Workflows

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539 Workflows visible to you, out of a total of 581
scRNAseq_CellQC
Stable

Take an anndata file, and perform basic QC with scanpy. Produces a filtered AnnData object.

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

scRNAseq Single Sample Processing STARSolo
Stable

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

scRNAseq Single Sample Processing Counts Matrix
Stable

Take a scRNAseq counts matrix from a single sample, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData object.

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

scRNAseq Single Sample Processing Cell Ranger
Stable

From the R1 and R2 fastq files of a single samples, make a scRNAseq counts matrix, and perform basic QC with scanpy. Then, do further processing by making a UMAP and clustering. Produces a processed AnnData

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

scRNAseq: Count and Load with Cell Ranger
Stable

Takes fastqs and reference data, to produce a single cell counts matrix into and save in annData format - adding a column called sample with the sample name.

Type: Galaxy

Creators: Sarah Williams, Mike Thang, Valentine Murigneaux

Submitter: Sarah Williams

PyCOMPSs Wordcount test, using files as task inputs, and dictionaries as task outputs (executed at Marenostrum IV supercomputer)
Stable

Name: Word Count Contact Person: support-compss@bsc.es Access Level: public License Agreement: Apache2 Platform: COMPSs

Description

Wordcount is an application that counts the number of words for a given set of files.

To allow parallelism every file is treated separately and merged afterwards.

Execution instructions

Usage:

runcompss --lang=python src/wordcount.py datasetPath

where:

  • datasetPath: Absolute path of the file to parse (e.g. /home/compss/tutorial_apps/python/wordcount/data/) ...

Type: COMPSs

Creators: Javier Conejero, The Workflows and Distributed Computing Team (https://www.bsc.es/discover-bsc/organisation/scientific-structure/workflows-and-distributed-computing/)

Submitter: Raül Sirvent

DOI: 10.48546/workflowhub.workflow.635.1

Workflow 2: Sciensano
No description specified

Type: Galaxy

Creators: None

Submitter: Dennis Dollée

Assembly-Hifi-HiC-phasing-VGP4/main

Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

  1. Hifi long reads [fastq]
  2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
  3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
  4. K-mer database [meryldb]
  5. Genome profile summary generated by Genomescope [txt]
  6. Name of first assembly
  7. Name of second assembly ...

Type: Galaxy

Creators: Delphine Lariviere, Galaxy, VGP

Submitter: WorkflowHub Bot

Autosubmit mHM test domains
Work-in-progress

Autosubmit mHM test domains

Type: Autosubmit

Creator: Bruno P. Kinoshita

Submitter: Bruno P. Kinoshita

V-pipe (main multi-virus version)
Stable

Logo

bio.tools Snakemake Deploy Docker image ...

Type: Snakemake

Creators: Ivan Topolsky, Kim Philipp Jablonski

Submitter: Ivan Topolsky

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