Workflows

What is a Workflow?
747 Workflows visible to you, out of a total of 808
How Usable Are Published Permeability Data?
Stable

Current version of this workflow: https://workflowhub.eu/workflows/1109. Please use only with the new version. KNIME workflow to gather ChEMBL permeability data is availbale: https://workflowhub.eu/workflows/1169.

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

KNIME workflow to gather ChEMBL permeability data
Stable
No description specified

Type: KNIME

Creator: Kateřina Storchmannová

Submitter: Kateřina Storchmannová

ERGA HiC Pri Scaffolding+QC YaHS v2409 (WF4)
Stable

The workflow takes trimmed HiC forward and reverse reads, and Pri/Alt assemblies to produce a scaffolded primary assembliy (and alternate contigs) using YaHS. It also runs all the QC analyses (gfastats, BUSCO, and Merqury).

Type: Galaxy

Creators: Diego De Panis, ERGA

Submitter: Diego De Panis

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

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

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