Workflows

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817 Workflows visible to you, out of a total of 891
Find transcripts - TSI

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

About this workflow:

  • Run this workflow per tissue.
  • Inputs: masked_genome.fasta and the trimmed RNAseq reads ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.877.1

QC and trimming of RNAseq reads - TSI

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

About this workflow:

  • Repeat this workflow separately for datasets from different tissues.
  • Inputs = collections ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.876.1

JAX NGS Operations Nextflow DSL2 Pipelines
Stable

DOI

JAX NGS Operations Nextflow DSL2 Pipelines

This repository contains production bioinformatic analysis pipelines for a variety of bulk 'omics data analysis. Please see the Wiki documentation associated with this repository for all documentation and available analysis workflows.

Type: Nextflow

Creators: Michael Lloyd, Brian Sanderson, Barry Guglielmo, Sai Lek, Peter Fields, Harshpreet Chandok, Carolyn Paisie, Gabriel Rech, Ardian Ferraj, Anuj Srivastava

Submitter: Michael Lloyd

DOI: 10.48546/workflowhub.workflow.874.1

Tango: Numerical reconciliation of bacterial fermentation in cheese production
Stable

Complete workflow for TANGO as reported in Lecomte et al (2024), "Revealing the dynamics and mechanisms of bacterial interactions in cheese production with metabolic modelling", Metabolic Eng. 83:24-38 https://doi.org/10.1016/j.ymben.2024.02.014

  1. Parameters for individual models are obtained by optimization
  2. Individual dynamics and community dynamics are simulated
  3. Figures for the manuscript are assembled from the results.

Type: Common Workflow Language

Creators: None

Submitter: David James Sherman

PyCOMPSs Matrix Multiplication, out-of-core using files, MareNostrum V, reproducibility example, without data persistence
Stable

Name: Matrix multiplication with Files, reproducibility example, without data persistence Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Matrix multiplication is a binary operation that takes a pair of matrices and produces another matrix.

If A is an n×m matrix and B is an m×p matrix, the result AB of their multiplication is an n×p matrix defined only if the number of columns m in A is equal to the number ...

Type: COMPSs

Creator: Raül Sirvent

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.839.1

PyCOMPSs Matrix Multiplication, out-of-core using files, reproducibility example
Stable

Name: Matrix multiplication with Files, reproducibility example Contact Person: [email protected] Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Matrix multiplication is a binary operation that takes a pair of matrices and produces another matrix.

If A is an n×m matrix and B is an m×p matrix, the result AB of their multiplication is an n×p matrix defined only if the number of columns m in A is equal to the number of rows m in B. When multiplying ...

Type: COMPSs

Creator: Raül Sirvent

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.838.1

ProGFASTAGen - Protein-Graph FASTA Generation (and Identification) Workflows
Stable

ProGFASTAGen

The ProGFASTAGen (Protein-Graph-FASTA-Generator or ProtGraph-FASTA-Generator) repository contains workflows to generate so-called precursor-specific-FASTAs (using the precursors from MGF-files) including feature-peptides, like VARIANTs or CONFLICTs if desired, or global-FASTAs (as described in ProtGraph). The single workflow scripts have been implemented with Nextflow-DSL-2 ...

Type: Nextflow

Creators: Dominik Lux, Julian Uszkoreit

Submitter: Dominik Lux

DOI: 10.48546/workflowhub.workflow.837.1

Parabricks-Genomics-nf

Parabricks-Genomics-nf is a GPU-enabled pipeline for alignment and germline short variant calling for short read sequencing data. The pipeline utilises NVIDIA's Clara Parabricks toolkit to dramatically speed up the execution of best practice bioinformatics tools. Currently, this pipeline is configured specifically for NCI's Gadi HPC.

NVIDIA's Clara Parabricks can deliver a significant ...

Type: Nextflow

Creator: Georgina Samaha

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.836.1

Library curation BOLD
Work-in-progress

Perl CI DOI

Library curation BOLD

alt text

This repository contains scripts and synonymy data for pipelining the automated curation of BOLD data dumps in BCDM TSV ...

Type: Snakemake

Creators: Rutger Vos, Fabian Deister, Ben Price, Special thanks to Sujeevan Ratnasingham and the team at CBG for the creation of the BCDM data exchange format that this pipeline operates on

Submitter: Rutger Vos

DOI: 10.48546/workflowhub.workflow.833.1

Use Case 13: Novel Cell Surface Targets for Individual Cancer Patients Analyzed with Common Fund Datasets
Work-in-progress

The input to this workflow is a data matrix of gene expression that was collected from a pediatric patient tumor patient from the KidsFirst Common Fund program [1]. The RNA-seq samples are the columns of the matrix, and the rows are the raw expression gene count for all human coding genes (Table 1). This data matrix is fed into TargetRanger [2] to screen for targets which are highly expressed in the tumor but lowly expressed across most healthy human tissues based on gene expression data collected ...

Type: Common Workflow Language

Creators: None

Submitter: Daniel Clarke

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