GAND

GAND project repository for reproducible analysis.

Reproducible Workflow

Nextflow

Building a nextflow pipeline that will handle everything from data download (when relevant or possible), to report building.

Data Download

The data should be stored in the data directory under the appropriate category. To reduce the memory footprint of this repository, we do not provide the data here.

scRNA Data

Nextflow will handle data download automatically using a data download workflow.

We download two data sets:

1. ScRNA-seq data taken from this publication under GEO accession number GSE244477. To facilitate, formatting and naming of data sets, we provide a data manifest.txt which contains the names and conditions of each individual data set.

2. A reference data sets for cell type annotation (GEO: GSE123335)

The nextflow.config contains a dwl section which allows you to select which data sets should be downloaded. Simply toggle the booleans to true to selectively downloaded data sets. The download URLs are alreaddy added.

dwl {
        dwl_scrna = false
        scrna_url = ["https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE244477&format=file"]
        dwl_ref = false
        ref_url = ["https://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123335/suppl/GSE123335%5FE14%5Fcombined%5Fmatrix.txt.gz",
                    "https://ftp.ncbi.nlm.nih.gov/geo/series/GSE123nnn/GSE123335/suppl/GSE123335%5FE14%5Fcombined%5Fmatrix%5FClusterAnnotations.txt.gz"]
    }

BigWig

TBD

Containers & Environments

Conda yml

Conda .yml files are available for each sub-workflow in the envs directory. The current workflow will automatically make use of the appropriate environment.

NOTE: The config file contains beforeScript clause that will be remove in final iterations.

Containers

Singularity/Docker containers will be made available.

Data upload

Nextflow pipeline for data upload?