test

test subworkflow

Tests are annoying to develop, but really useful once they have been.

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Donut Falls
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flowchart LR

A[Downloads fastq file] --> B[Runs through Donut Falls]

Loading

Most of the tests use the subset15000.fq.gz from nf-core's test-datasets repository.

Tutorial

• Step 1. Get the relevant file

wget -q https://bridges.monash.edu/ndownloader/files/23754659 -O great_dataset.tar.gz
    tar -xvf great_dataset.tar.gz

There should now be a file called reads.fastq.gz in your current directory.

• Step 2. Move the file into a directory

mkdir tutorial
mv reads.fastq.gz tutorial/.

• Step 3. Create sample sheet

echo "sample,fastq" > sample_sheet.csv
echo "test,tutorial/reads.fastq.gz" >> sample_sheet.csv

• Step 4. Run the workflow with default parameters

nextflow run UPHL-BioNGS/Donut_Falls -profile singularity --sample_sheet sample_sheet.csv --outdir donut_falls_tutorial

• Step 5. Wait until completed

Final results will be in donut_falls_tutorial

• Step 6. Test other parameters

This dataset is generally good enough to test other parameters. Try adjusting the assembler.

nextflow run UPHL-BioNGS/Donut_Falls -profile singularity --sample_sheet sample_sheet.csv --outdir donut_falls_tutorial_raven --assembler raven

Test profile

There is also a test profile that can be run

nextflow run UPHL-BioNGS/Donut_Falls -profile singularity,test --outdir testing