# Hackathon July 2020 --- <!-- Put the link to this slide here so people can follow --> slide: https://hackmd.io/@nf-core-hackathon-july-2020/ByaotZZkv --- # New pipelines :new:  --- ## Primary focus Developing new pipelines --- ## Group members - Nurlan Kerimov - Erik Fasterius - Matthias Hörtenhuber - Paweł Ciurka - Kamil Malisz - Daniel Wojciechowski - Tomasz Wrzesinski - Matthias Marquardt - Jesper Gådin --- ## QTLMAP pipeline (by Nurlan Kerimov from University of Tartu) ### Aim - Automatize Quantitative Trait Loci (QTL) mapping. - The pipeline will take genotype (vcf) and molecular phenotype data (TSV file) together with some phenotype reference files and will generate QTL summary statistics according to given parameters. - See https://github.com/eQTL-Catalogue/qtlmap for more info --- ## QTLMAP pipeline ### Progress - Testing is missing - Some tools used in pipeline are not in conda (we use pre-built binary executables currently) --- ## The RIF-Seq pipeline (by Erik Fasterius from National Bioinformatics Infrastructure Sweden, NBIS) ### Aim - Analyse a new type of highly multiplexed and RNA-isolation-free RNA-seq data from the Nilsson lab at Stockholm University. - The pipeline will demultiplex, perform QC, estimate gene expression as well as perform differential expression and downstream analyses (such as enrichment analyses) from this new data. --- ## The RIF-Seq pipeline ### Progress - A Snakemake-based pipeline has been in development since 2019, which now also has a nf-core-based version in nextflow. - It was created from the nf-core template and initially used DSL1 but has since started using DSL2. - Work on linting, documentation and other things related to getting it ready for incorporation into nf-core is currently ongoing. --- ## The RIF-Seq pipeline ### Availability - As the owners of the new method have yet to publish their technology, the RIF-Seq pipeline is currently residing in a private GitHub repository. - Permission to view and contribute to the code can be granted to hackathon-attandees, though, if there is an interest in this. --- ## The Sim-Seqer pipeline (by Paweł Ciurka, Kamil Malisz, Daniel Wojciechowski, Tomasz Wrzesiński, Ardigen) ### Aim - Sim Seqer is planned to be a tool that allows the user, who has a set of annotated antibodies (as from of csv file), to look for antibodies in a reference set which have matching annotations (such as V genes or canonical folds) and similar CDR peptide sequences. --- ## The Sim-Seqer pipeline ### Done - Input and parameters validation - Aligner process - Reference chunking and filtering process ### In Progress - Put together main workflow - Results collection - Pipeline tests --- ## GWAS pipeline (by Jesper Gådin) ### Aim - Genome Wide Association analysis pipeline - working towards first release ---  --- ## Cageseq (contribution by Matthias Hörtenhuber) ### Aim - Write documentation for cageseq 1.0 release --- ### Progress - Finished readme. - See automated pipeline documentation section in tools presentation :upside_down_face: - Almost done with schema.json. --- ## popbom Pipeline (by Matthias Marquardt, University of Tübingen) ### Aim It is an acronym for: Prediction Of Phenotype Based On Metagenome. Species abundancies in samples are used to train ML models for predictions of illnesses. --- ## popbom Pipeline ### Progress - Rewriten the assignment of species abundancies based on nextflow workshop. The choices are kraken2, centrifuge and metaphlan3. - The next step is to include a Random Forrest script as a first ML method with the goal to extend it to other methods later. --- ### Thank you! :sheep: