A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
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- Workflows (41+3)
Dr. Ferhat Ay and his lab are currently located at the La Jolla Institute of Immunology. Our lab focuses on the study of the 3D genome including the development of statistical tools to better interrogate functions and associations between the 3D genome and other biological factors.
Download all genome from https://www.ncbi.nlm.nih.gov/labs/virus/vssi/#/virus?SeqType_s=Nucleotide
with filter host:viridiplantae and Refseq on.
Workflow to take DataOne data packages (raw datasets + metadata written in Ecological Metadata Standard) as input and create a DwC occurence.csv file almost ready to put in a Dawrin core Archive using eml-annotations at the attribute level
Submitter: Yvan Le Bras
A porting of the Trinity RNA assembly pipeline, https://trinityrnaseq.github.io, that uses Nextflow to handle the underlying sub-tasks.
This enables additional capabilities to better use HPC resources, such as packing of tasks to fill up nodes and use of node-local disks to improve I/O.
By design, the pipeline separates the workflow logic (main file) and the cluster-specific configuration (config files), improving portability.
Based on a pipeline by Sydney Informatics Hub:
Workflow for tracking objects in Cell Profiler:
Submitter: Beatriz Serrano-Solano
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’.
Creator: David F. Nieuwenhuijse, Alexey Sokolov
Submitter: Ross Thorne