Workflows
What is a Workflow?Filters
Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs
Description
Simple is an application that takes one value and increases it by five units. The purpose of this application is to show how tasks are managed by COMPSs.
Execution instructions
Usage:
runcompss --lang=python src/simple.py initValue
where:
- initValue: Initial value for counter
Execution Examples
runcompss --lang=python src/simple.py 1
runcompss
...
Type: COMPSs
Creators: Javier Conejero, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing/)
Submitter: Raül Sirvent
The aim of this workflow is to handle the routine part of shotgun metagenomics data processing on Galaxy Australia.
The workflow is using the tools MetaPhlAn2 for taxonomy classification and HUMAnN2 for functional profiling of the metagenomes. The workflow is based on the Galaxy Training tutorial 'Analyses of metagenomics data - The global picture' (Saskia Hiltemann, Bérénice Batut) https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html#shotgun-metagenomics-data. ...
Type: Galaxy
Creators: Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut, The workflow is based on the Galaxy Training tutorial Analyses of metagenomics data. Thank you to the Galaxy Australia team, Igor Makunin and Mike Thang for help with the workflow
Submitter: Valentine Murigneux
Type: Nextflow
Creators: Damon-Lee Pointon, Will Eagles, Ying Sims, Matthieu Muffato, Priyanka Surana
Submitter: Matthieu Muffato
A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.
A workflow for mapping and consensus generation of SARS-CoV2 whole genome amplicon nanopore data implemented in the Nextflow framework. Reads are mapped to a reference genome using Minimap2 after trimming the amplicon primers with a fixed length at both ends of the amplicons using Cutadapt. The consensus is called using Pysam based on a majority read support threshold per position of the Minimap2 alignment and positions with less than 30x coverage are masked using ‘N’.
covid-sequence-analysis-workflow
This is the official repository of the SARS-CoV-2 variant surveillance pipeline developed by Danish Technical University (DTU), Eotvos Lorand University (ELTE), EMBL-EBI, Erasmus Medical Center (EMC) under the Versatile Emerging infectious disease Observatory (VEO) project. The project consists of 20 European partners. It is funded by the European Commission.
The ...