UMCUGenetics/DxNextflowPRS

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Introduction

UMCUGenetics/DxNextflowPRS

Usage

First, prepare a samplesheet with your input data that looks as follows: (note: use absolute filepaths) samplesheet.csv:

sample,bam,bai
Sample1,sample1.bam,sample1.bam.bai
Sample2,sample2.bam,sample2.bam.bai

HPC

On the HPC you can submit a pipeline run using the run_dxnextflowprs.sh script. This submits the pipeline in an sbatch and runs nextflow with a slurm profile.

./DxNextflowPRS/run_dxnextflowprs.sh \
    --input <samplesheet.csv> \
    --outdir <path> \
    --email <address> \
    [options]

Alternatively

The pipeline can also be executed using a regular nextflow run command.

nextflow run DxNextflowPRS/main.nf \
    --input <samplesheet.csv> \
    --outdir <path> \
    --email <adress> \
    --profile <standard|docker|singularity> \
    [options]

NF-test

Tests are also automatically run on pull requests. A pipeline level test can be executed using:

cd DxNextflowPRS
nf-test test ./tests/default.nf.test --profile <docker|singularity>

This will test the pipeline execution using the -stub-run option; mocking process execution.

Similarly, individual units of the pipeline can be tested using tags.

cd DxNextflowPRS
# All local modules/subworkflows
nf-test test . --tag=local
# All local subworkflows
nf-test test . --tag=subworkflows/local
# All local modules
nf-test test . --tag=modules/local

# To see all available tags
nf-test list  --tags

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.