Workflows

What is a Workflow?
18 Workflows visible to you, out of a total of 18
Stable

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData Depreciated: use individual workflows insead for multiple samples

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

Stable

Takes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

Stable

Take a scRNAseq counts matrix from a single sample, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData object.

Depreciated: use individual workflows insead for multiple samples

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

Stable

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData

Depreciated: use individual workflows insead for multiple samples

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

Stable

Basic processing of a QC-filtered Anndata Object. UMAP, clustering e.t.c

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

Stable

Take an anndata file, and perform basic QC with scanpy. Produces a filtered AnnData object.

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

Stable

Takes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

Stable

Loads a single cell counts matrix into an annData format - adding a column called sample with the sample name. (Input format - matrix.mtx, features.tsv and barcodes.tsv)

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

Work-in-progress

The aim of this workflow is to handle the routine part of shotgun metagenomics data processing on Galaxy Australia.

The workflow is using the tools MetaPhlAn2 for taxonomy classification and HUMAnN2 for functional profiling of the metagenomes. The workflow is based on the Galaxy Training tutorial 'Analyses of metagenomics data - The global picture' (Saskia Hiltemann, Bérénice Batut) https://training.galaxyproject.org/training-material/topics/metagenomics/tutorials/general-tutorial/tutorial.html#shotgun-metagenomics-data. ...

Type: Galaxy

Creators: Valentine Murigneux, Mike Thang, Saskia Hiltemann, Bérénice Batut, The workflow is based on the Galaxy Training tutorial Analyses of metagenomics data. Thank you to the Galaxy Australia team, Igor Makunin and Mike Thang for help with the workflow

Submitter: Valentine Murigneux

DOI: 10.48546/workflowhub.workflow.624.1

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

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