IWC - Intergalactic Workflow Commission
Space: This Team is not associated with a Space
Public web page: https://github.com/galaxyproject/iwc
Organisms: Not specified
The EuroScienceGateway project is producing and maintaining workflows. We need to register those workflows in WorkflowHub:
- To give visibility to the workflows created by the project and by the different networks and communities within the project
- To give visibility to the workflows used by project that were created
- To share workflows across the project, within project networks and externally
- To credit and cite the people making the workflows and the ...
Creators: Stian Soiland-Reyes, Carole Goble, Finn Bacall
Submitter: Stian Soiland-Reyes
COVID-19 sequence analysis on Illumina Amplicon PE data
This workflow implements an iVar based analysis similar to the one in ncov2019-artic-nf, covid-19-signal and the Thiagen Titan workflow. These workflows (written in Nextflow, Snakemake and WDL) are widely in use in COG UK, ...
COVID-19: variation analysis on WGS PE data
This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.
COVID-19: variation analysis reporting
This workflow takes VCF datasets of variants produced by any of the "*-variant-calling" workflows in https://github.com/galaxyproject/iwc/tree/main/workflows/sars-cov-2-variant-calling and generates tabular reports of variants by samples and by variant, along with an overview plot of variants and their allele-frequencies across all samples.
Generic variation analysis reporting
This workflow generates reports from a list of variants generated by Variant Calling Workflow.
The workflow accepts a single input:
- A collection of VCF files
The workflow produces two outputs (format description below):
- A list of variants grouped by Sample
- A list of variants grouped by Variant
Here is example of output by sample. In this table all varinats in all samples are epxlicitrly listed:
| Sample | ...
Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.
Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.
VGP Workflow #1
This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.
Inputs
- A collection of Hifi long reads in FASTQ format
- k-mer length
- Ploidy
Outputs
- Meryl Database of kmer counts
...
VGP Workflow #1
This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.
Inputs
- A collection of Hifi long reads in FASTQ format
- k-mer length
- Ploidy
Outputs
- Meryl Database of kmer counts
...
Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.
Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.
SARS-CoV-2 variant prediction using Read It And Keep, fastp, bbmap and iVar
COVID-19: consensus construction
This workflow aims at generating reliable consensus sequences from variant calls according to transparent criteria that capture at least some of the complexity of variant calling.
It takes a collection of VCFs (with DP and DP4 INFO fields) and a collection of the corresponding aligned reads (for the purpose of calculating genome-wide coverage) such as produced by any of the variant calling workflows in ...
GROMACS dcTMD free energy calculation
Perform an ensemble of targeted MD simulations of a user-specified size using the GROMACS PULL code and calculate dcTMD free energy and friction profiles for the resulting dissocation pathway. Note that pathway separation is not performed by the workflow; the user is responsible for checking the ensemble themselves.
The input protein (PDB) and ligand (SDF) files provided are parameterized by the 'Protein-ligand complex parameterization' subworkflow.
Note ...
A workflow for the analysis of pox virus genomes sequenced as half-genomes (for ITR resolution) in a tiled-amplicon approach
ROIforMSI
Source codes for manuscript "Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation"
"ExampleWorkflow.ipynb" is a methods document to demonstrate the workflow of our multimodal fusion-based spatial segmentation.
"Utilities.py" contains all the tools to implement our method.
"gui.py" and "registration_gui.py" are files to implement linear and nonlinear registration.
(Licence: GPL-3)
COVID-19: variation analysis on ARTIC ONT data
This workflow for ONT-sequenced ARTIC data is modeled after the alignment/variant-calling steps of the ARTIC pipeline. It performs, essentially, the same steps as that pipeline’s minion command, i.e. read mapping with minimap2 and variant calling with medaka. Like the Illumina ARTIC workflow it uses ivar for primer trimming. Since ONT-sequenced reads have a much ...
COVID-19: variation analysis on WGS SE data
This workflows performs single end read mapping with bowtie2 followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff 4.5covid19.
Protein-ligand complex parameterization
Parameterizes an input protein (PDB) and ligand (SDF) file prior to molecular dynamics simulation with GROMACS.
This is a simple workflow intended for use as a subworkflow in more complex MD workflows. It is used as a subworkflow by the GROMACS MMGBSA and dcTMD workflows.
This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.
Racon polish with long reads, x4