Sofia, James - Add KMCP modules </small> --- # [nanoseq](https://github.com/nf-core/nanoseq/tree/update_3_1_dev) (day 2) <small> 👨‍👩‍👦‍👦: 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 </small> --- # [hgtseq](https://github.com/nf-core/hgtseq) (day 2) <small> > **Goal**: bug fixing 👨‍👩‍👦‍👦: Simone - 🚧 [#28](https://github.com/nf-core/hgtseq/pull/28) - Resolving conflicts to update template - 🚧 [#30](https://github.com/nf-core/hgtseq/pull/30) - New local module </small> --- # [differentialabundance](https://github.com/nf-core/differentialabundance) (day 2) <small> > **Goal**: add-pre differential matrix subsetting, new plot and more input 👨‍👩‍👦‍👦: Jon, Oskar, Erika - ✅ [#11](https://github.com/nf-core/differentialabundance/pull/103) - Jon - Update differential module interface, add pre-contrast subsetting options - 🚧 Erika - Add biotype plot to report - 🚧 Oskar - Enable multiple GTFs for GSEA </small> --- # [proteinfold](https://nf-co.re/proteinfold) (day 2) > **Goal**: Add new software and functionalities! 👨‍👩‍👦‍👦: Athanasios, Leila - 🚧 [#86](https://github.com/nf-core/proteinfold/issues/86) - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows - 🚧 [85](https://github.com/nf-core/proteinfold/issues/85) - Leila - Update ColabFold version --- # [funcscan](https://github.com/nf-core/funcscan) (day 2) > **Goal**: Solve new issues! 👨‍👩‍👦‍👦: Jasmin - 🚧 [#251](https://github.com/nf-core/funcscan/pull/251) PR out: Implement new pyrodigal module into pipeline - 🚧 Implement changes of prodigal update --- # [ampliseq](https://github.com/nf-core/ampliseq) (day 2) 👨‍👩‍👦‍👦: Daniel & Daniel - ✅ [#563](https://github.com/nf-core/ampliseq/pull/563) - Renamed DADA2 taxonomic classification files to include the chosen reference taxonomy abbreviation. - 🚧 [#564](https://github.com/nf-core/ampliseq/pull/564) - Added phylogenetic placement. --- # [bamtofastq](https://github.com/qbic-pipelines/bamtofastq) (day 2) > **Goal**: DSL2 conversion! 👨‍👩‍👦‍👦: SusiJo, Friederike, matrulda - 🚧 Adding tests - 👀 Still reviewing the huge PR - --- # [PhuEgo](https://github.com/haoqichen20/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](https://github.com/Ensembl/ensembl-vep/tree/release/109/nextflow) (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 <iframe src="https://giphy.com/embed/TuDaPP6VwTObsqzG4p" width="480" height="478" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/marchmadness-TuDaPP6VwTObsqzG4p">via GIPHY</a></p> --- Summary today: - :sparkles: 8 New pipelines (without first release) - :alien: 3 non nf-core pipelines - :older_adult: 10 existing pipelines - 2 DSL2 conversion --- # :sparkles: New pipelines <iframe src="https://giphy.com/embed/LQ3cfzLDUQnfEWChJx" width="480" height="270" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/true-and-the-rainbow-kingdom-true-and-the-rainbow-kingdom-bartleby-LQ3cfzLDUQnfEWChJx">via GIPHY</a></p> --- # [pangenome](https://github.com/nf-core/pangenome) (day 3) <small> > **Goal**: Reimplement the pangenome pipeline following proper nf-core guidelines. 👨‍👩‍👦‍👦: Simon - ✅ Add VG_DECONSTRUCT as a local module. - ✅ Update tests. - 🚧 Community subworkflow. - 🚧 Squeeze subworkflow. </small> --- # [variantcatalogue](https://github.com/scorreard/nfcore-variantcatalogue/tree/master) (night 2) <small> > **Goal**: Coding the Variant catalogue pipeline up to nf-core 👨‍👩‍👦‍👦: Solenne - ✅ Code ready for review - 🚧 Improve documentation </small> --- # [viralintegration](https://github.com/nf-core/viralintegration) (day 3) <small> > **Goal**: Finalize first release and work on enhancements. 👨‍👩‍👦: Alyssa - 🚧 [#2](https://github.com/nf-core/viralintegration/issues/2) - add metaphlan3 module - 👀 [#52](https://github.com/nf-core/viralintegration/pull/52) - get final review for first release (being reviewed by @keslingmj) - 🚧 [#58](https://github.com/nf-core/viralintegration/issues/58) - organize into subworkflows (done but waiting on first release to open PR for review!) </small> --- # [metapep](https://github.com/nf-core/metapep) (day 3) 👨‍👩‍👦‍👦: Till & Sabrina - ✅ Unforked nf-core/metapep repository - ✅ [#56](https://github.com/nf-core/metapep/pull/56),[#61](https://github.com/nf-core/metapep/pull/61) - Improved documentation about data model - ✅ [#55](https://github.com/nf-core/metapep/pull/55) Updated framework of epitopeprediction to epytope 3.3.0 - ✅ [#58](https://github.com/nf-core/metapep/pull/58) Made various ids deterministic to ensure reproducibility - ✅ [#62](https://github.com/nf-core/metapep/pull/62) Updated the nf-core module prodigal to the latest version --- # [spinningjenny](https://github.com/nf-core/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](https://github.com/krokicki/nf-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](https://github.com/nextflow-io/nextflow/issues/3606)) - ✅ Wa new #microscopy channel discussing microscopy-related pipelines - 🚧 Add tests_full & Add test (with stubs) --- # [bamtofastq](https://github.com/qbic-pipelines/bamtofastq) (day 3) > **Goal**: DSL2 conversion & adding to nf-core! 👨‍👩‍👦‍👦: SusiJo, Friederike, matrulda - ✅ Transferred to nf-core - 🚧 Adding metro map - 👀 Reviewing DSL2 conversion --- # [magmap](https://github.com/LNUc-EEMiS/magmap) (day 3) <small> > **Goal**: fix some bugs and add more statistics output 👨‍👩‍👦‍👦: - ✅ [#17](https://github.com/LNUc-EEMiS/magmap/pull/17) - Emelie and Danilo - Adding featurecounts and some associated modules - ✅ [#16](https://github.com/LNUc-EEMiS/magmap/pull/16) - Danilo, Daniel and Emelie - update readme and bug fix! - 🚧 []() - Emelie and Danilo - Adding more statistics output - ✅ [#22](https://github.com/LNUc-EEMiS/magmap/pull/22) - Emelie and Danilo - Adding new input index to feed sourmash - ✅ Danilo, Emelie and Daniel: minimal working pipeline! :tada: </small> --- --- # [sammyseq](https://github.com/daisymut/sammyseq) (day3) 👨‍👩‍👦‍👦: Margherita - 🚧 [#832](https://github.com/nf-core/test-datasets/issues/832) Preparing test data following the standards --- # [PhuEgo](https://github.com/haoqichen20/PhuEgo) (day 3) 👨‍👩‍👦‍👦: Haoqi Chen - Break apart python codes into individual nextflow process. Overall designed the pipeline. --- # [Nextflow-VEP](https://github.com/Ensembl/ensembl-vep/tree/release/109/nextflow) (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 <iframe src="https://giphy.com/embed/P1OUwUpTlLzEGAUHpN" width="480" height="270" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/Avatar-avatar-james-cameron-the-way-of-water-P1OUwUpTlLzEGAUHpN">via GIPHY</a></p> --- # [ensembl sequence pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/22) (day 3) <small> 👨‍👩‍👦‍👦: 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! 🎉🎉🎉 </small> --- # [Aquatic Symbiosis Cobiont Check pipeline](https://github.com/sanger-tol/cobiontcheck) (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](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/8#issuecomment-1487091898) (day 3) <small> 👨‍👩‍👦‍👦: 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 </small> --- # :older_adult: Bug fixes & features for existing pipelines <iframe src="https://giphy.com/embed/8A2jEyKYXS2IZVBo0d" width="480" height="360" frameBorder="0" class="giphy-embed" allowFullScreen></iframe><p><a href="https://giphy.com/gifs/8A2jEyKYXS2IZVBo0d">via GIPHY</a></p> --- # DSL2 conversion --- # [DualRNA-Seq](https://github.com/piotr-faba-ardigen/dualrnaseq) (day 3) <small> > **Goal**: DSL2 conversion! 👨‍👩‍👦‍👦: Bożena, Błażej, Mauro, Michał, Paweł, Paweł, Olha, Piotr, Dorota - 🚧 [#44](https://github.com/nf-core/dualrnaseq/issues/44) - Update tximport_host process from DSL1 process to DSL2 module - 🚧 [#48](https://github.com/nf-core/dualrnaseq/issues/48) - A new module to combine the host ambig and unique counts - ✅ [#54](https://github.com/nf-core/dualrnaseq/issues/54) - Update extract_annotations_* to DSL2 - ✅ [#56](https://github.com/nf-core/dualrnaseq/issues/56) - Create subworkflow to create combined host/path transcriptome file - 🚧 [#57](https://github.com/nf-core/dualrnaseq/issues/57) - Combine host annotations with quantification results - ✅ [#62](https://github.com/nf-core/dualrnaseq/issues/62) - Add salmon quantification to salmon_alignment_base subworkflow - 🚧 [#64](https://github.com/nf-core/dualrnaseq/issues/64) - create a module for generating bacterial transcriptome fasta file - 🚧 [#66](https://github.com/nf-core/dualrnaseq/issues/66) - Add a module for count_total_reads and count_total_read_pairs processes - ✅ [#69](https://github.com/nf-core/dualrnaseq/issues/69) - Add module extract processed reads to the pipeline - 🚧 [#70](https://github.com/nf-core/dualrnaseq/issues/70) - 'Parent' is hard-coded in the replace_attribute_host_genome_gff_star_salmon process - 🚧 [#73](https://github.com/nf-core/dualrnaseq/issues/73) - rethink check_replicates process for DSL2 </small> --- # [Aquatic Symbiosis Cobiont Check pipeline](https://github.com/sanger-tol/cobiontcheck) (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) <small> People: Selina, Aida Judi, Ian, Thiseas, James - 👀 [#964](https://github.com/nf-core/eager/pull/964) - Selina - Adding Bowtie 2 - 🚧 [#3210](https://github.com/nf-core/modules/issues/3210) - Selina - new angsd contamination subworkflow - 👀 - Thiseas - aDNA Damage Manipulation - 👀 - Judith - Adding MtNucRatio [#958](https://github.com/nf-core/eager/pull/958) - 🚧 - Judith - Starting with DamageProfiler [#966](https://github.com/nf-core/eager/issues/966) - 👀 - Ian - Finished initial implementation of metagenomics profiling [967](https://github.com/nf-core/eager/pull/967) </small> --- # sarek (day 3) <small> > **Goal**: Make it more awesome! 👨‍👩‍👦: Friederike, Maxime, Matilda, Michael, Susanne, Alison - ✅ [#981](https://github.com/nf-core/sarek/pull/981) Documentation on how to generate resource files for ASCAT (Alison) - :eyes: [982](https://github.com/nf-core/sarek/pull/982) Avoid using `exit` statements (Rike) - :eyes: [#808](https://github.com/nf-core/sarek/issues/808) ControlFREEC ploidy (Rike) - 🚧 [#702](https://github.com/nf-core/sarek/issues/702) Making ASCAT output reproducible: Bioconda recipe for ascat merged ✅, intergration in progress (SusiJo) + new mulled container ✅ + update module - currently testing </small> --- # [viralrecon](https://github.com/nf-core/viralrecon) (day 3) <small> > **Goal**: Implement & test the freyja subworkflow for wastewater variant analysis within viralrecon 👨‍👩‍👦: Joon - 🚧 [#299](https://github.com/nf-core/viralrecon/issues/299) Implement & test the freyja subworkflow </small> --- # [taxprofiler](https://github.com/nf-core/taxprofiler) (day 3) <small> > **Goal**: Continue working on issues for 1.0.0 👨‍👩‍👦‍👦: Sofia, Lili, James - 🚧 [#273](https://github.com/nf-core/taxprofiler/issues/273) Lili- Add a new profiler: MetaPhlAn4. - 👀 [#210](https://github.com/nf-core/taxprofiler/issues/210) - Sofia, James - Add KMCP modules - 👀 [#257](https://github.com/nf-core/taxprofiler/issues/257)- Sofia-Substitute samtools/bam2fq module with samtools/fastq module. </small> --- # [proteinfold](https://nf-co.re/proteinfold) (day 3) <small> > **Goal**: Add new software and functionalities! 👨‍👩‍👦‍👦: Athanasios, Leila - 🚧 [#86](https://github.com/nf-core/proteinfold/issues/86) - Athanasios - Integrate Jalview visualisation into the AlphaFold2 and Colabfold workflows - 🚧 [#85](https://github.com/nf-core/proteinfold/issues/85) - Leila - Update ColabFold version - 🚧 [#84](https://github.com/nf-core/proteinfold/issues/84) - Leila - Update AlphaFold2 version </small> --- # [ampliseq](https://github.com/nf-core/ampliseq) (day 3) <small> 👨‍👩‍👦‍👦: Daniel & Daniel - ✅ [#564](https://github.com/nf-core/ampliseq/pull/564) - Added phylogenetic placement. - 🚧 []() - Integrate phylogenetic placement into downstream analysis </small> --- # [funcscan](https://github.com/nf-core/funcscan) (day 3) <small> 👨‍👩‍👦‍👦: Jasmin - ✅ [#251](https://github.com/nf-core/funcscan/pull/251): Implement new pyrodigal module into pipeline - 🚧 [#253](https://github.com/nf-core/funcscan/pull/253) ready for review: Implement changes of prodigal update - 🚧 [#173](https://github.com/nf-core/funcscan/issues/173) Implement RGI update – more database stuff :raised_hands: - 🚧 [#3217](https://github.com/nf-core/modules/issues/3217) Compress pyrodigal output files </small> --- # [atacseq](https://github.com/nf-core/atacseq) (day 3) <small> 👨‍👩‍👦‍👦: Björn - 👀 [#259](https://github.com/nf-core/atacseq/pull/259) Add support for optional control data </small> --- # [rnaseq](https://github.com/nf-core/rnaseq) (day 3) <small> 👨‍👩‍👦‍👦: Harshil? Just released nf-core/rnaseq v3.11.0 :tada: </small> --- # [treeval](https://github.com/sanger-tol/treeval) (day 3) <small> 👨‍👩‍👦‍👦: Will Eagles - Updated longread_coverage workflow with all modules now included. - Began conversion of hic_mapping snakemake workflow into nf-core. </small> --- # [ensembl genome_prepare pipeline](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/16) (day 3) 🚧: [#16](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/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](https://github.com/priyanka-surana/wgc-nextflow-hackathon-mar23/issues/8#issuecomment-1488831043) (day 3) <small> 👨‍👩‍👦‍👦: 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. </small> --- # 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) <small> > "its good that I am doing the wrap up and quoting myself" \- Friederike Hanssen (March 2023) </small> <p style="font-size:20%"> ❤️ from James </p> <style> body { background-image: url(https://raw.githubusercontent.com/nf-core/logos/master/nf-core-logos/nf-core-logo-square.svg); background-size: 7.5%; background-repeat: no-repeat; background-position: 3% 96%; background-color: #181a1b; } .reveal body { font-family: 'Roboto', sans-serif; font-weight: 300; color: white; } .reveal p { font-family: 'Roboto', sans-serif; font-weight: 300; color: white; } .reveal h1 { font-family: 'Roboto', sans-serif; font-style: bold; font-weight: 400; color: white; font-size: 62px; } .reveal h2 { font-family: 'Roboto', sans-serif; font-weight: 300; color: white; } .reveal h3 { font-family: 'Roboto', sans-serif; font-style: italic; font-weight: 300; color: white; } .reveal p { font-family: 'Roboto', sans-serif; font-weight: 300; color: white; } .reveal li { font-family: 'Roboto', sans-serif; font-weight: 300; color: white; } .reveal pre { background-color: #272822 !important; display: inline-block; border-radius: 7px; color: #aaaba9; } .reveal pre code { color: #eeeeee; background-color: #272822; font-size: 100%; } .reveal code { background-color: #272822; font-size: 75%; } .reveal .progress { color: #24B064; } .reveal .controls button { color: #24B064; } .reveal blockquote { display: block; position: relative; width: 90%; margin: 20px auto; padding: 5px; background: rgba(255, 255, 255, 0.05); box-shadow: 0px 0px 2px rgb(0 0 0 / 20%); } .multi-column{ display: grid; grid-auto-flow: column; } </style>

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