Workflows

What is a Workflow?
834 Workflows visible to you, out of a total of 910
Kallisto RNAseq Workflow

Workflow Kallisto RNAseq

(pseudoalignment on transcripts)

All tool CWL files and other workflows can be found here:
Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl
Workflows: https://git.wur.nl/unlock/cwl/-/tree/master/cwl/workflows

How to setup and use an UNLOCK workflow:
https://m-unlock.gitlab.io/docs/setup/setup.html

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst

Submitter: Bart Nijsse

Nanopore Guppy Basecalling Assembly Workflow

- deprecated -

Workflow for sequencing with ONT Nanopore, from basecalling to assembly.

  • Guppy (basecalling of raw reads)
  • MinIONQC (quality check)
  • FASTQ merging from multi into one file
  • Kraken2 (taxonomic classification)
  • Krona (classification visualization)
  • Flye (de novo assembly)
  • Medaka (assembly polishing)
  • QUAST (assembly quality reports)

All tool CWL files and other workflows can be found here: Tools: https://git.wur.nl/unlock/cwl/-/tree/master/cwl Workflows: ...

Type: Common Workflow Language

Creators: Bart Nijsse, Jasper Koehorst, Germán Royval

Submitter: Jasper Koehorst

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EJP-RD WP13 case-study CAKUT momix analysis
Stable

Joint multi-omics dimensionality reduction approaches for CAKUT data using peptidome and proteome data

Brief description In (Cantini et al. 2020), Cantini et al. evaluated 9 representative joint dimensionality reduction (jDR) methods for multi-omics integration and analysis and . The methods are Regularized Generalized Canonical Correlation Analysis (RGCCA), Multiple co-inertia analysis (MCIA), Multi-Omics Factor Analysis (MOFA), Multi-Study Factor Analysis (MSFA), iCluster, Integrative NMF ...

Type: Snakemake

Creators: Ozan Ozisik, Juma Bayjan, Cenna Doornbos, Friederike Ehrhart, Matthias Haimel, Laura Rodriguez-Navas, José Mª Fernández, Eleni Mina, Daniël Wijnbergen

Submitter: Juma Bayjan

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EJP-RD WP13 case-study: CAKUT peptidome and miRNome data analysis using the DIABLO and PLS-DA methods from the mixOmics R package
Stable

For integrative analysis of CAKUT multi-omics data DIABLO method of the mixOmics package (version 6.10.9. Singh et. al. 2019) was used with sPLS-DA (sparse Partial Least Squares Discriminant Analysis Discriminant Analysis) and PLS-DA classification.

Type: Snakemake

Creators: Juma Bayjan, Ozan Ozisik, Cenna Doornbos, Friederike Ehrhart

Submitter: Juma Bayjan

EJP-RD WP13 case-study: CAKUT proteome, peptidome and miRNome data analysis using WikiPathways
Stable

In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics datasets. For this, each of the three -omics datasets was first analyzed to identify differentially expressed elements, and pathways associated with the significant miRNA-protein links were detected. A miRNA-protein link is deemed significant, and may possibly be implying causality, if both a miRNA and its target are significantly differentially expressed.

The peptidome and ...

Type: Snakemake

Creators: Woosub Shin, Friederike Ehrhart, Juma Bayjan, Cenna Doornbos, Ozan Ozisik

Submitter: Juma Bayjan

PacBio HiFi genome assembly using hifiasm v2.1
Stable

PacBio HiFi genome assembly using hifiasm v2.1

General usage recommendations

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

See change log

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian ...

Type: Galaxy

Creators: Gareth Price, Katherine Farquharson

Submitter: Johan Gustafsson

DOI: 10.48546/workflowhub.workflow.221.3

Purge duplicates from hifiasm assembly v1.0
Stable

Purge-duplicates-from-hifiasm-assembly

General recommendations for using Purge-duplicates-from-hifiasm-assembly

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian ...

Type: Galaxy

Creators: Gareth Price, Gareth Price

Submitter: Johan Gustafsson

DOI: 10.48546/workflowhub.workflow.237.2

BAM to FASTQ + QC v1.0
Stable

BAM-to-FASTQ-QC

General recommendations for using BAM-to-FASTQ-QC

Please see the Genome assembly with hifiasm on Galaxy Australia guide.

Acknowledgements

The workflow & the doc_guidelines template used are supported by the Australian BioCommons via Bioplatforms Australia funding, the Australian Research Data Commons (https://doi.org/10.47486/PL105) ...

Type: Galaxy

Creator: Gareth Price

Submitter: Johan Gustafsson

DOI: 10.48546/workflowhub.workflow.220.2

ChIPseq_PE/main

ChIP-seq paired-end Workflow

Inputs dataset

  • The workflow needs a single input which is a list of dataset pairs of fastqsanger.

Inputs values

  • adapters sequences: this depends on the library preparation. If you don't know, use FastQC to determine if it is Truseq or Nextera.
  • reference_genome: this field will be adapted to the genomes available for bowtie2.
  • effective_genome_size: this is used by MACS2 and may be entered manually (indications are provided for heavily used genomes).

...

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

IndexReferenceFasta-nf
Stable

IndexReferenceFasta-nf

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Type: Nextflow

Creator: Georgina Samaha

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.393.1

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