Workflows

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829 Workflows visible to you, out of a total of 902
BatchConvert
Work-in-progress

BatchConvert DOI:10.5281

A command line tool for converting image data into either of the standard file formats OME-TIFF or OME-Zarr.

The tool wraps the dedicated file converters bfconvert and bioformats2raw to convert into OME-TIFF or OME-Zarr, respectively. The workflow management system NextFlow is used to perform conversion in parallel for batches of images.

The tool also wraps s3 and Aspera clients (go-mc and aspera-cli, respectively). ...

Type: Nextflow

Creator: Bugra Oezdemir

Submitter: bugra oezdemir

DOI: 10.48546/workflowhub.workflow.453.3

CWL-based (single-sample) workflow for germline variant calling
Stable

A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.

On the respective GitHub folder are available:

  • The CWL wrappers and subworkflows for the workflow
  • A pre-configured YAML template, based on validation analysis of publicly available HTS data

Briefly, the workflow performs the following steps:

  1. Quality control of Illumina reads ...

Type: Common Workflow Language

Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos

Submitter: Konstantinos Kyritsis

DOI: 10.48546/workflowhub.workflow.527.1

CWL-based (multi-sample) workflow for germline variant calling
Stable

A CWL-based pipeline for calling small germline variants, namely SNPs and small INDELs, by processing data from Whole-genome Sequencing (WGS) or Targeted Sequencing (e.g., Whole-exome sequencing; WES) experiments.

On the respective GitHub folder are available:

  • The CWL wrappers and subworkflows for the workflow
  • A pre-configured YAML template, based on validation analysis of publicly available HTS data

Briefly, the workflow performs the following steps:

  1. Quality control of Illumina reads ...

Type: Common Workflow Language

Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos

Submitter: Konstantinos Kyritsis

DOI: 10.48546/workflowhub.workflow.526.1

CWL-based ChIP-Seq workflow
Stable

A CWL-based pipeline for processing ChIP-Seq data (FASTQ format) and performing:

  • Peak calling
  • Consensus peak count table generation
  • Detection of super-enhancer regions
  • Differential binding analysis

On the respective GitHub folder are available:

  • The CWL wrappers for the workflow
  • A pre-configured YAML template, based on validation analysis of publicly available HTS data
  • Tables of metadata (EZH2_metadata_CLL.csv and H3K27me3_metadata_CLL.csv), based on the same validation ...

Type: Common Workflow Language

Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos

Submitter: Konstantinos Kyritsis

DOI: 10.48546/workflowhub.workflow.525.1

CWL-based RNA-Seq workflow
Stable

A CWL-based pipeline for processing RNA-Seq data (FASTQ format) and performing differential gene/transcript expression analysis.

On the respective GitHub folder are available:

  • The CWL wrappers for the workflow
  • A pre-configured YAML template, based on validation analysis of publicly available HTS data
  • A table of metadata (mrna_cll_subsets_phenotypes.csv), based on the same validation analysis, to serve as an input example for the design of comparisons during differential expression ...

Type: Common Workflow Language

Creators: Konstantinos Kyritsis, Nikolaos Pechlivanis, Fotis Psomopoulos

Submitter: Konstantinos Kyritsis

DOI: 10.48546/workflowhub.workflow.524.1

SARS-CoV-2 Illumina Amplicon pipeline - SANBI - v1.2

SARS-CoV-2 variant prediction using Read It And Keep, fastp, bbmap and iVar

Type: Galaxy

Creators: Peter van Heusden, Bradley W. Langhorst

Submitter: Peter van Heusden

SARS-CoV-2 ONT Amplicon Sequencing SANBI 1.0
No description specified

Type: Galaxy

Creators: None

Submitter: Peter van Heusden

SARS-CoV-2 PostProcessing
No description specified

Type: Galaxy

Creators: None

Submitter: Peter van Heusden

Life Science cross-RI (Research Infrastructure) project
Stable

The project allowed us to manage and build structured code scripts on the Jupyter Notebook, a simple web application which is user-friendly, flexible to use in the research community. The script is developed to address the specific needs of research between different platforms of dataset. These stakeholders have developed their own platforms for the annotation and standardisation of both data and metadata produced within their respective field. -The INFRAFRONTIER - European Mutant Mouse Archive ...

Type: Jupyter

Creator: Elisabetta Spinazzola

Submitter: Elisabetta Spinazzola

Metagenome and metatranscriptome assembly in CWL
Stable

CWL-assembly

Codacy Badge Build Status

Description

This repository contains two workflows for metagenome and ...

Type: Common Workflow Language

Creators: None

Submitters: Germana Baldi, Varsha Kale

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