Workflows

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817 Workflows visible to you, out of a total of 891
AssemblyQC: A NextFlow pipeline for evaluating assembly quality
Stable

GitHub Actions CI Status GitHub Actions Linting StatusCite with Zenodo ...

Type: Nextflow

Creators: Usman Rashid, Chen Wu, Jason Shiller, Ken Smith, Ross Crowhurst, Marcus Davy, Ting-Hsuan Chen, Susan Thomson, Cecilia Deng

Submitter: Usman Rashid

nf-core/demo

An nf-core demo pipeline

Type: Nextflow

Creator: Christopher Hakkaart

Submitter: WorkflowHub Bot

TSI-Scaffolding-with-HiC (based on VGP-HiC-scaffolding)

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

Repeat masking - 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

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

brew3r/main

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

bacterial_genome_annotation/main

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

amr_gene_detection/main

Antimicrobial resistance gene detection from assembled bacterial genomes

Type: Galaxy

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

Submitter: WorkflowHub Bot

Java COMPSs LU Factorization for Sparse Matrices, MareNostrum V, 3 nodes, no data persistence
Stable

Name: SparseLU Contact Person: [email protected] 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

PyCOMPSs Matrix Multiplication, out-of-core using files. Example using DIRECTORY parameters executed at laptop, data persistence True.
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

Porto-Sinusoidal Vascular Disease transcriptomics analysis workflow
Work-in-progress

Workflow for gene set enrichment analsysis (GSEA) and co-expression analysis (WGCNA) on transcriptomics data to analyze pathways affected in Porto-Sinusoidal Vascular Disease.

Type: Common Workflow Language

Creators: Aishwarya Iyer, Friederike Ehrhart

Submitter: Aishwarya Iyer

DOI: 10.48546/workflowhub.workflow.1040.1

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