Workflows

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738 Workflows visible to you, out of a total of 793
GridSearch on kNN non data persistence

Name: GridSearchCV Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

GridSearch of kNN algorithm for the iris.csv dataset (https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad21398ea43cba4f7d537619d0e07d5ae3/iris.csv). This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.1095.1

GridSearch on kNN

Name: GridSearchCV Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs Machine: MareNostrum5

GridSearch of kNN algorithm for the iris.csv dataset (https://gist.githubusercontent.com/netj/8836201/raw/6f9306ad21398ea43cba4f7d537619d0e07d5ae3/iris.csv). This application used dislib-0.9.0

Type: COMPSs

Creator: Fernando Vázquez-Novoa

Submitter: Fernando Vázquez-Novoa

DOI: 10.48546/workflowhub.workflow.1094.1

kmer-profiling-hifi-trio-VGP2/main

Create Meryl Database used for the estimation of assembly parameters and quality control with Merqury. Part of the VGP pipeline.

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

kmer-profiling-hifi-VGP1/main

VGP Workflow #1

This workflow produces a Meryl database and Genomescope outputs that will be used to determine parameters for following workflows, and assess the quality of genome assemblies. Specifically, it provides information about the genomic complexity, such as the genome size and levels of heterozygosity and repeat content, as well about the data quality.

Inputs

  • A collection of Hifi long reads in FASTQ format
  • k-mer length
  • Ploidy

Outputs

  • Meryl Database of kmer counts

...

Type: Galaxy

Creator: VGP, Galaxy

Submitter: WorkflowHub Bot

qiime2-III-VI-downsteam/QIIME2-III-V-Phylogeny-Rarefaction-Taxonomic-Analysis

This workflow

  • Reconstruct phylogeny (insert fragments in a reference)
  • Alpha rarefaction analysis
  • Taxonomic analysis

Type: Galaxy

Creators: Debjyoti Ghosh, Helmholtz-Zentrum für Umweltforschung - UFZ

Submitter: WorkflowHub Bot

Genome-assessment-post-assembly
Stable

Post-genome assembly quality control workflow using Quast, BUSCO, Meryl, Merqury and Fasta Statistics. Updates November 2023.

  • Inputs: reads as fastqsanger.gz (not fastq.gz), and assembly.fasta. (To change format: click on the pencil icon next to the file in the Galaxy history, then "Datatypes", then set "New type" as fastqsanger.gz).
  • New default settings for BUSCO: lineage = eukaryota; for Quast: lineage = eukaryotes, genome = large.
  • Reports assembly stats into a table called metrics.tsv, ...

Type: Galaxy

Creators: Gareth Price, Anna Syme

Submitters: Johan Gustafsson, Anna Syme

DOI: 10.48546/workflowhub.workflow.403.4

End-to-end EI+ mass spectra prediction workflow using QCxMS
Stable

High-Performance Computing (HPC) environments are integral to quantum chemistry and computationally intense research, yet their complexity poses challenges for non-HPC experts. Navigating these environments proves challenging for researchers lacking extensive computational knowledge, hindering efficient use of domain specific research software. The prediction of mass spectra for in silico annotation is therefore inaccessible for many wet lab scientists. Our main goal is to facilitate non-experts ...

Type: Galaxy

Creators: Zargham Ahmad, Helge Hecht, Wudmir Rojas, RECETOX SpecDat

Submitters: Helge Hecht, Wudmir Rojas

DOI: 10.48546/workflowhub.workflow.897.2

Differential peak analysis with SnapATAC2

This workflow takes a cell-type-annotated AnnData object (processed with SnapATAC2) and performs peak calling with MACS3 on the cell types. Next, a cell-by-peak matrix is constructed and differential accessibility tests are performed for comparison of either two cell types or one cell type with a background of all other cells. Lastly, differentially accessible marker regions for each cell type are identified.

Type: Galaxy

Creator: Timon Schlegel

Submitter: Timon Schlegel

Multisample Batch Correction with SnapATAC2 and Harmony

This Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs:

  • preprocessing
  • filtering
  • concatenation
  • dimension reduction
  • batch correction (with Harmony and optionally Scanorama and MNC-correct)
  • leiden clustering
  • new SnapATAC2 version: from 2.5.3 to 2.6.4

Type: Galaxy

Creators: None

Submitter: Timon Schlegel

Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2

Workflow for Single-cell ATAC-seq standard processing with SnapATAC2. This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. Finally, the clusters are manually annotated with the help of marker genes. In an alternative step, the fragment file can also be generated from a BAM file.

  • newer Version: Updated SnapATAC2 version from 2.5.3 to 2.6.4

Type: Galaxy

Creator: Timon Schlegel

Submitter: Timon Schlegel

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