Workflows

What is a Workflow?
1463 Workflows visible to you, out of a total of 1558
Genome-assessment-post-assembly
Stable

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics, with updates November 2024.

Workflow inputs: reads as fastqsanger.gz (not fastq.gz), and primary assembly.fasta. (To change reads format: click on the pencil icon next to the file in the Galaxy history, then "Datatypes", then set "New type" as fastqsanger.gz). Note: the reads should be those that were used for the assembly (i.e., the filtered/cleaned reads), not the raw reads.

What it does: ...

Type: Galaxy

Creators: Kate Farquharson, Gareth Price, Simon Tang, Anna Syme

Submitters: Johan Gustafsson, Anna Syme

DOI: 10.48546/workflowhub.workflow.403.10

ORBiT
Stable

ORBiT

A Nextflow workflow for analysing Oxford Nanopore Technologies (ONT) RNAseq direct read sequening (DRS) or cDNA data.

This workflow emphasises sensitivity to detect rare and novel features within the data. Multiple aspects of this workflow are tailored to enhance sensitivity:

  • Alignment to reference genome rather than transcriptome
  • Multiple tools per analysis type (n = 2 isoforms, n = 3 fusions)
  • Reads quantification tools capable of detecting novel isoforms, and counting at the isoform ...

Type: Nextflow

Creators: Cali Willet, Amarinder Thind, Michael Geaghan, Mitchell O'Brien, Madison Gonebale, Marina Kennerson

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.2160.1

Transcription Speech to Text (imported from uploaded file)

This Workflow transcribes a video or audio with multiple speakers. After transcription, it allocates the names of the speakers and groups and cleans passages from the two main speakers for further analysis.

Associated Tutorial

This workflows is part of the tutorial Transcribing Audio and Video files with Automated Speech Recognition, available in the ...

Type: Galaxy

Creators: None

Submitter: GTN Bot

Gene EXpansion and CONtraction analysis pipeline
Stable

EXCON (v2.3.1)

A Nextflow pipeline for gene family EXpansion and CONtraction analysis across multiple species using CAFE5.

Given a set of genome assemblies and annotations, EXCON builds orthogroups with OrthoFinder, fits and compares multiple CAFE models to identify gene families evolving at significantly different rates, and automatically selects the best-fitting model for downstream analysis. Optionally, GO enrichment analysis can be run on expanded and contracted gene families, and ...

Type: Nextflow

Creator: Christopher Wyatt

Submitter: Chris Wyatt

DOI: 10.48546/workflowhub.workflow.2141.8

vvv2_align_SE_bwamem2_nanopore
Stable

Using:

  • vadr annotation (model to select)
  • vardict variant caller
  • coverage depth

Provides summarizing files:

  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only
  • vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

vvv2_align_PE_bwamem2
Stable

Using:

  • vadr annotation (model to select)
  • vardict variant caller
  • coverage depth

Provides summarizing files:

  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only
  • vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

vvv2_align_SE_bwamem2
Stable

Using:

  • vadr annotation (model to select)
  • vardict variant caller
  • coverage depth

Provides summarizing files:

  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only
  • vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

vvv2_align_SE_minimap2_pacbio
Stable

Using:

  • vadr annotation (model to select)
  • vardict variant caller
  • coverage depth

Provides summarizing files:

  • png image of variant calling with annotations and coverage depths
  • tsv file with all information of significant variants only
  • vcf file with all information of significant variants only (to allow downstream NextStrain analyses)

Type: Galaxy

Creators: Fabrice Touzain, This study was founded by the French National Research Agency and by Santé publique France as part of the project "EMERGEN". Anses Ploufragan research was also supported by Agglomération de Saint-Brieuc, Département des Côtes d'Armor and Région Bretagne

Submitter: Fabrice Touzain

Apache Airflow Classical Molecular Interaction Potentials
Stable

CMIP tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), ...

Type: Apache Airflow

Creators: Genís Bayarri, Adam Hospital

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.2157.1

CWL Classical Molecular Interaction Potentials
Stable

CMIP tutorial using BioExcel Building Blocks (biobb)

This tutorial aims to illustrate the process of computing classical molecular interaction potentials from protein structures, step by step, using the BioExcel Building Blocks library (biobb). Examples shown are Molecular Interaction Potentials (MIPs) grids, protein-protein/ligand interaction potentials, and protein titration. The particular structures used are the Lysozyme protein (PDB code 1AKI), ...

Type: Common Workflow Language

Creators: Genís Bayarri, Adam Hospital

Submitter: Genís Bayarri

DOI: 10.48546/workflowhub.workflow.2156.1

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