Workflows

What is a Workflow?
73 Workflows visible to you, out of a total of 73
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

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

About this workflow:

  • Inputs: transdecoder-peptides.fasta, transdecoder-nucleotides.fasta
  • Runs many steps ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.880.1

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

About this workflow:

  • Input: merged_transcriptomes.fasta.
  • Runs TransDecoder to produce longest_transcripts.fasta ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.879.1

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

About this workflow:

  • Inputs: multiple transcriptome.gtfs from different tissues, genome.fasta, coding_seqs.fasta, ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.878.1

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

About this workflow:

  • Run this workflow per tissue.
  • Inputs: masked_genome.fasta and the trimmed RNAseq reads ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.877.1

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

About this workflow:

  • Repeat this workflow separately for datasets from different tissues.
  • Inputs = collections ...

Type: Galaxy

Creators: Luke Silver, Anna Syme

Submitter: Anna Syme

DOI: 10.48546/workflowhub.workflow.876.1

Parabricks-Genomics-nf is a GPU-enabled pipeline for alignment and germline short variant calling for short read sequencing data. The pipeline utilises NVIDIA's Clara Parabricks toolkit to dramatically speed up the execution of best practice bioinformatics tools. Currently, this pipeline is configured specifically for NCI's Gadi HPC.

NVIDIA's Clara Parabricks can deliver a significant ...

Type: Nextflow

Creator: Georgina Samaha

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.836.1

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