Workflows

What is a Workflow?
660 Workflows visible to you, out of a total of 706

An nf-core demo pipeline

Type: Nextflow

Creator: Christopher Hakkaart

Submitter: WorkflowHub Bot

Scaffolding using HiC data with YAHS

This workflow has been created from a Vertebrate Genomes Project (VGP) scaffolding workflow.

Some minor changes have been made to better fit with TSI project data:

  • optional inputs of SAK info ...

Type: Galaxy

Creators: VGP Project, VGP, Galaxy

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.1054.1

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

Workflow information:

  • Input = genome.fasta.
  • Outputs = soft_masked_genome.fasta, hard_masked_genome.fasta, ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.875.3

Short paired-end read analysis to provide quality analysis, read cleaning and taxonomy assignation

Type: Galaxy

Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

This workflow takes a collection of BAM (output of STAR) and a gtf. It extends the input gtf using de novo annotation.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

Annotation of an assembled bacterial genomes to detect genes, potential plasmids, integrons and Insertion sequence (IS) elements.

Type: Galaxy

Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

Antimicrobial resistance gene detection from assembled bacterial genomes

Type: Galaxy

Creators: ABRomics , Pierre Marin, Clea Siguret, abromics-consortium

Submitter: WorkflowHub Bot

Stable

Name: SparseLU Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

The Sparse LU application computes an LU matrix factorization on a sparse blocked matrix. The matrix size (number of blocks) and the block size are parameters of the application.

As the algorithm progresses, the area of the matrix that is accessed is smaller; concretely, at each iteration, the 0th row and column of the current matrix are discarded. ...

Type: COMPSs

Creator: Raül Sirvent

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.1047.1

Stable

COMPSs Matrix Multiplication, out-of-core using files. Hypermatrix size used 2x2 blocks (MSIZE=2), block size used 2x2 elements (BSIZE=2)

Type: COMPSs

Creator: Raül Sirvent

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.1046.1

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

For this workflow:

Inputs:

  • assembled-genome.fasta
  • hard-repeat-masked-genome.fasta
  • If using the mRNAs option, ...

Type: Galaxy

Creator: Luke Silver

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.881.4

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