BioLabFree/nfdrug

workflow

flowchart TB
    subgraph MURUNDATA
    subgraph take
    v0["samples"]
    end
    v3([DATATETCHDRUG])
    v4([MUTILDATAPROCESS])
    v5([MUALLMODELS])
    v6([MUTRAIN])
    v7([VISIABLE])
    v8([SHAP])
    v0 --> v3
    v0 --> v4
    v3 --> v4
    v0 --> v5
    v4 --> v5
    v0 --> v6
    v5 --> v6
    v0 --> v7
    v6 --> v7
    v0 --> v8
    v3 --> v8
    v4 --> v8
    v5 --> v8
    v6 --> v8
    end

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Introduction

BioLabFree/nfdrug is a bioinformatics pipeline that predict drugs.

1. prepare matrix data
2. prepare drug data
3. prepre protein data

Usage

Note

If you are new to Nextflow and nf-core, please refer to this page on how to set-up Nextflow. Make sure to test your setup with -profile test before running the workflow on actual data.

Now, you can run the pipeline using:

nextflow run nfdrug/main.nf \
   -profile <docker/singularity/.../institute> \
   --input samplesheet.csv \
   --outdir <OUTDIR>

Warning

Please provide pipeline parameters via the CLI or Nextflow -params-file option. Custom config files including those provided by the -c Nextflow option can be used to provide any configuration except for parameters; see docs.

Credits

BioLabFree/nfdrug was originally written by kongjd.

We thank the following people for their extensive assistance in the development of this pipeline:

Contributions and Support

If you would like to contribute to this pipeline, please see the contributing guidelines.

Citations

An extensive list of references for the tools used by the pipeline can be found in the CITATIONS.md file.

This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.

The nf-core framework for community-curated bioinformatics pipelines.

Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.

Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x.