Workflows

What is a Workflow?
738 Workflows visible to you, out of a total of 793
ERGA HiFi PriAlt Purge+QC v2409 (WF3)
Stable

The workflow takes a trimmed HiFi reads collection, Pri/Alt contigs, and the values for transition parameter and max coverage depth (calculated from WF1) to run Purge_Dups. It produces purged Pri and Alt contigs assemblies, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1163.1

ERGA HiFi-only Assembly+QC Hifiasm v2409 (WF2)
Stable

The workflow takes a trimmed HiFi reads collection, and max coverage depth (calculated from WF1) to run Hifiasm in HiFi solo mode. It produces a Pri/Alt assembly, and runs all the QC analysis (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.1162.1

Meta-analysis of permeability literature data shows possibilities and limitations of popular methods
Stable

Article abstract

Permeability is an important molecular property in drug discovery, as it co-determines pharmacokinetics whenever a drug crosses the phospholipid bilayer, e.g., into the cell, in the gastrointestinal tract or across the blood-brain barrier. Many methods for the determination of permeability have been developed, including cell line assays, cell-free model systems like PAMPA mimicking, e.g., gastrointestinal epithelia or the skin, as well as the Black lipid membrane (BLM) and ...

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

miniTurboID of RAI14, EPHA2 and PHACTR4

KNIME workflow describing the analysis of mass spectrometry dataset related to the publication "Proximity interactomics identifies RAI14, EPHA2 and PHACTR4 as essential components of Wnt/planar cell polarity pathway in vertebrates". Workflow was built using the KNIME software container environment, version 4.7.7a, which can be created using "docker pull cfprot/knime:4.7.7a" command in Docker. The input data for the KNIME workflow (the report.tsv from DIA-NN) can be found on PRIDE repository under ...

Type: KNIME

Creator: Kristina Gomoryova

Submitter: Kristina Gomoryova

DOI: 10.48546/workflowhub.workflow.1083.1

ERGA Profiling HiFi v2409 (WF1)
Stable

The workflow takes a trimmed HiFi reads collection, runs Meryl to create a K-mer database, Genomescope2 to estimate genome properties and Smudgeplot to estimate ploidy. The main results are K-mer database and genome profiling plots, tables, and values useful for downstream analysis. Default K-mer length and ploidy for Genomescope are 21 and 2, respectively.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.603.1

ERGA DataQC HiFi v2409 (WF0)
Stable

The workflow takes a HiFi reads collection, runs FastQC and SeqKit, filters with Cutadapt, and creates a MultiQC report. The main outputs are a collection of filtred reads, a report with raw and filtered reads stats, and a table with raw reads stats.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.602.1

ERGA DataQC Illumina v2409 (WF0)
Stable

The workflow takes a paired-reads collection (like illumina WGS or HiC), runs FastQC and SeqKit, trims with Fastp, and creates a MultiQC report. The main outputs are a paired collection of trimmed reads, a report with raw and trimmed reads stats, and a table with raw reads stats.

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

DOI: 10.48546/workflowhub.workflow.601.1

Demultiplexing Doublet Benchmark
Work-in-progress

demux_doublet_sim

Repository for Nextflow pipeline used in demuxSNP demultipelxing paper

Overall workflow

  1. Simulate doublets
  1. Benchmark methods
  • Experiments 1: Vary doublet rate
  • Experiment 2: Vary SNP subsetting

Inputs

Most inputs are specified in nextflow.config: container__souporcell: path to souporcell apptainer image, ideally at top level of project. bam_path: Path to demultiplexed bam files. barcodes_path: Path to demultiplexed barcodes. tenx: Path to barcodes.tsv, features.tsv ...

Type: Nextflow

Creators: Michael Lynch, Leverages scripts developed by Weber et al (2021) DOI: https://doi.org/10.1093/gigascience/giab062

Submitter: Michael Lynch

DOI: 10.48546/workflowhub.workflow.1160.2

ECTI Atopic Dermatitis
Stable

Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment

This repository presents an objective, quantifiable method for assessing atopic dermatitis (AD) severity. The program integrates deep learning object detection with spatial analysis algorithms to accurately calculate the density of circular nano-size objects (CNOs), termed the Effective Corneocyte Topographical Index (ECTI). The ECTI demonstrates remarkable ...

Type: Python

Creator: Jen-Hung Wang

Submitter: Jen-Hung Wang

DOI: 10.48546/workflowhub.workflow.1161.1

EuCanImage FHIR ETL Implementation I: Hepatocellular Carcinoma

EuCanImage FHIR ETL Implementation

This repository contains the ETL implementation for EuCanImage, encouraging semantic interoperability of the clinical data obtained in the studies by transforming it into a machine-readable format following FHIR standards. This parser uses FHIR Resources in order to create the dictionaries following a FHIR compliant structure.

Type: Python

Creator: Aldar Cabrelles

Submitter: Aldar Cabrelles

DOI: 10.48546/workflowhub.workflow.1112.1

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