Workflows
What is a Workflow?Filters
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
Non-functional workflow to get a global view of possibilities for plant virus classification.
Galaxy version of pre-processing of reads from COVID-19 samples. QC + human read cleaning Based on https://github.com/Finn-Lab/Metagen-FastQC/blob/master/metagen-fastqc.sh
CWL version of the md_list.cwl workflow for HPC.
Workflow to build different indices for different tools from a genome and transcriptome.
This workflow expects an (annotated) genome in GBOL ttl format.
Steps:
- SAPP: rdf2gtf (genome fasta)
- SAPP: rdf2fasta (transcripts fasta)
- STAR index (Optional for Eukaryotic origin)
- bowtie2 index
- kallisto index
Continuous flexibility analysis of SARS-CoV-2 Spike prefusion structures
Type: Scipion
Creators: Carlos Oscar Sorzano Sanchez, Roberto Melero, Marta Martinez
Submitter: Laura del Cano
Scipion is a workflow engine mostly for Cryo-Electron Microscopy image processing. In this extremely simple workflow, we load the Relion 3.0 tutorial data and process it to 2.9A resolution.
This WF is based on the official Covid19-Galaxy assembly workflow as available from https://covid19.galaxyproject.org/genomics/2-assembly/ . It has been adapted to suit the needs of the analysis of metagenomics sequencing data. Prior to be submitted to INDSC databases, these data need to be cleaned from contaminant reads, including reads of possible human origin.
The assembly of the SARS-CoV-2 genome is performed using both the Unicycler and the SPAdes assemblers, similar to the original WV.
To ...
RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is CLAN.
RNA-RNA interactome analysis using ChiRA tools suite. The aligner used is BWA-MEM.