Workflows

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280 Workflows visible to you, out of a total of 291
A workflow for marine Genomic Observatories data analysis
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A workflow for marine Genomic Observatories data analysis

An EOSC-Life project

Build Status

The workflows developed in the framework of this project are based on pipeline-v5 of the MGnify resource.

This branch is a child of the pipeline_5.1 branch that contains all CWL descriptions of the MGnify ...

Type: Common Workflow Language

Creators: Haris Zafeiropoulos, Martin Beracochea

Submitter: Haris Zafeiropoulos

sars-cov-2-pe-illumina-artic-variant-calling/COVID-19-PE-ARTIC-ILLUMINA
iwc

COVID-19: variation analysis on ARTIC PE data

The workflow for Illumina-sequenced ampliconic data builds on the RNASeq workflow for paired-end data using the same steps for mapping and variant calling, but adds extra logic for trimming amplicon primer sequences off reads with the ivar package. In addition, this workflow uses ivar also to identify amplicons affected by primer-binding site mutations and, if possible, excludes reads derived from such ...

Type: Galaxy

Creator: Wolfgang Maier

Submitter: WorkflowHub Bot

CNV_pipeline
TransBioNet
Stable

StructuralVariants Workflow

Type: Nextflow

Creators: Laura Rodriguez-Navas, Adrián Muñoz-Civico, Daniel López-López

Submitter: Laura Rodriguez-Navas

FAIR CRCC - image conversion
CRC Cohort
Work-in-progress

Snakemake workflow: FAIR CRCC - image conversion

Snakemake GitHub actions status

A Snakemake workflow for converting whole-slide images (WSI) from the CRC Cohort ...

Type: Snakemake

Creator: Luca Pireddu

Submitter: Luca Pireddu

dna-seq-varlociraptor workflow
Snakemake-Workflows

Snakemake workflow: dna-seq-varlociraptor

Snakemake GitHub actions status DOI

A ...

Type: Snakemake

Creator: Johannes Köster

Submitter: Johannes Köster

Fastq-to-bam @ NCI-Gadi
Australian BioCommons, Sydney Informatics Hub
Stable

Fastq-to-BAM @ NCI-Gadi is a genome alignment workflow that takes raw FASTQ files, aligns them to a reference genome and outputs analysis ready BAM files. This workflow is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes on NCI Gadi to run all stages of the workflow in parallel, either massively parallel using the scatter-gather approach or parallel by sample. It consists of a number of stages and follows the BROAD Institute's best practice ...

Type: Shell Script

Creators: Cali Willet, Tracy Chew, Georgina Samaha, Rosemarie Sadsad, Andrey Bliznyuk, Ben Menadue, Rika Kobayashi, Matthew Downton, Yue Sun

Submitter: Georgina Samaha

DOI: 10.48546/workflowhub.workflow.146.1

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RNASeq-DE @ NCI-Gadi
Sydney Informatics Hub
Stable

RNASeq-DE @ NCI-Gadi processes RNA sequencing data (single, paired and/or multiplexed) for differential expression (raw FASTQ to counts). This pipeline consists of multiple stages and is designed for the National Computational Infrastructure's (NCI) Gadi supercompter, leveraging multiple nodes to run each stage in parallel.

Infrastructure_deployment_metadata: Gadi (NCI)

Type: Shell Script

Creators: Tracy Chew, Rosemarie Sadsad, Cali Willet

Submitter: Tracy Chew

DOI: 10.48546/workflowhub.workflow.152.1

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