Workflows
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EOSC4Cancer_D2.2
Galaxy workflow used for EOSC4Cancer D2.2 - Analytical methods for data extraction, processing and sharing using biomedical images - demonstrator
An overview of the components for the image processing demonstrator can be seen in the diagram below
Link to deliverable report on Zenodo: https://doi.org/10.5281/zenodo.15704480
Type: Galaxy
Creators: Jeanne Chèneby, Hakim Achterberg, Dario Longo, Francesco Gammaraccio, Robin Navest
Submitter: Robin Navest
Visualize and filter scATAC-seq anndata to produce a high quality count matrix
Associated Tutorial
This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
This workflow creates an count matrix anndata file given 10x scATAC-seq data.
Associated Tutorial
This workflows is part of the tutorial Pre-processing of 10X Single-Cell ATAC-seq Datasets, available in the GTN
Features
- Includes Galaxy Workflow Tests ...
pb_variants
A snakemake 9 based Pipeline for hifi snp, sv, cnv calling, phasing and more
Only PacBio data for now
!!THIS PIPLINE IS IN-DEVELOPMENT AND EXPERIMENTAL, USE AT YOUR OWN RISK!!
what this tool aims to deliver:
- newest and best tools suited for HiFi data (only for now)
- singletons and trio analysis (trio is coming sometime...)
- human-first (hg38 for now), others should be possible (untested...)
included tools:
- deepvariant or bcftools for snp calling
- snps get used for ...
Domestication of new parts and cloning simulation
Add new parts to your sequences before the cloning simulation and interact with the database.
input:
- input: csv file (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.
- JSON parameters file (optional) : The JSON file should contain the the parameters used in workflow tools. If this ...
Cloning simulation workflow for sequences present in DB
Run the GoldenGate cloning simulation for a list of constructs in a CSV file and interact with a database
inputs:
- Assmbly Plan (without header) : The CSV file should contain the constraints line by line in the first column, along with their associated fragments on each line. This data will be passed to the seq_from_DB tool.
- JSON parameters file (optional) : The JSON file should contain the the parameters used in workflow ...