Workflows

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829 Workflows visible to you, out of a total of 902
Workflow 5: OTU Clustering [16S Microbial Analysis With Mothur]

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

Workflow 3: Classification [Galaxy Training: 16S Microbial Analysis With Mothur]

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for pipeline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

Workflow 1: Further Quality Control [16S Microbial Analysis With Mothur]

16S Microbial Analysis with mothur (short)

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

Workflow 2: Data Cleaning And Chimera Removal [16S Microbial Analysis With Mothur]

The workflows in this collection are from the '16S Microbial Analysis with mothur' tutorial for analysis of 16S data (Saskia Hiltemann, Bérénice Batut, Dave Clements), adapted for piepline use on galaxy australia (Ahmed Mehdi). The workflows developed in galaxy use mothur software package developed by Schloss et al https://pubmed.ncbi.nlm.nih.gov/19801464/.

Please also refer to the 16S tutorials available at Galaxy https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/mothur-miseq-sop-short/tutorial.html ...

Type: Galaxy

Creators: Saskia Hiltemann, Bérénice Batut, Dave Clements, Ahmed Mehdi

Submitter: Sarah Williams

PyCOMPSs Wordcount test, using files as task inputs, and dictionaries as task outputs (executed at Marenostrum IV supercomputer)
Stable

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

Description

Wordcount is an application that counts the number of words for a given set of files.

To allow parallelism every file is treated separately and merged afterwards.

Execution instructions

Usage:

runcompss --lang=python src/wordcount.py datasetPath

where:

  • datasetPath: Absolute path of the file to parse (e.g. /home/compss/tutorial_apps/python/wordcount/data/) ...

Type: COMPSs

Creators: Javier Conejero, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing/)

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.635.1

Autosubmit mHM test domains
Work-in-progress

Autosubmit mHM test domains

Type: Autosubmit

Creator: Bruno P. Kinoshita

Submitter: Bruno P. Kinoshita

ERGA HiC Hap1Hap2 Scaffolding+QC YaHS v2309 (WF4)
Stable

The workflow takes trimmed HiC forward and reverse reads, and Hap1/Hap2 assemblies to produce Hap1 and Hap2 scaffolded assemblies using YaHS. It also runs all the QC analyses (gfastats, BUSCO, Merqury and Pretext).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.608.1

Java COMPSs LU Factorization for Sparse Matrices
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

Creators: Jorge Ejarque, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing)

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.515.1

Cancer variant annotation (hg38 VEP-based) with MAF export
Stable

A variation of the Cancer variant annotation (hg38 VEP-based) workflow at https://doi.org/10.48546/workflowhub.workflow.607.1.

Like that other workflow it takes a list of tumor/normal sample pair variants in VCF format (see the other workflow for details about the expected format) and

  1. annotates them using the ENSEMBL Variant Effect Predictor and custom annotation data
  2. turns the annotated VCF into a MAF file for import into cBioPortal
  3. generates human-readable variant- and gene-centric ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Wolfgang Maier

DOI: 10.48546/workflowhub.workflow.629.1

Variant calling from matched tumor/normal sample pair (hg38 version)
Stable

Call somatic, germline and LoH event variants from PE Illumina sequencing data obtained from matched pairs of tumor and normal tissue samples.

This workflow can be used with whole-genome and whole-exome sequencing data as input. For WES data, parts of the analysis can be restricted to the exome capture kits target regions by providing the optional "Regions of Interest" bed dataset.

The current version uses bwa-mem for read mapping and varscan somatic for variant calling and somatic status ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: Wolfgang Maier

DOI: 10.48546/workflowhub.workflow.628.1

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