Teams: BSC-CES
Organizations: Barcelona Supercomputing Center (BSC-CNS)

Expertise: Scientific workflow developement, workflow managers, Software Engineering, open source, fuzzy logic, graphs
Tools: CWL, Autosubmit, Cylc, ecFlow
Research Engineer (Workflow Engineer) at the Barcelona Supercomputing Center (BSC) in Barcelona, Spain. Working on the Autosubmit workflow manager.
Previously NIWA/Cylc, and Curii/CWL.
Expertise: Bioinformatics, Genomics, Metagenomics, Data Management
Tools: CWL, Jupyter notebook, Nextflow, Molecular Biology, Workflows, Microbiology, Transcriptomics, Perl, Python, R
Expertise: Metagenomics, amplicon analysis, Microbiology, Systems Biology
Tools: CWL
I am a bioinformatician working on microbial ecology and ecosystem functioning at the microbial dimension.
This BioExcel best practice guide outlines the development process for writing a workflow using the Common Workflow Language (CWL), from creating and selecting tools like BioBB, through early experimentation, reuse and testing, to optimization and ensuring reproducibility before publication in workflow repositories.
Creators: Stian Soiland-Reyes, Douglas Lowe, Robin Long
Submitter: Stian Soiland-Reyes
Abstract (Expand)
Authors: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Date Published: 7th Nov 2019
Publication Type: Journal
DOI: 10.1093/nar/gkz1035
Citation: Nucleic Acids Research,gkz1035
Abstract (Expand)
Authors: Michael R. Crusoe, Sanne Abeln, Alexandru Iosup, Peter Amstutz, John Chilton, Nebojša Tijanić, Hervé Ménager, Stian Soiland-Reyes, Carole Goble
Date Published: 14th May 2021
Publication Type: Unpublished
Citation: arXiv 2105.07028 [cs.DC]
Presented at Swedish eResearch Centre meeting, 13 may 2022
Creator: Carole Goble
Submitter: Carole Goble
Keynote Presented at the ICTeSSH 2021 Conference to Social Science and Humanities. ICTeSSH 2021, 30th June 2021
https://ictessh.uns.ac.rs/ In data intensive science multi-step tool-chains are widely used to help scientists manage, analyze, and share increasing volumes of complex data. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the exchange of processing know-how, and ...
Creator: Carole Goble
Submitter: Carole Goble
Keynote JOBIM 2021 (French Bioinformatics Conference)
FAIR Computational Workflows https://jobim2021.sciencesconf.org/ 8 July 2021
Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for ...
Creator: Carole Goble
Submitter: Carole Goble
Keynote at German Conference on Bioinformatics 2021 https://gcb2021.de/ FAIR Computational Workflows Computational workflows capture precise descriptions of the steps and data dependencies needed to carry out computational data pipelines, analysis and simulations in many areas of Science, including the Life Sciences. The use of computational workflows to manage these multi-step computational processes has accelerated in the past few years driven by the need for scalable data processing, the ...
Creator: Carole Goble
Submitter: Carole Goble
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...
Type: Common Workflow Language
Creators: Ekaterina Sakharova, Varsha Kale, Martin Beracochea, Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...
Type: Common Workflow Language
Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea
MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...
Type: Common Workflow Language
Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn
Submitter: Martin Beracochea
Workflow for LongRead Quality Control and Filtering
- NanoPlot (read quality control) before and after filtering
- Filtlong (read trimming)
- Kraken2 taxonomic read classification before and after filtering
- Minimap2 read filtering based on given references
Other UNLOCK workflows on WorkflowHub: https://workflowhub.eu/projects/16/workflows?view=default
All tool CWL files and other workflows can be found here: https://gitlab.com/m-unlock/cwl/workflows
**How to setup and use an UNLOCK ...
Type: Common Workflow Language
Creators: Bart Nijsse, Jasper Koehorst, Germán Royval
Submitter: Bart Nijsse
Workflow for quality assessment of paired reads and classification using NGTax 2.0 and functional annotation using picrust2. In addition files are exported to their respective subfolders for easier data management in a later stage. Steps:
- FastQC (read quality control)
- NGTax 2.0
- Picrust 2
- Export module for ngtax
Rare disease researchers workflow is that they submit their raw data (fastq), run the mapping and variant calling RD-Connect pipeline and obtain unannotated gvcf files to further submit to the RD-Connect GPAP or analyse on their own.
This demonstrator focuses on the variant calling pipeline. The raw genomic data is processed using the RD-Connect pipeline (Laurie et al., 2016) running on the standards (GA4GH) compliant, interoperable container ...
Type: Common Workflow Language
Creators: José Mª Fernández, Laura Rodriguez-Navas
Submitter: Laura Rodriguez-Navas
Type: Common Workflow Language
Creators: Pjotr Prins, Andrea Guarracino, Peter Amstutz, Thomas Liener, Adam M. Novak, Bonface Munyoki, Tazro Inutano, Michael Heuer, Michael R. Crusoe, Stian Soiland-Reyes
Submitter: Michael R. Crusoe
Analysis of variation within individual COVID-19 samples using bowtie2, bwa, fastp, multiqc , picard ,samtools, snpEff Workflow, tools and data are available on https://github.com/fjrmoreews/cwl-workflow-SARS-CoV-2/tree/master/Variation This worklow was ported into CWL from a Galaxy Workflow ( https://github.com/galaxyproject/SARS-CoV-2/tree/master/genomics/4-Variation migrated to CWL).
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using SAMTools.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using GATK4.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Author: AMBARISH KUMAR er.ambarish@gmail.com; ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using VARSCAN.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
Author: AMBARISH KUMAR er.ambarish@gmail.com & ambari73_sit@jnu.ac.in
This is a proposed standard operating procedure for genomic variant detection using GATK4.
It is hoped to be effective and useful for getting SARS-CoV-2 genome variants.
It uses Illumina RNASEQ reads and genome sequence.
This BioExcel best practice guide discusses the workflow engines available for the Common Workflow Language (CWL).
Creators: Robin Long, Douglas Lowe, Stian Soiland-Reyes
Submitter: Stian Soiland-Reyes