A prototype implementation of the Air Quality Prediction pipeline in Galaxy, using CWL tools.

ABR_Threshold_Detection

What is this?

This code can be used to automatically determine hearing thresholds from ABR hearing curves.

One of the following methods can be used for this purpose:

• neural network (NN) training,
• calibration of a self-supervised sound level regression (SLR) method

on given data sets with manually determined hearing thresholds.

Installation:

Run inside the src directory:

Installation as python package

pip install -e ./src (Installation as python
...

StructuralVariants Workflow

This workflow demonstrates the usage of the Community Earth System Model on Galaxy Europe.

A fully coupled B1850 compset with resolution f19_g17 is run for 1 month.

HiFi de novo genome assembly workflow

HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.

Please refer to the following documentation for detailed description of each workflow section:

• Pre-assembly quality control (QC) ...

Generic consensus building

This workflow generates consensus sequences using a list of variants generated by Variant Calling Workflow.

The workflow accepts a single input:

• A collection of VCF files

The workflow produces a single output:

• Consensus sequence for each input VCF file

The workflow can be accessed at usegalaxy.org

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):

1. A list of variants grouped by Sample
2. 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 | ...

Generic variant calling

A generic workflow for identification of variants in a haploid genome such as genomes of bacteria or viruses. It can be readily used on MonkeyPox. The workflow accepts two inputs:

• A genbank file with the reference genomes
• A collection of paired fastqsanger files

The workflow outputs a collection of VCF files for each sample (each fastq pair). These VCF files serve as input to the Reporting workflow.

Workflow can be accessed ...

A workflow for the quality assessment of mass spectrometry (MS) based proteomics analyses

ESCALIBUR

Escalibur Population Genomic Analysis Pipeline is able to explore key aspects centering the population genetics of organisms, and automates three key bioinformatic components in population genomic analysis using Workflow Definition Language (WDL: https://openwdl.org/), and customised R, Perl, Python and Unix shell scripts. Associated programs are packaged into a platform independent singularity image, for which the definition file is provided.

The workflow for analysis using Escalibur ...