Workflows

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556 Workflows visible to you, out of a total of 600
dna-seq-varlociraptor workflow

Snakemake workflow: dna-seq-varlociraptor

Snakemake GitHub actions status DOI

A ...

Type: Snakemake

Creator: Johannes Köster

Submitter: Johannes Köster

Fastq-to-bam @ NCI-Gadi
Stable

Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...

Type: Shell Script

Creators: Cali Willet, Tracy Chew, Georgina Samaha, Rosemarie Sadsad, Andrey Bliznyuk, Ben Menadue, Rika Kobayashi, Matthew Downton, Yue Sun

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.146.1

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RNASeq-DE @ NCI-Gadi
Stable

RNASeq-DE @ NCI-Gadi processes RNA sequencing data (single, paired and/or multiplexed) for differential expression (raw FASTQ to counts). This pipeline consists of multiple stages and is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes to run each stage in parallel.

Infrastructure_deployment_metadata: Gadi (NCI)

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.152.1

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Air Quality Prediction Prototype
Work-in-progress

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

Type: Galaxy

Creators: Oliver Woolland, Douglas Lowe

Submitter: Oliver Woolland

Lysozyme in Water COMPSs workflow
Stable

Lysozyme in Water simplest version, from COMPSs Tutorial. The original idea of this worklfow comes from http://www.mdtutorials.com/gmx/lysozyme/index.html

Type: COMPSs

Creators: Javier Conejero, Justin Lemkul

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.379.1

ABR Threshold Detection

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
...

Type: Python

Creators: None

Submitter: Elida Schneltzer

HTR-Collections-test
Work-in-progress

An example workflow for the Specimen Data Refinery tool, allowing an individual tool to be used

Type: Galaxy

Creators: Laurence Livermore, Oliver Woolland, Oliver Woolland

Submitter: Oliver Woolland

DOI: 10.48546/workflowhub.workflow.375.1

DLA-Collections-test
Work-in-progress

An example workflow for the Specimen Data Refinery tool, allowing an individual tool to be used

Type: Galaxy

Creators: Laurence Livermore, Oliver Woolland

Submitter: Oliver Woolland

DOI: 10.48546/workflowhub.workflow.374.1

De novo digitisation
Work-in-progress

An example workflow to allow users to run the Specimen Data Refinery tools on data provided in an input CSV file.

Type: Galaxy

Creators: Paul Brack, Oliver Woolland, Laurence Livermore

Submitter: Oliver Woolland

DOI: 10.48546/workflowhub.workflow.373.1

CNV_pipeline
Stable

StructuralVariants Workflow

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, Daniel López-López

Submitter: Laura Rodriguez-Navas

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