Workflows

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43 Workflows visible to you, out of a total of 46
Work-in-progress

Workflow for Metagenomics from raw reads to annotated bins.

Steps:

  • workflow_quality.cwl:

  • FastQC (control)

  • fastp (trimming)

  • Kraken2 (Taxonomic Read Classification

  • SPAdes (Assembly)

  • QUAST (Assembly quality report)

  • BBmap (Read mapping to assembly)

  • samtobam (sam to indexed bam)

  • metabatContigDepths (jgisummarizebamcontigdepths)

  • MetaBat2 (binning)

Type: Common Workflow Language

Creators: None

Submitter: Jasper Koehorst

Stable

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

alt text

Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular

...

Stable

COnSensus Interaction Network InFErence Service

Inference framework for reconstructing networks using a consensus approach between multiple methods and data sources.

alt text

Reference

[Manica, Matteo, Charlotte, Bunne, Roland, Mathis, Joris, Cadow, Mehmet Eren, Ahsen, Gustavo A, Stolovitzky, and María Rodríguez, Martínez. "COSIFER: a python package for the consensus inference of molecular

...

Type: Common Workflow Language

Creators: Laura Rodriguez-Navas, José Mª Fernández

Submitter: Laura Rodriguez-Navas

Work-in-progress

Workflow to take DataOne data packages (raw datasets + metadata written in Ecological Metadata Standard) as input and create a DwC occurence.csv file almost ready to put in a Dawrin core Archive using eml-annotations at the attribute level

Type: Galaxy

Creators: None

Submitter: Yvan Le Bras

Stable

A porting of the Trinity RNA assembly pipeline, https://trinityrnaseq.github.io, that uses Nextflow to handle the underlying sub-tasks.

This enables additional capabilities to better use HPC resources, such as packing of tasks to fill up nodes and use of node-local disks to improve I/O.

By design, the pipeline separates the workflow logic (main file) and the cluster-specific configuration (config files), improving portability.

Based on a pipeline by Sydney Informatics Hub:

...

Type: Nextflow

Creator: Marco De La Pierre

Submitter: Marco De La Pierre

Work-in-progress

A pipeline for mapping, calling, and annotation of SARS-CoV2 variants.

Type: Nextflow

Creator: Krisztian Papp

Submitter: Ross Thorne

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