Workflows

What is a Workflow?
738 Workflows visible to you, out of a total of 793
Workflow for running the Community Earth System Model in fully coupled mode
Stable

This workflow demonstrates the usage of the Community Earth System Model on Galaxy Europe.

A fully coupled B1850 compset with resolution f19_g17 is run for 1 month.

Type: Galaxy

Creators: None

Submitter: Anne Fouilloux

MGnify - raw-reads analysis pipeline
Stable

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...

Type: Common Workflow Language

Creators: Ekaterina Sakharova, Varsha Kale, Martin Beracochea, Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Submitter: Martin Beracochea

DOI: 10.48546/workflowhub.workflow.362.1

MGnify - amplicon analysis pipeline
Stable

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...

Type: Common Workflow Language

Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Submitter: Martin Beracochea

MGnify - assembly analysis pipeline
Stable

MGnify (http://www.ebi.ac.uk/metagenomics) provides a free to use platform for the assembly, analysis and archiving of microbiome data derived from sequencing microbial populations that are present in particular environments. Over the past 2 years, MGnify (formerly EBI Metagenomics) has more than doubled the number of publicly available analysed datasets held within the resource. Recently, an updated approach to data analysis has been unveiled (version 5.0), replacing the previous single pipeline ...

Type: Common Workflow Language

Creator: Alex L Mitchell, Alexandre Almeida, Martin Beracochea, Miguel Boland, Josephine Burgin, Guy Cochrane, Michael R Crusoe, Varsha Kale, Simon C Potter, Lorna J Richardson, Ekaterina Sakharova, Maxim Scheremetjew, Anton Korobeynikov, Alex Shlemov, Olga Kunyavskaya, Alla Lapidus, Robert D Finn

Submitter: Martin Beracochea

HiFi de novo genome assembly workflow

HiFi de novo genome assembly workflow

HiFi-assembly-workflow is a bioinformatics pipeline that can be used to analyse Pacbio CCS reads for de novo genome assembly using PacBio Circular Consensus Sequencing (CCS) reads. This workflow is implemented in Nextflow and has 3 major sections.

Please refer to the following documentation for detailed description of each workflow section:

Type: Nextflow

Creators: None

Submitter: Naga Kasinadhuni

ML phylogenetic reconstruction

Phylogenetic reconstruction using genome-wide and single-gene alignment data. Here we use maximum likelihood reconstruction program IQTree. Data can be prepared using the phylogenetic data preparation workflow prior to phylogenetic reconstruction. Resulting trees can be viewed interactively using Galaxy's 'Phyloviz' or 'Phylogenetic Tree Visualization'

Type: Galaxy

Creator: Miguel Roncoroni

Submitter: Miguel Roncoroni

preparing genomic data for phylogeny recostruction (GTN)

This workflow begins from a set of genome assemblies of different samples, strains, species. The genome is first annotated with Funnanotate. Predicted proteins are furtner annotated with Busco. Next, 'ProteinOrtho' finds orthologs across the samples and makes orthogroups. Orthogroups where all samples are represented are extracted. Orthologs in each orthogroup are aligned with ClustalW. Test dataset: https://zenodo.org/record/6610704#.Ypn3FzlBw5k

Type: Galaxy

Creator: Miguel Roncoroni

Submitter: Miguel Roncoroni

generic-variant-calling-wgs-pe/main

Generic variation analysis on WGS PE data

This workflows performs paired end read mapping with bwa-mem followed by sensitive variant calling across a wide range of AFs with lofreq and variant annotation with snpEff. The reference genome can be provided as a GenBank file.

Type: Galaxy

Creator: Anton Nekrutenko

Submitter: WorkflowHub Bot

Generic consensus construction from VCF calls

Generic consensus building

This workflow generates consensus sequences using a list of variants generated by Variant Calling Workflow.

The workflow accepts a single input:

  • A collection of VCF files

The workflow produces a single output:

  • Consensus sequence for each input VCF file

The workflow can be accessed at usegalaxy.org

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Anton Nekrutenko

Generic variation analysis reporting
Stable

Generic variation analysis reporting

This workflow generates reports from a list of variants generated by Variant Calling Workflow.

The workflow accepts a single input:

  • A collection of VCF files

The workflow produces two outputs (format description below):

  1. A list of variants grouped by Sample
  2. A list of variants grouped by Variant

Here is example of output by sample. In this table all varinats in all samples are epxlicitrly listed:

| Sample | ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Anton Nekrutenko

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