diff --git a/src/pages/nfcamp/2019/alex.md b/src/pages/nfcamp/2019/alex.md index 312480ea..b287c549 100644 --- a/src/pages/nfcamp/2019/alex.md +++ b/src/pages/nfcamp/2019/alex.md @@ -1,14 +1,16 @@ -title=Migrating legacy workflows to Nextflow -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Migrating legacy workflows to Nextflow +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Migrating legacy workflows to Nextflow ### Alexander Peltzer -*Bioinformatics Research Scientist, Quantitative Biology Center Tübingen, Germany* +*Bioinformatics Research Scientist, Quantitative Biology Center Tübingen, Germany* Many researchers and institutions face similar issues: Having in-house legacy workflows written in bash or other formats and now facing issues with reproducibility, maintenance of these pipelines and the increasing computational demands poses severe threats to being able to address modern computational questions using such legacy workflows. In this talk, I intend to highlight the efforts we took at the QBIC to maintain compatibility between existing workflows but simultaneously porting all of our existing legacy pipelines to the Nextflow and nf-core frameworks to be able to answer these threats. With a specific application case on one of the most widely used ancient DNA pipelines, I intend to highlight the benefits of these migrated pipeline in comparison to the previously existing workflow in a 1:1 setting. @@ -16,6 +18,6 @@ Many researchers and institutions face similar issues: Having in-house legacy wo Alexander Peltzer is a bioinformatics research scientist at the Quantitative Biology Center in Tübingen and is working in maintaining and developing modern solutions for data management and analysis for various omics technologies there. Before, he obtained a PhD in bioinformatics at the University of Tübingen and the Max Planck Institute for the Science of Human History where he worked on computational methods for ancient DNA reconstruction. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/alper.md b/src/pages/nfcamp/2019/alper.md index da5d27d1..d33e342b 100644 --- a/src/pages/nfcamp/2019/alper.md +++ b/src/pages/nfcamp/2019/alper.md @@ -1,33 +1,35 @@ -title=DolphinNext: A graphical user interface for distributed data processing of high throughput genomics -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: DolphinNext: A graphical user interface for distributed data processing of high throughput genomics +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## DolphinNext: A graphical user interface for distributed data processing of high throughput genomics ### Alper Kucukural -*Assistant Professor, UMass Medical School, USA* +*Assistant Professor, UMass Medical School, USA* Emergence of new biomedical technologies, like next-generation sequencing (NGS) which is producing vast amounts of genomic data every day, is driving a big data revolution in biology. The dramatic increase in the volume, as well as the production rate of genomic data, has now made the data analysis new bottleneck for scientific discovery. Naturally, the need for highly-parallel data processing frameworks is greater than ever. It is also important for these frameworks to have certain design characteristics such as flexibility, portability, and reproducibility. Processing of sequencing data usually involves many different programs, each of which performs a specific step in the overall pipeline. Flexibility ensures that the pipelines can support a variety of use cases or data types without the need to modify existing pipelines or create new ones. Portability gives user the freedom to choose computational resources as he/she deems fit. Reproducibility across computing environments, which warrants credibility of the results, is a particularly important feature in the face of the sheer volume of data and complexity of the pipelines. There exist several platforms that offer graphical user interfaces for designing and execution of complex pipelines (e.g. Galaxy, GenePattern, GeneProf). Unfortunately, none of these platforms supports parallelism or portability across computing environments. To address these and additional shortcomings discussed in this paper, we have created DolphinNext, an easy-to-use graphical user interface for creating and deploying complex workflows for parallel processing of high throughput genomic data. DolphinNext relies on Nextflow which is a framework enabling scalable and reproducible workflows using software containers. The central idea behind the creation of DolphinNext is to facilitate building and deployment of complex pipelines using a graphically-enabled modular approach. DolphinNext provides: -1. A drag and drop user interface that abstracts Nextflow pipelines and allows users to create pipelines without familiarity with Nextflow. -2. Reproducible pipelines by providing version tracking, and by creating a stand-alone version of any pipeline instance to run independently or to share in the publications. -3. Seamless portability to distributed computational environments such as high performance clusters or cloud based solutions. +1. A drag and drop user interface that abstracts Nextflow pipelines and allows users to create pipelines without familiarity with Nextflow. +2. Reproducible pipelines by providing version tracking, and by creating a stand-alone version of any pipeline instance to run independently or to share in the publications. +3. Seamless portability to distributed computational environments such as high performance clusters or cloud based solutions. 4. A graphical user interface to monitor pipeline execution that allows restarting of intermediate processes even after parameter changes. ### Bio -Dr. Kucukural designs and implements reusable, robust and production grade bioinformatics analysis pipelines and pipeline generation tools for processing next-generation sequencing data. +Dr. Kucukural designs and implements reusable, robust and production grade bioinformatics analysis pipelines and pipeline generation tools for processing next-generation sequencing data. He mainly works on NGS data analysis; RNA-Seq, RIP-Seq, Chip-Seq, CLIP-Seq and derivatives. He implemented algorithms to reduce noise by calling the peaks caused by experimental and alignment biases especially for RIP and CLIP-Seq data. -Dr. Kucukural worked on analyzing deep sequencing data to discover key elements of splicing of pre-mRNAs to have better understanding of post-transcriptional regulations of RNAs. Moreover, he has deep knowledge of finding genome wide mRNA targets of RNA binding proteins (RBPs). Analyzing RNA targets of tdp43 RBP with deep sequencing on Rat and human was another focus of his research to understand the mechanisms of neuro-degenerative diseases such as Alzheimer and ALS. +Dr. Kucukural worked on analyzing deep sequencing data to discover key elements of splicing of pre-mRNAs to have better understanding of post-transcriptional regulations of RNAs. Moreover, he has deep knowledge of finding genome wide mRNA targets of RNA binding proteins (RBPs). Analyzing RNA targets of tdp43 RBP with deep sequencing on Rat and human was another focus of his research to understand the mechanisms of neuro-degenerative diseases such as Alzheimer and ALS. He also worked for protein structure characterization and prediction. He applied techniques from graph theory on protein structure analysis and implemented the theories from computer sciences to biology to find solutions in drug design and small molecular docking fields. He developed applications using genetic algorithms to discover biomarkers and implemented feature detection methods using various clustering, classification and machine learning algorithms such as hidden markov models and support vector machines. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/anna.md b/src/pages/nfcamp/2019/anna.md index 3eaa5f54..c0f4cfb7 100644 --- a/src/pages/nfcamp/2019/anna.md +++ b/src/pages/nfcamp/2019/anna.md @@ -1,9 +1,11 @@ -title=FA-nf - A Bioinformatics pipeline for functional annotation implemented in Nextflow -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: FA-nf - A Bioinformatics pipeline for functional annotation implemented in Nextflow +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## FA-nf - A Bioinformatics pipeline for functional annotation implemented in Nextflow @@ -13,21 +15,21 @@ status=published ### Toni Hermoso *Bioinformatician, Centre for Genomics Regulation, Spain* -With the advantages of NGS technologies it became possible to obtain a whole genome sequence and its genome assembly of any novel organism at a relatively low cost and short time. To be able to work with this novel genome assembly, scientists need to know positions of the genic elements, especially protein-coding genes, and their putative function. Therefore, function annotation (FA) is an important step in de-novo genome processing and can provide important information about putative role of concrete gene. Such annotation usually includes assigning functional domains, i.e. from Pfam or Panther, ontology terms (GO), and specific elements, i.e. cleavage sites. - +With the advantages of NGS technologies it became possible to obtain a whole genome sequence and its genome assembly of any novel organism at a relatively low cost and short time. To be able to work with this novel genome assembly, scientists need to know positions of the genic elements, especially protein-coding genes, and their putative function. Therefore, function annotation (FA) is an important step in de-novo genome processing and can provide important information about putative role of concrete gene. Such annotation usually includes assigning functional domains, i.e. from Pfam or Panther, ontology terms (GO), and specific elements, i.e. cleavage sites. + There are two main outcomes from functional annotation: the first one is an annotation itself, which allows scientists to perform various analysis to understand better genome function. The second one, is an additional quality check for genome assembly and predicted genes. Therefore, it is possible to identify suspicious genes which may belong to another species due to contamination, or non-functional overpredicted genes, erroneously annotated. - + Here we will present a pipeline for a functional annotation of novel proteins from non-model organisms implemented in Nextflow. The pipeline allows to put together different widely-used tools in the field of functional annotation, including some Java applications and REST API services scripts. This software diversity and complexity is handled thanks to software containers (Docker or Singularity), allowing an easier maintenance and versioning of bundled programs. Data exchange and resulting reports are stored in a database, which can be either sitting on the very filesystem as a single database file using SQLite, or through a preset MySQL DBMS server. For that latter case, we also managed to set up a HPC-compatible MySQL on-demand approach that enabled parallel and subsequent processes of the pipeline to query a single MySQL server instance from different cluster nodes. -The provided output is compatible with commonly-used standard resources for downstream analysis, such as UCSC genome browser or Bioconductor packages. +The provided output is compatible with commonly-used standard resources for downstream analysis, such as UCSC genome browser or Bioconductor packages. This pipeline was used in many genomic projects we collaborated with, among others, those of melon, common bean, wasp, and Iberian lynx. -### Bio +### Bio -**Anna Vlasova**, Bioinformatician at Institute of Molecular Pathology, Vienna, Austria. +**Anna Vlasova**, Bioinformatician at Institute of Molecular Pathology, Vienna, Austria. **Toni Hermoso Pulido**, Bioinformatics Core Facility, Centre for Genomic Regulation, Barcelona. Degree in Biochemistry and PhD in Biotechnology at Autonomous University of Barcelona. Since 2009 he joined CRG as a member of the just established Bioinformatics Core Facility where he has been supporting scientific web services and databases, research training and data analyses at the centre. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/anthony.md b/src/pages/nfcamp/2019/anthony.md index e5cd6f35..f2efd102 100644 --- a/src/pages/nfcamp/2019/anthony.md +++ b/src/pages/nfcamp/2019/anthony.md @@ -1,32 +1,34 @@ -title=Pay As You Go Cloud Bioinformatics for Pathogens -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Pay As You Go Cloud Bioinformatics for Pathogens +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Pay As You Go Cloud Bioinformatics for Pathogens ### Anthony Underwood -*Bioinformatics Implementation Manager, Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, UK* +*Bioinformatics Implementation Manager, Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, UK* ### Ben Taylor -*Senior Software Developer, Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, UK* +*Senior Software Developer, Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, UK* -Nextflow provides a mechanism to develop high throughput parallelizable pipelines on a small desktop machine and then scale out to larger infrastructures such as HPC clusters. If you do not have a cluster Nextflow allows the same pipeline to run in the cloud such as on AWS Batch where hundreds or thousands of jobs can run in parallel. However: +Nextflow provides a mechanism to develop high throughput parallelizable pipelines on a small desktop machine and then scale out to larger infrastructures such as HPC clusters. If you do not have a cluster Nextflow allows the same pipeline to run in the cloud such as on AWS Batch where hundreds or thousands of jobs can run in parallel. However: 1. it is not trivial to set up 2. users need to be comfortable on the command line 3. and there’s a risk you could rack up large bills We have developed a CloudFormation template and web application to make scaling up Nextflow-based pipelines via deployment in AWS far simpler. Using this approach: - + 1. a new pipeline can be deployed with just a few clicks 2. end users can start and monitor the pipeline using a web page -3. limits can be enforced to prevent unexpected bills. +3. limits can be enforced to prevent unexpected bills. By using AWS Lambda to provide the services that bind everything together, you only pay to store your data and for the EC2 compute used by batch when the pipeline is actually running. - + We will talk about why and how we did this and ask for feedback on how our approach could be improved. ### Bio @@ -35,6 +37,6 @@ We will talk about why and how we did this and ask for feedback on how our appro **Ben Taylor** is a senior software developer in the Centre for Genomic Pathogen Surveillance developing software that optimises common bioinformatics processes and delivers them through user-friendly interfaces. He’s previously worked for the UK Government and private companies to make it easier to use Cloud Infrastructure. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/anton.md b/src/pages/nfcamp/2019/anton.md index 0949c071..215b0f44 100644 --- a/src/pages/nfcamp/2019/anton.md +++ b/src/pages/nfcamp/2019/anton.md @@ -1,9 +1,11 @@ -title=NF-web: a web interface for Nextflow -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: NF-web: a web interface for Nextflow +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## NF-web: a web interface for Nextflow @@ -14,8 +16,8 @@ We are presenting an open-source web application for running Nextflow pipelines ### Bio -Senior Software Developer in Cellular Genetics Informatics support group at Sanger Institute. Developing internal services (NF-web) and paper supplement websites, working with computational infrastructure (Openstack, Kubernetes), maintaining the department JupyterHub deployment. Contributed to the development of multiple workflow engines (primarily CWL - cwltool, REANA, Rabix). Bachelor of System Analysis and Master of Computer Science, Kyiv Polytechnic Institute. +Senior Software Developer in Cellular Genetics Informatics support group at Sanger Institute. Developing internal services (NF-web) and paper supplement websites, working with computational infrastructure (Openstack, Kubernetes), maintaining the department JupyterHub deployment. Contributed to the development of multiple workflow engines (primarily CWL - cwltool, REANA, Rabix). Bachelor of System Analysis and Master of Computer Science, Kyiv Polytechnic Institute. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/evan.md b/src/pages/nfcamp/2019/evan.md index ca80a555..1e1c7710 100644 --- a/src/pages/nfcamp/2019/evan.md +++ b/src/pages/nfcamp/2019/evan.md @@ -1,25 +1,27 @@ -title=Scientific workflows beyond the Ivory Tower -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Scientific workflows beyond the Ivory Tower +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Scientific workflows beyond the Ivory Tower ### Evan Floden -*Seqera Labs & Centre for Genomic Regulation (CRG), Spain* +*Seqera Labs & Centre for Genomic Regulation (CRG), Spain* Evan will discuss the progress of Seqera Labs over the past 12 months as well unveil some exciting new developments for the Nextflow project. ### Bio -Evan is a workflow developer helping scientists and engineers to find solutions to their problems using Nextflow. +Evan is a workflow developer helping scientists and engineers to find solutions to their problems using Nextflow. His background is in Biotechnology and Bioinformatics and he worked on the Nextflow project -during his PhD from 2014 before co-founding Seqera Labs. Evan's interests include genomics, scientific workflow -optimization, home automation and bicycle touring. +during his PhD from 2014 before co-founding Seqera Labs. Evan's interests include genomics, scientific workflow +optimization, home automation and bicycle touring. -### Registration +### Registration To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/francesco.md b/src/pages/nfcamp/2019/francesco.md index b17aa938..07d6352f 100644 --- a/src/pages/nfcamp/2019/francesco.md +++ b/src/pages/nfcamp/2019/francesco.md @@ -1,9 +1,11 @@ -title=Nextflow and the human microbiome: from data to insights -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Nextflow and the human microbiome: from data to insights +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Nextflow and human microbiome: from data to insights @@ -12,10 +14,10 @@ status=published Using Nextflow at scale gives the possibility to extensively analyse complex datasets such as the human gut microbiome, and investigate microbial composition both at the taxonomical and functional level. This is a fundamental step towards a broader and deeper comprehension of the role the human microbiome has in diseases progression, prevention and treatment. Key examples will be presented to highlight the impact and the contribution Nextflow is providing in this field. -### Bio +### Bio Head of Data Science, leading a team of bioinformaticians and biostatisticians focused on quantitative and functional human microbiome analysis for drugs development and biomarkers discovery. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/lee-tutorial.md b/src/pages/nfcamp/2019/lee-tutorial.md index e9908e93..32eb2df4 100644 --- a/src/pages/nfcamp/2019/lee-tutorial.md +++ b/src/pages/nfcamp/2019/lee-tutorial.md @@ -1,9 +1,11 @@ -title=Running Nextflow on AWS Batch -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Running Nextflow on AWS Batch +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Running Nextflow on AWS Batch @@ -21,6 +23,6 @@ This tutorial will walk you through how to setup AWS infrastructure and Nextflow Lee is a Technical Business Development Manager specializing in Genomics and Life Sciences workloads on AWS. He has over 10 years of hands-on experience as a practicing research scientist and software engineer in bioinformatics, computational systems biology, and data science developing tools ranging from high throughput pipelines for *omics data processing to HIPAA compliant software for clinical data capture and analysis. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/lee.md b/src/pages/nfcamp/2019/lee.md index a0b098ab..b45d4c88 100644 --- a/src/pages/nfcamp/2019/lee.md +++ b/src/pages/nfcamp/2019/lee.md @@ -1,9 +1,11 @@ -title=Governance & Guardrails: Managing your AWS account to ensure your data is secure and your budget is safe -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Governance & Guardrails: Managing your AWS account to ensure your data is secure and your budget is safe +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Governance & Guardrails: Managing your AWS account to ensure your data is secure and your budget is safe @@ -16,6 +18,6 @@ The most common questions asked by new AWS customers involve finding the tools a Lee is a Technical Business Development Manager specializing in Genomics and Life Sciences workloads on AWS. He has over 10 years of hands-on experience as a practicing research scientist and software engineer in bioinformatics, computational systems biology, and data science developing tools ranging from high throughput pipelines for *omics data processing to HIPAA compliant software for clinical data capture and analysis. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/luca.md b/src/pages/nfcamp/2019/luca.md index d16d1500..89c051c7 100644 --- a/src/pages/nfcamp/2019/luca.md +++ b/src/pages/nfcamp/2019/luca.md @@ -1,21 +1,23 @@ -title=Parallel and scalable workflow for the analysis of RNA modifications using Oxford Nanopore direct RNA sequencing -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Parallel and scalable workflow for the analysis of RNA modifications using Oxford Nanopore direct RNA sequencing +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- -## Parallel and scalable workflow for the analysis of RNA modifications using Oxford Nanopore direct RNA sequencing +## Parallel and scalable workflow for the analysis of RNA modifications using Oxford Nanopore direct RNA sequencing ### Luca Cozzuto -*Bioinformatics Research Scientist, Centre for Genomic Regulation (CRG), Spain* +*Bioinformatics Research Scientist, Centre for Genomic Regulation (CRG), Spain* -The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA (cDNA), and as such, is virtually capable of detecting any given RNA modification present in the molecule that is being sequenced. Although the technology has been publicly available since 2017, the complexity of the raw current intensity output data generated by nanopore sequencing, together with lack of systematic and reproducible pipelines for the analysis of direct RNA sequencing datasets, have greatly hindered the access of this technology to the general user. Here we provide an in silico scalable and parallelizable workflow for the analysis of direct RNA sequencing reads, which converts raw current intensities into multiple types of processed data, providing metrics of the quality of the run, per-gene counts, RNA modification predictions and polyA tail length predictions. The workflow, which has been built using the Nextflow framework and is distributed with Docker and Singularity containers, can be executed on any Unix-compatible OS on a computer, cluster or cloud without the need of installing any additional software or dependencies. Moreover, the workflow is easily scalable, as it can incorporate updated software versions or algorithms that may be released in the future in a modular manner. We expect that our pipeline will make the analysis of direct RNA sequencing datasets highly simplified and accessible to the non-bioinformatic expert, and thus boost our understanding of the epitranscriptome with single molecule resolution. +The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA (cDNA), and as such, is virtually capable of detecting any given RNA modification present in the molecule that is being sequenced. Although the technology has been publicly available since 2017, the complexity of the raw current intensity output data generated by nanopore sequencing, together with lack of systematic and reproducible pipelines for the analysis of direct RNA sequencing datasets, have greatly hindered the access of this technology to the general user. Here we provide an in silico scalable and parallelizable workflow for the analysis of direct RNA sequencing reads, which converts raw current intensities into multiple types of processed data, providing metrics of the quality of the run, per-gene counts, RNA modification predictions and polyA tail length predictions. The workflow, which has been built using the Nextflow framework and is distributed with Docker and Singularity containers, can be executed on any Unix-compatible OS on a computer, cluster or cloud without the need of installing any additional software or dependencies. Moreover, the workflow is easily scalable, as it can incorporate updated software versions or algorithms that may be released in the future in a modular manner. We expect that our pipeline will make the analysis of direct RNA sequencing datasets highly simplified and accessible to the non-bioinformatic expert, and thus boost our understanding of the epitranscriptome with single molecule resolution. ### Bio -Luca Cozzuto is a bioinformatician expert of NGS data who studied biotechnology at University of Naples Federico II. He got his PhD at European School of Molecular Medicine and since 2010 is part of the Bioinformatics Core at Center for Genomics Regulation in Barcelona. He is mainly involved in providing data analysis, pipeline developments and training to researchers. +Luca Cozzuto is a bioinformatician expert of NGS data who studied biotechnology at University of Naples Federico II. He got his PhD at European School of Molecular Medicine and since 2010 is part of the Bioinformatics Core at Center for Genomics Regulation in Barcelona. He is mainly involved in providing data analysis, pipeline developments and training to researchers. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/matthias.md b/src/pages/nfcamp/2019/matthias.md index 232fa9e8..7a1be846 100644 --- a/src/pages/nfcamp/2019/matthias.md +++ b/src/pages/nfcamp/2019/matthias.md @@ -1,34 +1,36 @@ -title=Robust and reproducible pipelines to support routine clinical diagnostic and research projects in oncology -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Robust and reproducible pipelines to support routine clinical diagnostic and research projects in oncology +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Robust and reproducible pipelines to support routine clinical diagnostic and research projects in oncology ### Matthias Monfort -*Research Engineer, Institut Curie, France* +*Research Engineer, Institut Curie, France* -Institut Curie is a European Comprehensive Cancer Center which comprises a research center and three cancer hospitals. The bioinformatics platform support both research and patient care in particular by providing different kinds of analysis pipelines to address different use cases. +Institut Curie is a European Comprehensive Cancer Center which comprises a research center and three cancer hospitals. The bioinformatics platform support both research and patient care in particular by providing different kinds of analysis pipelines to address different use cases. -On the one hand, diagnostic pipelines are used by hospital teams in their daily clinical routine to process patient samples. As the therapeutic decisions rely on their results, the reproducibility and robustness of these pipelines are a major concern. +On the one hand, diagnostic pipelines are used by hospital teams in their daily clinical routine to process patient samples. As the therapeutic decisions rely on their results, the reproducibility and robustness of these pipelines are a major concern. -On the other hand, research pipelines are more exploratory programs with frequent changes (tool versions, state-of-the-art for the domain) requiring more flexibility and a high level of customization (overriding default settings, adjusting some tools parameters) ; such pipelines have to be easily tunable, versatile, portable, and sometimes sharable with other stakeholders. +On the other hand, research pipelines are more exploratory programs with frequent changes (tool versions, state-of-the-art for the domain) requiring more flexibility and a high level of customization (overriding default settings, adjusting some tools parameters) ; such pipelines have to be easily tunable, versatile, portable, and sometimes sharable with other stakeholders. -To reach these objectives, the bioinformatics platform has made the choice of Nextflow as a common workflow manager for implementing these pipelines which raised technical and organisational challenges that we propose to expose and discussed. We will focus on how: -- we defined common guidelines both for Nextflow usage but also for more generic concerns (language independent, e.g. algorithmic) in order to migrate historical pipelines composed by thousand lines of legacy code, accumulated for years, involving different languages -- we have turned the progressive deployment of Nextflow in our technical environment into an opportunity to generalize and improve our skills and practices regarding some well known best practices in many different areas such as containerisation, reproducibility, modularity and so on. +To reach these objectives, the bioinformatics platform has made the choice of Nextflow as a common workflow manager for implementing these pipelines which raised technical and organisational challenges that we propose to expose and discussed. We will focus on how: +- we defined common guidelines both for Nextflow usage but also for more generic concerns (language independent, e.g. algorithmic) in order to migrate historical pipelines composed by thousand lines of legacy code, accumulated for years, involving different languages +- we have turned the progressive deployment of Nextflow in our technical environment into an opportunity to generalize and improve our skills and practices regarding some well known best practices in many different areas such as containerisation, reproducibility, modularity and so on. -To address some of the concerns mentioned above (portability, scalability, reproducibility, robustness, etc.) we have implemented a MPI (Message Passing Interface) version of the first steps of the variant calling NGS pipelines. Those steps are the alignment, the sorting and the marking of duplicates. We will provide a feedback experience on how we integrated programs optimized with MPI within Nextflow and see how much effort it takes and how it could affect the performances. +To address some of the concerns mentioned above (portability, scalability, reproducibility, robustness, etc.) we have implemented a MPI (Message Passing Interface) version of the first steps of the variant calling NGS pipelines. Those steps are the alignment, the sorting and the marking of duplicates. We will provide a feedback experience on how we integrated programs optimized with MPI within Nextflow and see how much effort it takes and how it could affect the performances. ### Bio -Matthias validated the bioinformatics master of the University of Bordeaux by doing a 6 months internship in Eileen Furlong's laboratory at EMBL Heidelberg under the joint supervision of Charles Girardot. He then joined the Furlong team right after as a bioinformatician and software developer. Dynamix, his master project, is a genome browser plugin for automated genome browsing and was released in Bioinformatics (2017). +Matthias validated the bioinformatics master of the University of Bordeaux by doing a 6 months internship in Eileen Furlong's laboratory at EMBL Heidelberg under the joint supervision of Charles Girardot. He then joined the Furlong team right after as a bioinformatician and software developer. Dynamix, his master project, is a genome browser plugin for automated genome browsing and was released in Bioinformatics (2017). Matthias joined Emmanuel Barillot's team, in the Cancer System Biology Unit at the Curie institute of Paris, in november 2018 and currently works for the Bio-IT/HPC platform under Philippe Hupé's supervision. The platform picked Nextflow to industrialise data processing and analysis workflows, used both for research purposes as well as assisted medical diagnosis. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/olga.md b/src/pages/nfcamp/2019/olga.md index f9b3e413..4c648762 100644 --- a/src/pages/nfcamp/2019/olga.md +++ b/src/pages/nfcamp/2019/olga.md @@ -1,22 +1,24 @@ -title=Nextflow at Chan Zuckerberg Biohub -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Nextflow at Chan Zuckerberg Biohub +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- -## Nextflow at Chan Zuckerberg Biohub +## Nextflow at Chan Zuckerberg Biohub ### Olga Botvinnik -*Data Scientist, Chan Zuckerberg Biohub, USA* +*Data Scientist, Chan Zuckerberg Biohub, USA* -At CZ Biohub, we scale biology to thousands of samples, perform computation both in the cloud and on-prem, and need workflow managers that work with us rather than against us. +At CZ Biohub, we scale biology to thousands of samples, perform computation both in the cloud and on-prem, and need workflow managers that work with us rather than against us. ### Bio Genomics expert applying computation to biology. PhD in single-cell RNA-sequencing. “Grand unified theory of cells”, hashing, sequencing weird creatures, STEM outreach. MIT, Broad Institute, UCSC, UCSD, CZ Biohub. twitch.tv/BioinformaticsBeyonce Open science/data/source. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/paolo-tutorial.md b/src/pages/nfcamp/2019/paolo-tutorial.md index 184d7dc8..4743ea06 100644 --- a/src/pages/nfcamp/2019/paolo-tutorial.md +++ b/src/pages/nfcamp/2019/paolo-tutorial.md @@ -1,14 +1,16 @@ -title=What's new in Nextflow DLS-2 and beyond -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: What's new in Nextflow DLS-2 and beyond +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## What's new in Nextflow: DSL-2 and beyond ### Paolo Di Tommaso -*Research Software engineer, Seqera Labs, Centre for Genomic Regulation (CRG), Spain* +*Research Software engineer, Seqera Labs, Centre for Genomic Regulation (CRG), Spain* This tutorial will give a practical introduction to new features such as modules and sub-workflows that will be included in up-coming Nextflow releases. @@ -16,10 +18,10 @@ and sub-workflows that will be included in up-coming Nextflow releases. ### Bio -Paolo Di Tommaso is a computer scientist and bioinformaticians. He has a long experience as software developer and architect. His main interests are parallel programming, HPC, cloud computing and containerisation technologies. He is an open source advocate and he is the creator and project leader of the Nextflow workflow framework. Recently co-founded [Seqera Labs](http://www.seqera.io), a spin-off -of the Centre for Genomic Regulation (CRG) focused on the development of Nextflow technology. +Paolo Di Tommaso is a computer scientist and bioinformaticians. He has a long experience as software developer and architect. His main interests are parallel programming, HPC, cloud computing and containerisation technologies. He is an open source advocate and he is the creator and project leader of the Nextflow workflow framework. Recently co-founded [Seqera Labs](http://www.seqera.io), a spin-off +of the Centre for Genomic Regulation (CRG) focused on the development of Nextflow technology. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/paolo.md b/src/pages/nfcamp/2019/paolo.md index be51de55..d93866fa 100644 --- a/src/pages/nfcamp/2019/paolo.md +++ b/src/pages/nfcamp/2019/paolo.md @@ -1,26 +1,28 @@ -title=What's new in Nextflow DLS-2 and beyond -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: What's new in Nextflow DLS-2 and beyond +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## What's new in Nextflow: DSL-2 and beyond ### Paolo Di Tommaso -*Research Software engineer, Seqera Labs, Centre for Genomic Regulation (CRG), Spain* +*Research Software engineer, Seqera Labs, Centre for Genomic Regulation (CRG), Spain* -Paolo will talk about the current state of the project, focusing on the development +Paolo will talk about the current state of the project, focusing on the development of new long-await features, such as modularization, sub-workflows and more, which are commonly referenced as DSL-2. ### Bio -Paolo Di Tommaso is a computer scientist and bioinformaticians. He has a long experience as software developer and architect. His main interests are parallel programming, HPC, cloud computing and containerisation technologies. He is an open source advocate and he is the creator and project leader of the Nextflow workflow framework. Recently co-founded [Seqera Labs](http://www.seqera.io), a spin-off -of the Centre for Genomic Regulation (CRG) focused on the development of Nextflow technology. +Paolo Di Tommaso is a computer scientist and bioinformaticians. He has a long experience as software developer and architect. His main interests are parallel programming, HPC, cloud computing and containerisation technologies. He is an open source advocate and he is the creator and project leader of the Nextflow workflow framework. Recently co-founded [Seqera Labs](http://www.seqera.io), a spin-off +of the Centre for Genomic Regulation (CRG) focused on the development of Nextflow technology. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/phil-tutorial.md b/src/pages/nfcamp/2019/phil-tutorial.md index 4f3994b9..323ae7f5 100644 --- a/src/pages/nfcamp/2019/phil-tutorial.md +++ b/src/pages/nfcamp/2019/phil-tutorial.md @@ -1,26 +1,28 @@ -title=Getting started with nf-core -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Getting started with nf-core +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Getting started with nf-core ### Philip Ewels -*Bioinformatics Team Leader, SciLifeLab, Sweden* +*Bioinformatics Team Leader, SciLifeLab, Sweden* The nf-core community provides a range of tools to help new users get to grips with nextflow - both by providing complete pipelines that can be used out of the box, and also by helping developers with best practices. Companion tools can create a bare-bones pipeline from a template scattered with TO-DO pointers and CI with linting tools check code quality. Guidelines and documentation help to get nextflow newbies on their feet in no time. Best of all, the nf-core community is always on hand to help. In this tutorial we discuss the best-practice guidelines developed by the nf-core community, why they're important and give insight into the best tips and tricks for budding nextflow pipeline developers. -### Bio +### Bio Phil Ewels is the Team Leader for Bioinformatics development at the National Genomics Infrastructure (NGI) at SciLifeLab in Stockholm, Sweden. SciLifeLab is a national centre for molecular biosciences for Sweden; the NGI is the largest platform at SciLifeLab. We provide library preparation, sequencing and bioinformatics analysis support for research groups across the country. Phil has been working at SciLifeLab for five years and moved to Sweden after a PhD and postdoc at the University of Cambridge and Babraham Institute in Cambridge, UK. He has has a history of lab and bioinformatics work in epigenetics and has a soft spot for software development with a focus on user friendliness. More recently he's developed MultiQC - a tool that parses log file outputs from multiple samples and bioinformatics tools and generates a single interactive HTML report. Now at SciLifeLab, he and his team focus on the development and scaling up of new lab protocols and bioinformatics solutions for the ISO accredited NGI Genomics Production facility. They develop new analysis pipelines and try to ensure that the tools they write are scalable, reproducible and transferable. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/phil.md b/src/pages/nfcamp/2019/phil.md index 51d2e799..6426e16d 100644 --- a/src/pages/nfcamp/2019/phil.md +++ b/src/pages/nfcamp/2019/phil.md @@ -1,25 +1,27 @@ -title=nf-core community updates -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: nf-core community updates +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## nf-core community updates ### Philip Ewels -*Bioinformatics Team Leader, SciLifeLab, Sweden* +*Bioinformatics Team Leader, SciLifeLab, Sweden* nf-core (http://nf-co.re) is a community effort to collect, curate and collaborate on high quality nextflow bioinformatics workflows. Shared pipelines give increased reproducibility between groups and greater collective development power. To help users and developers we have written an nf-core companion tool with a workflow template, code linting and helper functions for downloading pipelines for offline use and staying up to date. All nf-core pipelines make the best use of Nextflow features possible, with support for Conda, Docker and Singularity, with reference genomes available from the cloud. Consistency between pipelines means that all work in a similar manner with comparable requirements. Now in its second year, the nf-core community continues to develop at a rapid pace. More and more pipelines are being added to the list of stable releases, and the suite of framework tools continues to grow. In this talk I will describe recent updates from the nextflow nf-core community - what's new with pipelines, best-practices, tips & tricks and the nf-core companion tools. -### Bio +### Bio Phil Ewels is the Team Leader for Bioinformatics development at the National Genomics Infrastructure (NGI) at SciLifeLab in Stockholm, Sweden. SciLifeLab is a national centre for molecular biosciences for Sweden; the NGI is the largest platform at SciLifeLab. We provide library preparation, sequencing and bioinformatics analysis support for research groups across the country. Phil has been working at SciLifeLab for five years and moved to Sweden after a PhD and postdoc at the University of Cambridge and Babraham Institute in Cambridge, UK. He has has a history of lab and bioinformatics work in epigenetics and has a soft spot for software development with a focus on user friendliness. More recently he's developed MultiQC - a tool that parses log file outputs from multiple samples and bioinformatics tools and generates a single interactive HTML report. Now at SciLifeLab, he and his team focus on the development and scaling up of new lab protocols and bioinformatics solutions for the ISO accredited NGI Genomics Production facility. They develop new analysis pipelines and try to ensure that the tools they write are scalable, reproducible and transferable. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/program.md b/src/pages/nfcamp/2019/program.md index a41b7631..45025a60 100644 --- a/src/pages/nfcamp/2019/program.md +++ b/src/pages/nfcamp/2019/program.md @@ -1,13 +1,15 @@ -title=Nextflow Camp 2019 Program -date=2019-06-05 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Nextflow Camp 2019 Program +date: 2019-06-05 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- -## Nextflow Camp 2019 Program +## Nextflow Camp 2019 Program -Draft program for the Nexflow Camp (times and activities may be changed in the final line-up due to unforeseen exigencies). +Draft program for the Nexflow Camp (times and activities may be changed in the final line-up due to unforeseen exigencies). #### Thursday, 19 September @@ -15,105 +17,105 @@ Draft program for the Nexflow Camp (times and activities may be changed in the f - - -9.00 - 9.10 + + +9.00 - 9.10 Welcome & introduction
- + - -9.10 - 9.45 + +9.10 - 9.45 nf-core community updates
Phil Ewels
Bioinformatics Team Leader, SciLifeLab, Sweden
[slides] [video] - + - -9.45 - 10.20 + +9.45 - 10.20 Migrating legacy workflows to Nextflow
Alex Peltzer
Bioinformatics Research Scientist, Quantitative Biology Center, Germany - -10.20 - 10.45 + +10.20 - 10.45 Scientific workflows beyond the Ivory Tower
Evan Floden
Seqera Labs, Centre for Genomic Regulation, Spain - -10.45 - 11.15 + +10.45 - 11.15 Coffee break - -11.15 - 13.00 + +11.15 - 13.00 Tutorial - Getting started with nf-core
Phil Ewels
Bioinformatics Team Leader, SciLifeLab, Sweden - -13.00 - 14:00 + +13.00 - 14:00 Lunch - -14.00 - 14.35 + +14.00 - 14.35 Keynote - Accelerating Bioinformatics with Nextflow and the Cloud
Sam Minot
Fred Hutchinson Cancer Research Center, USA - -14.35 - 15.10 + +14.35 - 15.10 Governance & Guardrails: Managing your AWS account to ensure your data is secure and your budget is safe
Lee Pang
Amazon Web Services, USA - -15.10 - 15.22 + +15.10 - 15.22 Nextflow and human microbiome: from data to insights
Francesco Strozzi
Enterome Bioscience, France - -15.10 - 15.22 + +15.10 - 15.22 NF-web: a web interface for Nextflow
Anton Khodak
Wellcome Sanger Institute, UK - -15.34 - 16.05 + +15.34 - 16.05 Coffee break - -16.05 - 18.00 + +16.05 - 18.00 Tutorial - Running Nextflow on AWS Batch
Lee Pang
Amazon Web Services, USA - -18.00 - 20.00 + +18.00 - 20.00 Open - networking - -20.00 + +20.00 Event dinner @@ -127,99 +129,99 @@ Draft program for the Nexflow Camp (times and activities may be changed in the f - - + + - -9.30 - 10.05 + +9.30 - 10.05 What's new in Nextflow: DSL-2 and beyond
Paolo Di Tommaso
Seqera Labs, Centre for Genomic Regulation, Spain - + - -10.05 - 10.40 + +10.05 - 10.40 U-DAWS: Developing and maintaining reproducible workflows for bioinformatics data
Venkat Malladi
UT Southwestern, USA - + - -10.40 - 11.15 + +10.40 - 11.15 Coffee break - -11.15 - 11.40 + +11.15 - 11.40 Pay As You Go Cloud Bioinformatics for Pathogens
Anthony Underwood
Ben Taylor
Centre for Genomic Pathogen Surveillance, Wellcome Trust Sanger Institute, UK - -11.40 - 13.00 + +11.40 - 13.00 Tutorial - Deep dive into Nextflow DSL-2
Paolo Di Tommaso
Seqera Labs, Centre for Genomic Regulation, Spain - + - -13.00 - 14:00 + +13.00 - 14:00 Lunch - -14.00 - 14.25 + +14.00 - 14.25 Robust and reproducible pipelines to support routine clinical diagnostic and research projects in oncology
Matthias Monfort
Institut Curie, France - + - -14.25 - 14.50 + +14.25 - 14.50 FA-nf - A Bioinformatics pipeline for functional annotation implemented in Nextflow
Anna Vlasova
Institute of Molecular Pathology, Austria
Toni Hermoso
- Centre for Genomic Regulation, Spain + Centre for Genomic Regulation, Spain - + - -14.50 - 15.10 + +14.50 - 15.10 Nextflow at Chan Zuckerberg Biohub
Olga Botvinnik
Chan Zuckerberg Biohub, USA - + -15.10 - 15.30 +15.10 - 15.30 Parallel and scalable workflow for the analysis of RNA modifications using Oxford Nanopore direct RNA sequencing
Luca Cozzuto
Centre for Genomic Regulation (CRG), Spain - -15.30 - 16.00 + +15.30 - 16.00 Coffee break - -16.00 - 17.30 + +16.00 - 17.30 Tutorial - DolphinNext: A graphical user interface for distributed data processing of high throughput genomics
Alper Kucukural
Onur Yukselen
UMass Medical School, USA - + - -17.30 - 17.45 + +17.30 - 17.45 Closing remarks @@ -227,6 +229,6 @@ Draft program for the Nexflow Camp (times and activities may be changed in the f -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/richard.md b/src/pages/nfcamp/2019/richard.md index 8fd94bc8..51eb37a0 100644 --- a/src/pages/nfcamp/2019/richard.md +++ b/src/pages/nfcamp/2019/richard.md @@ -1,9 +1,11 @@ -title=Making use of Nextflow-managed WGS analysis for routine disease surveillance in British livestock -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Making use of Nextflow-managed WGS analysis for routine disease surveillance in British livestock +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Making use of Nextflow-managed WGS analysis for routine disease surveillance in British livestock @@ -12,10 +14,10 @@ status=published Bovine tuberculosis is endemic in some parts of England and Wales and as part of the effort to control this disease, the Animal and Plant Health Agency has implemented routine whole genome sequencing of Mycobacterium bovis isolated from cattle. As there are approximately 5000 isolates from across GB each year we have developed an efficient yet comprehensive sample-to-result process. Data processing is fully automated via Nextfow using AWS, and includes a process to assign each sample to a WGS cluster based on matching pre-defined SNPs. This aids field staff in determining the likely source of infection, and aids in understanding the wider epidemiological picture. Furthermore, an approach for linking genetic relatedness and geographical neighborhood has been developed to aid visualization of the data in a readily usable format. These outputs are used in near-real time to manage disease outbreaks. -### Bio +### Bio Dr Richard J Ellis has been at Animal and Plant Health Agency (and its predecessors) for over 10 years and since 2016 has been Head of Genome Analysis. He also oversees molecular biology and bioinformatics at the Agency. Prior to this he held post-doctoral positions at Cardiff University and Imperial College London. He has over 25 years’ experience in molecular microbiology, particularly studying the structure of complex communities and bacterial population genetics. His work now focuses on the application of next generation sequencing technologies for understanding the evolution and spread of pathogens (both bacterial and viral), for investigating diseases of unknown aetiology, and the development of new diagnostic procedures and surveillance programmes. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/sam.md b/src/pages/nfcamp/2019/sam.md index aa2f6662..e440d682 100644 --- a/src/pages/nfcamp/2019/sam.md +++ b/src/pages/nfcamp/2019/sam.md @@ -1,9 +1,11 @@ -title=Accelerating Bioinformatics with Nextflow and the Cloud -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Accelerating Bioinformatics with Nextflow and the Cloud +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Accelerating Bioinformatics with Nextflow and the Cloud @@ -12,10 +14,10 @@ status=published Biologists tend to approach computational analysis in an extremely practical way — coding just enough to answer the question at hand, and knowing that our questions are constantly changing. With that mindset it can be difficult to justify adopting any technology platform which offers increased capabilities in exchange for rigidity or lock-in. In my own research activities I have found that Nextflow offers a very attractive bargain, lots of functionality with very little lock-in. In this talk I will share my own experience moving my microbiome research, which involves computationally microbial metagenomic analysis, into Nextflow, including our approach to cloud computing and the process of rolling out a new technology platform to a large community of researchers across my institution. -### Bio +### Bio -Sam Minot works as a Staff Scientist at Fred Hutch within the Vaccine and Infectious Disease Division focusing on gene-level metagenomics and biomedical research. He graduated from Bowdoin College in 2008 and received his Ph.D. in Cell and Molecular Biology in 2012 from the University of Pennsylvania. He's a big fan of culinary microbiology but tries not to talk about the gut microbiome at dinner parties. +Sam Minot works as a Staff Scientist at Fred Hutch within the Vaccine and Infectious Disease Division focusing on gene-level metagenomics and biomedical research. He graduated from Bowdoin College in 2008 and received his Ph.D. in Cell and Molecular Biology in 2012 from the University of Pennsylvania. He's a big fan of culinary microbiology but tries not to talk about the gut microbiome at dinner parties. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/venkat.md b/src/pages/nfcamp/2019/venkat.md index 9c6be18a..9388395f 100644 --- a/src/pages/nfcamp/2019/venkat.md +++ b/src/pages/nfcamp/2019/venkat.md @@ -1,9 +1,11 @@ -title=U-DAWS: Developing and maintaining reproducible workflows for bioinformatics data -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: U-DAWS: Developing and maintaining reproducible workflows for bioinformatics data +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## U-DAWS: Developing and maintaining reproducible workflows for bioinformatics data @@ -11,16 +13,16 @@ status=published *Director Biofinformatics Core Facility, UT Southwestern, USA* -The current effort at UT Southwestern is to enable researchers to run their own reproducible analysis and enable data exploration. Therefore a workflow system requires: (1) that computational resource allocation can be defined for each step; (2) a particular step can be run in parallel across all samples; (3) serial steps can be submitted to a queue or be activated on a cloud node when previous steps complete; (4) steps can be restarted in the case of machine failure; (5) workflow versions can run reproducibly; (6) common steps can be shared between different analysis and (7) visualization tools are available to aid researchers in understanding very complex data. +The current effort at UT Southwestern is to enable researchers to run their own reproducible analysis and enable data exploration. Therefore a workflow system requires: (1) that computational resource allocation can be defined for each step; (2) a particular step can be run in parallel across all samples; (3) serial steps can be submitted to a queue or be activated on a cloud node when previous steps complete; (4) steps can be restarted in the case of machine failure; (5) workflow versions can run reproducibly; (6) common steps can be shared between different analysis and (7) visualization tools are available to aid researchers in understanding very complex data. Here we present UTSW Data Analysis Workflows for Sequencing (U-DAWS), a system we developed to develop scalable reproducible sequence analysis workflows using Git, Nextflow, Containers, Shiny and Azure. Git projects with sub-modules allows us to share common steps, maintain version control and test new development with continuous integration. Nextflow provides the features necessary to run workflows on a high-performance compute cluster. Shiny provides a versatile method for creating easy to use analysis tools using R, in an easy point and click interface for users. Finally, Azure provides us with the ability to widely distribute and scale our pipelines. In this talk I will describe our architecture and philosophy of building pipelines. Additionally, I will talk about our development of Astrocyte, our GUI interface for running pipelines. Then, I will discuss our efforts with moving our pipelines to Azure. -### Bio +### Bio -Venkat Malladi is a computational biologist and software engineer with expertise in high-throughput sequencing analysis and reproducible software development. He is currently working on implementing and distribution of genomic analysis pipelines to facilitate reproducibility. He directs the daily operations for the BICF and works with collaborators to identify appropriate data and analysis and provide biological context to results obtained. +Venkat Malladi is a computational biologist and software engineer with expertise in high-throughput sequencing analysis and reproducible software development. He is currently working on implementing and distribution of genomic analysis pipelines to facilitate reproducibility. He directs the daily operations for the BICF and works with collaborators to identify appropriate data and analysis and provide biological context to results obtained. -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfcamp/2019/zamin.md b/src/pages/nfcamp/2019/zamin.md index 18deae4b..1ec588b7 100644 --- a/src/pages/nfcamp/2019/zamin.md +++ b/src/pages/nfcamp/2019/zamin.md @@ -1,9 +1,11 @@ -title=Shareable and scalable pathogen genomics with Nextflow, containers and Clockwork -date=2019-05-28 -type=col8 -tags=nextflow,nfcamp,2019,workshop -status=published -~~~~~~ +--- +title: Shareable and scalable pathogen genomics with Nextflow, containers and Clockwork +date: 2019-05-28 +type: col8 +tags: nextflow,nfcamp,2019,workshop +status: published +layout: "@layouts/Page.astro" +--- ## Shareable and scalable pathogen genomics with Nextflow, containers and Clockwork @@ -11,7 +13,7 @@ status=published *Research Group Leader, European Bioinformatics Institute (EMBL-EBI), UK* -Genomics is becoming ubiquitous in microbiology, and there are a plethora of variant analysis tools. I will give a tutorial on our new Clockwork pipeline which we have built for our 100,000 M. tuberculosis genomes project. +Genomics is becoming ubiquitous in microbiology, and there are a plethora of variant analysis tools. I will give a tutorial on our new Clockwork pipeline which we have built for our 100,000 M. tuberculosis genomes project. There are 4 key components which might be of interest. First: the pipeline is open source, containerised with singularity, and has been successfully been run on Azure, EBI internal cluster, our own laptops, and in training courses in India and Peru. Second: the pipeline includes automated submission to the European Nucleotide Archive (taking metadata in spreadsheet form), removal of human/HIV sequence contamination before submission, variant calling with both samtools and cortex, and state-of-the-art variant adjudication with genome graphs to give high sensitivity and specificity calls, and automated tracking in a database. Third, the pipeline also allows joint genotyping, in order to produce a single "wide" VCF giving consistent genotype calls and likelihoods for all samples at all sites. @@ -22,6 +24,6 @@ I'll talk through how to do this, and also some of the challenges we have seen i Zamin Iqbal is a computational biologist at the EBI. He works on fundamental methods for genome analysis (eg cortex, BIGSI) and translation of these methods into clinical and public health practise (e.g drug resistance prediction for TB with Mykrobe). -### Registration +### Registration -To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). \ No newline at end of file +To attend Nextflow Camp 2019 register at [this link](https://www.crg.eu/en/event/coursescrg-nextflow-2019). diff --git a/src/pages/nfhack/2018/alessia.md b/src/pages/nfhack/2018/alessia.md index 543cad66..4ab395b6 100644 --- a/src/pages/nfhack/2018/alessia.md +++ b/src/pages/nfhack/2018/alessia.md @@ -1,14 +1,14 @@ -title=Nextflow on the go -date=2018-10-16 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Nextflow on the go +date: 2018-10-16 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Nextflow on the go ### Alessia Visconti -*Research Fellow, King's College London, UK* +*Research Fellow, King's College London, UK* [YAMP](https://github.com/alesssia/YAMP) (Yet Another Metagenomics Pipeline) is a workflow that enables the analysis of whole shotgun metagenomic data while using containerization to ensure computational reproducibility and facilitate collaborative research. Being based on Nextflow, YAMP can be executed on any UNIX-like system and offers seamless support for multiple job schedulers as well as for the Amazon AWS cloud. @@ -18,14 +18,14 @@ The test was carried on during the ARM, Atos and Cavium BioData Hackathon challe During the two-day Hackathon, Team GoGut successfully and easily ported YAMP onto ARM’s latest mobile architecture, the ARM Cavium ThunderX2, showing that the analysis of microbial sequences, and of biological data at large, can be successfully taken out of centralised data centres, and that Nextflow offers a mature solution also for mobile applications. -### Deck +### Deck -### Bio +### Bio [Alessia Visconti](https://www.researchgate.net/profile/Alessia_Visconti) is a research fellow in Computational Biology at the Department of Twin Research and Genetic Epidemiology, King’s College London. Her research activity deals with the study of the genomics and epigenomics of human diseases, with a focus on melanoma, cognition and neurodevelopmental disorders, and IgA nephropathy. Recently, she became interested in the human microbiome and its connections to human health and diseases. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/antonio.md b/src/pages/nfhack/2018/antonio.md index fd681780..91ba1e8c 100644 --- a/src/pages/nfhack/2018/antonio.md +++ b/src/pages/nfhack/2018/antonio.md @@ -1,14 +1,14 @@ -title=Nextflow for supporting the European Reference Laboratory for GMO Food and Feed -date=2018-11-15 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Nextflow for supporting the European Reference Laboratory for GMO Food and Feed +date: 2018-11-15 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Nextflow for supporting the European Reference Laboratory for GMO Food and Feed ### Antonio Puertas Gallardo -*Bioinformatician, Directorate General Joint Research Centre, European Commission* +*Bioinformatician, Directorate General Joint Research Centre, European Commission* The European Union Reference Laboratory for Genetically Modified Food and Feed (EU-RL GMFF), hosted by the Joint Research Centre (JRC) of the European Commission, must, pursuant to Article 32 of Regulation (EC) N. 882/2004, provide National Reference Laboratories with reference methods and tools for GMO analysis. Commission Regulation (EC) No 641/2004 requires the EU-RL GMFF to maintain a database containing GMO events sequence. The polymerase chain reaction (PCR) has proven to be the most accurate and reliable technique available for GMO detection, identification and quantification and is applicable to a wide range of samples, from seeds to highly processed food and feed. The validation of PCR-based detection methods is a fundamental task that requires integrating the combination of both the experimental approach and of bioinformatics analyses for sequence similarity searches. The EU-RL GMFF is requested to perform in silico validation of the proposed detection methods, with respect to specificity. @@ -20,11 +20,11 @@ We are now exploring with Nexflow a new framework based on new workflows in orde -### Bio +### Bio Born and raised in Argentina, Antonio Puertas Gallardo has studied Electronic Engineering. -He arrived to the European Commission in 2003 as IT System Manager. He was responsible for Joint -Research Centre (JRC) data centre since 2005 to 2008. Then he was in charge for JRC Central Storage infrastructure since 2006 to 2012. He was also IT System manager and responsible for HPC in the JRC +He arrived to the European Commission in 2003 as IT System Manager. He was responsible for Joint +Research Centre (JRC) data centre since 2005 to 2008. Then he was in charge for JRC Central Storage infrastructure since 2006 to 2012. He was also IT System manager and responsible for HPC in the JRC since 2008 to 2013. In 2014 he moved to the JRC Bioinformatics team. Today he is dealing with HPC @@ -33,6 +33,6 @@ he started to work with Natural Language Processing and Machine Understanding. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/diogo.md b/src/pages/nfhack/2018/diogo.md index 60bd4c8c..9d42b689 100644 --- a/src/pages/nfhack/2018/diogo.md +++ b/src/pages/nfhack/2018/diogo.md @@ -1,25 +1,25 @@ -title=FlowCraft: A modular, extensible and flexible tool to build, monitor and report Nextflow pipelines -date=2018-10-30 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: FlowCraft: A modular, extensible and flexible tool to build, monitor and report Nextflow pipelines +date: 2018-10-30 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## FlowCraft: A modular, extensible and flexible tool to build, monitor and report Nextflow pipelines ### Diogo Nuno Silva -*Postdoctoral researcher, Instituto de Medicina Molecular João Lobo Antunes, Portugal* +*Postdoctoral researcher, Instituto de Medicina Molecular João Lobo Antunes, Portugal* -Nextflow has emerged as a promising framework for building parallelized, scalable and reproducible workflows using software containers. Amongst its most attractive features are the support for multi-scale containerization and its portability, which allows the same code to be executed on multiple platforms with different batch schedulers and container systems. +Nextflow has emerged as a promising framework for building parallelized, scalable and reproducible workflows using software containers. Amongst its most attractive features are the support for multi-scale containerization and its portability, which allows the same code to be executed on multiple platforms with different batch schedulers and container systems. -Usually, the generation of Nextflow pipelines entails the creation of a main Nextflow file with all the declarations of the pipeline’s processes, its channels and operators, and optional configuration and auxiliary files that are necessary for its execution. However, due to the fast pace and continuous development of software for genomic analyses and the need for a quick response to this change by altering existing pipelines, it would be important to make this process more agile and dynamic. Furthermore, the analyses’ goals also change over time and variations of existing pipelines are needed to answer new questions. +Usually, the generation of Nextflow pipelines entails the creation of a main Nextflow file with all the declarations of the pipeline’s processes, its channels and operators, and optional configuration and auxiliary files that are necessary for its execution. However, due to the fast pace and continuous development of software for genomic analyses and the need for a quick response to this change by altering existing pipelines, it would be important to make this process more agile and dynamic. Furthermore, the analyses’ goals also change over time and variations of existing pipelines are needed to answer new questions. -The FlowCraft project aims to address these issues by proposing a new tool that leverages the combination of Nextflow and docker/singularity containers to assemble, monitor and report scientific pipelines. The premise of FlowCraft is simple: the users create a broad set of components written in Nextflow language that can then be freely and easily assembled into ready-to-use pipelines taking full advantage of Nextflow execution. These components are modular pieces of software or scripts (e.g. FastQC or Trimmomatic) that have a set of attributes, including input and output types and other parameters. FlowCraft’s engine then connects them, handling the linking and forking of channels automatically, among several other features. +The FlowCraft project aims to address these issues by proposing a new tool that leverages the combination of Nextflow and docker/singularity containers to assemble, monitor and report scientific pipelines. The premise of FlowCraft is simple: the users create a broad set of components written in Nextflow language that can then be freely and easily assembled into ready-to-use pipelines taking full advantage of Nextflow execution. These components are modular pieces of software or scripts (e.g. FastQC or Trimmomatic) that have a set of attributes, including input and output types and other parameters. FlowCraft’s engine then connects them, handling the linking and forking of channels automatically, among several other features. -This modularity has two major advantages: (i) each process on a FlowCraft Nextflow pipeline can be written once and re-used to quickly build fairly complex pipelines for different ends with minimal effort; and (ii) adding/modifying parts of a pipeline does not require modification in the codebase of other components. This means that new additions to any pipeline can be easily introduced, and modifications to existing pipelines only require replacing the corresponding components. +This modularity has two major advantages: (i) each process on a FlowCraft Nextflow pipeline can be written once and re-used to quickly build fairly complex pipelines for different ends with minimal effort; and (ii) adding/modifying parts of a pipeline does not require modification in the codebase of other components. This means that new additions to any pipeline can be easily introduced, and modifications to existing pipelines only require replacing the corresponding components. -FlowCraft further extends the capabilities of Nextflow by providing an Inspection mode that monitors the execution of a pipeline in real time, either in a terminal using a curses interface, or via the [FlowCraft web application](https://www.youtube.com/watch?v=liG1hlEcs5M). Furthermore, it is currently under development a Report mode that allows the interactive visualization of the results from each component in the web application. +FlowCraft further extends the capabilities of Nextflow by providing an Inspection mode that monitors the execution of a pipeline in real time, either in a terminal using a curses interface, or via the [FlowCraft web application](https://www.youtube.com/watch?v=liG1hlEcs5M). Furthermore, it is currently under development a Report mode that allows the interactive visualization of the results from each component in the web application. The final aim of this project is to have a flexible, extensible and modular system built on top of Nextflow for building, monitoring and reporting scientific pipelines in any omics field. Flowcraft can be found at [this link](https://github.com/assemblerflow/flowcraft/) and the complete user guide is hosted at [this link](http://flowcraft.readthedocs.io/en/latest/). @@ -28,11 +28,11 @@ The final aim of this project is to have a flexible, extensible and modular syst -### Bio +### Bio Diogo is a freshly minted postdoctoral researcher working on genomics of fungal and bacterial pathogens. He is graduated in Environmental Biology, have a masters in Human and Environmental Biology and a PhD in Bioinformatics and Evolutionary Biology. During his research he have grown a keen fondness for computational biology and all things (bio)informatics. He started hacking on Nextflow as soon as I discovered the framework (about one year ago) and since then he's never looked back on ways of building workflows and scientific pipelines. He is currently active in developing workflows for the analysis of bacterial and fungal genomic data and using Nextflow whenever possible/relevant. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/evan.md b/src/pages/nfhack/2018/evan.md index c87b582a..b5e97be3 100644 --- a/src/pages/nfhack/2018/evan.md +++ b/src/pages/nfhack/2018/evan.md @@ -1,14 +1,14 @@ -title=Nextflow support and enhancements -date=2018-10-20 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Nextflow support and enhancements +date: 2018-10-20 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Nextflow support and enhancements ### Evan Floden -*PhD Student, Centre for Genomic Regulation (CRG), Spain* +*PhD Student, Centre for Genomic Regulation (CRG), Spain* A brief introduction to the commercial support and training available for Nextflow users. The focus is on those organisations running mission critical applications and teams who want to learn about the technology in-depth, starting from basic through to advanced concepts. @@ -17,11 +17,11 @@ A brief introduction to the commercial support and training available for Nextfl -### Bio +### Bio Evan Floden is about to complete his PhD in the Comparative Bioinformatics group at the CRG. He has been actively involved in the Nextflow project for the past three years and recently co-founded [Seqera Labs](http://www.seqera.io) to provide commercial support, training and enhancements for Nextflow users. Prior to his PhD, he worked as a bioinformatician at Rfam at the Sanger Institute and as a development scientist at Aroa Biosurgery. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/francesco.md b/src/pages/nfhack/2018/francesco.md index 67d3c76f..ffbf2171 100644 --- a/src/pages/nfhack/2018/francesco.md +++ b/src/pages/nfhack/2018/francesco.md @@ -1,20 +1,20 @@ -title=Industrial Personalised Immunotherapy Pipeline Development with Nextflow -date=2018-10-22 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Industrial Personalised Immunotherapy Pipeline Development with Nextflow +date: 2018-10-22 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Agile pipelines with Nextflow: how to go from development to production without pain ### Francesco Strozzi -*Head of Bioinformatics at Enterome Bioscience, France* +*Head of Bioinformatics at Enterome Bioscience, France* -Nextflow allows creating pipelines in a very agile way, starting from simple blocks and processes to test new software and parameters. Once a single block of the pipeline works as expected and there are no errors, the developer can simply add a new process and start exploring and testing a new layer of the pipeline. The main Nextflow features allowing this agile development are the data flow model, jobs traceability and the possibility to resume workflows, without the need to re-run unchanged and already completed steps. +Nextflow allows creating pipelines in a very agile way, starting from simple blocks and processes to test new software and parameters. Once a single block of the pipeline works as expected and there are no errors, the developer can simply add a new process and start exploring and testing a new layer of the pipeline. The main Nextflow features allowing this agile development are the data flow model, jobs traceability and the possibility to resume workflows, without the need to re-run unchanged and already completed steps. -The advanced logging and reporting system that Nextflow offers are also critical features helping with jobs profiling and monitoring. Finally, the support for multiple executors and the transparent use of software containers allow to prototype pipelines locally and then to port them in production on large HPC systems or on the cloud. +The advanced logging and reporting system that Nextflow offers are also critical features helping with jobs profiling and monitoring. Finally, the support for multiple executors and the transparent use of software containers allow to prototype pipelines locally and then to port them in production on large HPC systems or on the cloud. -In this talk, agile pipelines development with Nextflow will be presented from the point of view of Enterome Bioscience, a biotech company working on the human gut microbiome. In the company, cutting-edge bioinformatics pipelines are central to support the development of diagnostics and therapeutics on this innovative field. +In this talk, agile pipelines development with Nextflow will be presented from the point of view of Enterome Bioscience, a biotech company working on the human gut microbiome. In the company, cutting-edge bioinformatics pipelines are central to support the development of diagnostics and therapeutics on this innovative field. The ensemble of Nextflow features allows the Bioinformatics Team to transition without pain from a development stage, where pipelines are designed locally or on very small datasets, to a production phase where full datasets are processed with complete pipeline versions on the AWS cloud. A perspective on pipeline unit testing will be also presented, as a topic of possible broader interest for the Nextflow community. @@ -22,11 +22,11 @@ The ensemble of Nextflow features allows the Bioinformatics Team to transition w -### Bio +### Bio Bioinformatics Head at Enterome Bioscience, [Francesco Strozzi](https://www.linkedin.com/in/francescostrozzi/) has more than 14 years of experience in bioinformatics and with the management of bioinformatic teams across genomics, biotechnology and biomedicine fields. In his career he focused on the development of data analysis pipelines, data architecture strategies, and the application of computational methods to support and drive research projects and production platforms. Francesco has more than 6 years of experience with metagenomics and computational microbiology to characterise single microorganisms and complex communities, including the human gut, soil and rumen microbiome. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/julia.md b/src/pages/nfhack/2018/julia.md index 929d8291..c47a64af 100644 --- a/src/pages/nfhack/2018/julia.md +++ b/src/pages/nfhack/2018/julia.md @@ -1,14 +1,14 @@ -title=Exploiting orthology and de novo transcriptome assembly to refine target sequence information -date=2018-10-20 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Exploiting orthology and de novo transcriptome assembly to refine target sequence information +date: 2018-10-20 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Exploiting orthology and de novo transcriptome assembly to refine target sequence information ### Julia Soellner -*PhD student, Boehringer Ingelheim & University Tuebingen, Germany* +*PhD student, Boehringer Ingelheim & University Tuebingen, Germany* The ability to generate recombinant proteins facilitates several steps in drug discovery research, e.g. investigating drug-target-interactions or assessing a compound’s efficacy and safety. For this, the target’s exact protein sequence is required. Public databases such as Ensembl, UniProt and RefSeq are an important source of sequence information. However, many sequences for non-human organisms are predicted by computational pipelines and may thus be incomplete or contain errors. We present a Nextflow pipeline which exploits paired-end RNA-Seq reads for sequence validation and refinement by making use of sequence homology relationships across different species. We applied the pipeline to refine and validate the orthologues of all known human protein sequences in six species. @@ -16,10 +16,10 @@ The ability to generate recombinant proteins facilitates several steps in drug d -### Bio +### Bio Julia is a bioinformatician by training and she is currently in the second year of my PhD. Her PhD project is conducted at Boehringer Ingelheim under the supervision of Prof. Kay Nieselt at University Tuebingen. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/luca.md b/src/pages/nfhack/2018/luca.md index 23ad61f1..be315f54 100644 --- a/src/pages/nfhack/2018/luca.md +++ b/src/pages/nfhack/2018/luca.md @@ -1,14 +1,14 @@ -title=Scaling genomics in the AWS cloud -date=2018-10-22 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Scaling genomics in the AWS cloud +date: 2018-10-22 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Scaling genomics in the AWS cloud ### Luca Carrogu -*Software Development Engineer at Amazon Web Services, Italy* +*Software Development Engineer at Amazon Web Services, Italy* An update on all the latest technical developments from AWS's Engineering team that we’re building for the research and engineering community. We’ll deep dive on some that are particularly relevant to to Nextflow's users and developers and ask for input from the audience to help us understand what other things we can engineer with the advice and insights from people in the audience. @@ -16,11 +16,11 @@ An update on all the latest technical developments from AWS's Engineering team t -### Bio +### Bio [Luca Carrogu](https://www.linkedin.com/in/lucacarrogu/) is a Software Development Engineer. In 2009 he graduated in Electronic Engineering at Università di Cagliari and right after graduation joined NICE Software as a full stack developer. In 2016 NICE was acquired by Amazon Web Services where he joined the HPC team. His main field of interest is to facilitate HPC workflow for non-technical user. Currently he is working on EnginFrame, which is a Grid Portal that enables user-friendly and application-oriented HPC job submission, control and monitoring, and on CfnCluster, which is a framework that deploys and maintains high performance computing clusters on Amazon Web Services.] -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/luke-goodsell.md b/src/pages/nfhack/2018/luke-goodsell.md index 4ee0bf6f..a8ed488c 100644 --- a/src/pages/nfhack/2018/luke-goodsell.md +++ b/src/pages/nfhack/2018/luke-goodsell.md @@ -1,29 +1,29 @@ -title=Industrial Personalised Immunotherapy Pipeline Development with Nextflow -date=2018-10-11 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Industrial Personalised Immunotherapy Pipeline Development with Nextflow +date: 2018-10-11 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Industrial Personalised Immunotherapy Pipeline Development with Nextflow ### Luke Goodsell -*Team Leader, Bioinformatics Software Development, Achilles Therapeutics, UK* +*Team Leader, Bioinformatics Software Development, Achilles Therapeutics, UK* Cancer immunotherapy is a promising means of treatment that uses the patient's own immune system to destroy cancer cells. For over three decades, labs have been exploring ways to identify tumour specific surface proteins (neoantigens) and use them to induce the patient's immune cells to specifically target their cancer. This process is labour intensive and has highly variable results, in part due to tumour heterogeneity. - + [Achilles Therapeutics](https://achillestx.com/) is developing a process for delivering a patient-specific immunotherapy that exploits recent research into tumour evolution to reliably identify and target the neoantigens that occur early in a tumour's development and thus are present in every tumour cell (i.e. clonal). At the heart of this process is a bioinformatic pipeline that takes DNA- and RNA-sequencing data and reports clonal, actionable neoantigens. Achilles inherited an R-based pipeline suited for answering cutting-edge research questions from one of its academic founding labs, but adapting this for industrial use posed many challenges including: adaptations for high-throughput operation, guaranteeing reproducibility, portability to other compute environments (particularly AWS), conformance to required standards for clinical use, end-to-end automation and quality control, "fail-safe" operation and rapid prototyping of new features. - + This presentation will describe how the Achilles bioinformatics team used Nextflow (and other tools) to adapt a research-focussed sequence-processing pipeline into an efficient, reliable, portable and risk-managed system suitable for delivering a clinical personalised immunotherapy. This will include tips and tricks for developing modular Nextflow workflows and for ensuring early detection of errors. ### Deck -### Bio +### Bio [Luke Goodsell](https://www.linkedin.com/in/luke-goodsell-910a2793/) leads the Bioinformatics Software Development team at Achilles Therapeutics, where he has worked for 2 years. Before that he worked as a Computational Biologist at Oxford Gene Technology after completing his PhD in Structural, Computational and Chemical Biology. He is interested in applying data analysis techniques and software engineering experience to identify answers to bioinformatics questions and implementing robust, dependable software that uses those findings. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/paolo.md b/src/pages/nfhack/2018/paolo.md index 8daff670..b39b0cdf 100644 --- a/src/pages/nfhack/2018/paolo.md +++ b/src/pages/nfhack/2018/paolo.md @@ -1,14 +1,14 @@ -title=The state of Nextflow -date=2018-10-20 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: The state of Nextflow +date: 2018-10-20 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## The state of Nextflow ### Paolo Di Tommaso -*Research Software engineer, Centre for Genomic Regulation (CRG), Spain* +*Research Software engineer, Centre for Genomic Regulation (CRG), Spain* This presentation will give an overview of the current state of Nextflow technology, the achieved milestones, the upcoming changes and the open challenges facing the reproducibility of of in-silico genomic data analysis. @@ -16,14 +16,14 @@ This presentation will give an overview of the current state of Nextflow technol -### Bio +### Bio -Paolo Di Tommaso is a computer scientist and bioinformaticians. He has 20 years long experience as software developer and architect. His main interests are parallel programming, HPC, cloud computing and containerisation technologies. He is an open source advocate and he is the creator and project leader of the Nextflow workflow framework. Recently co-founded [Seqera Labs](http://www.seqera.io), a spin-off -of the Centre for Genomic Regulation (CRG) focused on the development of Nextflow technology. +Paolo Di Tommaso is a computer scientist and bioinformaticians. He has 20 years long experience as software developer and architect. His main interests are parallel programming, HPC, cloud computing and containerisation technologies. He is an open source advocate and he is the creator and project leader of the Nextflow workflow framework. Recently co-founded [Seqera Labs](http://www.seqera.io), a spin-off +of the Centre for Genomic Regulation (CRG) focused on the development of Nextflow technology. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/phil.md b/src/pages/nfhack/2018/phil.md index 925a859e..702ccee4 100644 --- a/src/pages/nfhack/2018/phil.md +++ b/src/pages/nfhack/2018/phil.md @@ -1,14 +1,14 @@ -title=nf-core: A community effort to collect curated Nextflow pipelines -date=2018-10-11 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: nf-core: A community effort to collect curated Nextflow pipelines +date: 2018-10-11 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## nf-core: A community effort to collect curated Nextflow pipelines ### Philip Ewels -*Head of Genomics Applications Development at SciLifeLab National Genomics Infrastructure, Sweden* +*Head of Genomics Applications Development at SciLifeLab National Genomics Infrastructure, Sweden* The [Swedish National Genomics Infrastructure](https://ngisweden.scilifelab.se/) (NGI) has been a key user and proponent of nextflow since soon after its initial release. We have produced several popular pipelines as well as writing recommendations on best practices. Our oldest pipeline for RNA sequencing analysis is used in production at NGI Stockholm and has been used to process nearly 20,000 samples since April 2017. @@ -22,13 +22,13 @@ There has been fantastic feedback from the user community about nf-core. The fir -### Bio +### Bio [Phil Ewels](https://www.linkedin.com/in/philewels/) is the head of the Genomics Applications Development facility at the National Genomics Infrastructure (NGI) at SciLifeLab in Stockholm, Sweden. SciLifeLab is a national centre for molecular biosciences for Sweden; the NGI is the largest platform at SciLifeLab. We provide library preparation, sequencing and bioinformatics analysis support for research groups across the country. Phil has been working at SciLifeLab for four years and moved to Sweden after a PhD and postdoc at the University of Cambridge and Babraham Institute in Cambridge, UK. He has has a history of lab and bioinformatics work in epigenetics and has a soft spot for software development with a focus on user friendliness. More recently he's developed [MultiQC](https://multiqc.info/) - a tool that parses log file outputs from multiple samples and bioinformatics tools and generates a single interactive HTML report. Now head of the Genomics Applications Development facility, he and his team focus on the development and scaling up of new lab protocols and bioinformatics solutions for the ISO accredited NGI Genomics Production facility. They develop new analysis pipelines and try to ensure that the tools they write are scalable, reproducible and transferable. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/roger.md b/src/pages/nfhack/2018/roger.md index 075bc927..5634b4c5 100644 --- a/src/pages/nfhack/2018/roger.md +++ b/src/pages/nfhack/2018/roger.md @@ -1,14 +1,14 @@ -title=QCloud: A web-based quality control system for mass spectrometry-based proteomics laboratories -date=2018-10-30 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: QCloud: A web-based quality control system for mass spectrometry-based proteomics laboratories +date: 2018-10-30 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## QCloud: A web-based quality control system for mass spectrometry-based proteomics laboratories ### Roger Olivella -*Proteomics Unit, Center for Genomic Regulation (CRG), Spain* +*Proteomics Unit, Center for Genomic Regulation (CRG), Spain* [QCloud](https://qcloud.crg.eu) is a web-based system to support proteomics laboratories in daily quality assessment using a user-friendly interface, easy setup, automated data processing and archiving, and unbiased instrument evaluation. QCloud supports the most common targeted and untargeted proteomics workflows, it accepts data formats from different vendors and it enables a user-selected vocabulary to report incidences and annotate the acquired data. @@ -16,11 +16,11 @@ status=published -### Bio +### Bio Roger graduated at the Universitat Autònoma de Barcelona in Physics. Then he worked as a software engineer in several research centers until he started to work as a bioinformatician at the IRB in 2013. Finally, he moved to the Proteomics Unit at the CRG in 2015 until today. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/simone.md b/src/pages/nfhack/2018/simone.md index 61a90c9f..4b26bd4f 100644 --- a/src/pages/nfhack/2018/simone.md +++ b/src/pages/nfhack/2018/simone.md @@ -1,14 +1,14 @@ -title=Using Nextflow to create scalable and reproducible pipelines at Genomics Medicine Ireland -date=2018-11-02 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Using Nextflow to create scalable and reproducible pipelines at Genomics Medicine Ireland +date: 2018-11-02 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Using Nextflow to create scalable and reproducible pipelines at Genomics Medicine Ireland ### Simone Coughlan -*Bioinformatician, Genomics Medicine Ireland, Ireland* +*Bioinformatician, Genomics Medicine Ireland, Ireland* [Genomics Medicine Ireland](https://genomicsmed.ie/) (GMI) is an Irish life sciences company performing large-scale studies in the Irish population using whole genome sequencing (WGS) and additional omics technologies. It works in collaboration with the healthcare system, patients, researchers and industry to advance understanding of the genetic basis of multiple diseases, to aid in the discovery of new diagnostics and therapeutics. In order to do this, our data analysis pipelines must be reproducible and easily scale to large numbers of samples. At GMI, we have created multiple Nextflow pipelines, which also employ the use of containerisation technologies and Conda environments to ensure full reproducibility. These include pipelines to perform analysis of genotyping arrays, concordance analysis of genotyping and sequencing data, copy number variation calling and downstream processing of files for a validated secondary analysis pipeline. In summary, the ability to rapidly prototype workflows using any tool, resume execution upon failure, scale easily and maintain a consistent environment across runs make Nextflow well suited to our work. @@ -16,10 +16,10 @@ status=published -### Bio +### Bio Dr [Simone Coughlan](https://www.linkedin.com/in/simone-coughlan-9b789830/) is a bioinformatics scientist at Genomics Medicine Ireland, an Irish Life Sciences company undertaking large scale analysis of genomics and other omics data to help discover new diagnostics and therapeutics. She has a PhD in Bioinformatics from the National University of Ireland Galway and a background in parasite and bacterial genomics before turning to humans where she is now involved in research across multiple diseases. Writing robust, scalable pipelines is an essential part of the job and Nextflow allows her to do this with minimal fuss! -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/tiffany.md b/src/pages/nfhack/2018/tiffany.md index b90d41a7..3792b213 100644 --- a/src/pages/nfhack/2018/tiffany.md +++ b/src/pages/nfhack/2018/tiffany.md @@ -1,14 +1,14 @@ -title=IARC Nextflow pipelines: towards efficient cancer genomics analyses -date=2018-10-16 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: IARC Nextflow pipelines: towards efficient cancer genomics analyses +date: 2018-10-16 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## IARC Nextflow pipelines: Towards efficient cancer genomics analyses ### Tiffany Delhomme -*PhD student, IARC (WHO), France* +*PhD student, IARC (WHO), France* A current effort is emerging inside the [IARC](https://www.iarc.fr/) to enable researchers to produce accurate cancer genomics results. This involves both a state-of-the-art method selection but also an efficient way to use them. To ensure this, IARC bioinformaticians are actively developing cancer genomics pipelines emphasizing performance, easy usage, reproducibility and computational efficiency. Our approach for that consists in using the Nextflow language to write our pipelines, and the combination of Docker, Singularity and Conda to distribute them and install dependencies. In this talk I will describe the global architecture of our cancer genomics pipelines. Then, I will focus my talk on one of the most complicated pipeline we have developed, which is used to estimate intra-tumor heterogeneity from whole-genome sequencing of multiple tumor regions of a cancer patient. @@ -17,10 +17,10 @@ A current effort is emerging inside the [IARC](https://www.iarc.fr/) to enable r -### Bio +### Bio [Tiffany Delhomme](https://www.researchgate.net/profile/Tiffany_Delhomme2) is currently working at the Section of Genetics, International Agency for Research on Cancer, in the Genetics Cancer Susceptibility Group. She is a PhD candidate trying to decipher cancer genomics issues using computational/statistical methods. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). diff --git a/src/pages/nfhack/2018/vladimir-kiselev.md b/src/pages/nfhack/2018/vladimir-kiselev.md index 71498e34..3ff1c141 100644 --- a/src/pages/nfhack/2018/vladimir-kiselev.md +++ b/src/pages/nfhack/2018/vladimir-kiselev.md @@ -1,14 +1,14 @@ -title=Nextflow at the heart of UK genomics -date=2018-10-11 -type=col8 -tags=nextflow,nfhack18,workshop -status=published -~~~~~~ +--- +title: Nextflow at the heart of UK genomics +date: 2018-10-11 +tags: nextflow,nfhack18,workshop +layout: "@layouts/Page.astro" +--- ## Nextflow at the heart of UK genomics ### Vladimir Kiselev -*Head of Cellular Genetics Informatics, Wellcome Sanger Institute, UK* +*Head of Cellular Genetics Informatics, Wellcome Sanger Institute, UK* The [Wellcome Sanger Institute](https://www.sanger.ac.uk/) is one of the biggest genomics centres in the world. To accommodate its compute needs it has ~10'000 cores on our LSF compute farm and ~12'000 cores on our OpenStack cloud environment. The Cellular Genetics programme is one of five of the Institute's programmes and investigates cell biology and human disease by focusing on cell types implicated in these processes. We utilise Nextflow to run our pipelines on both LSF and OpenStack environments. In my talk I will present our recent experiences and will concentrate on Kubernetes integration in Nextflow. @@ -16,10 +16,10 @@ The [Wellcome Sanger Institute](https://www.sanger.ac.uk/) is one of the biggest -### Bio +### Bio [Vladimir](https://www.sanger.ac.uk/people/directory/vladimir-yu-kiselev) graduated from the Moscow Institute of Physics and Technology in 2008 with a degree in Applied Physics and Mathematics. He then changed direction and did a PhD in Computational Biology at the University of Edinburgh. From 2011 he worked on multiple Bioinformatics projects at the European Bioinformatics Institute, the Babraham Institute and the Wellcome Trust Sanger Institute. In 2018 he became the Head of the core IT team at the Cellular Genetics programme of the Sanger Institute. -### More information +### More information -The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0). \ No newline at end of file +The event program is available at [this link](https://github.com/nextflow-io/nf-hack18/blob/master/schedule.md). For registration and other information check it out [this page](http://www.crg.eu/en/event/coursescrg-nextflow-reproducible-silico-genomics-0).