How to implement a test dataset

[oandrefonseca]

Description of feature

@mribeirodantas. Do you know if the scrna-seq pipeline on nf-core has testing data? I am thinking of creating a toy dataset to test over GitAction.

[mribeirodantas]

Yes, it does. You can check the input sample sheet that the nf-core/scrnaseq pipeline uses for the test profile here: https://github.com/nf-core/test-datasets/raw/scrnaseq/samplesheet-2-0.csv. Much more here: https://github.com/nf-core/test-datasets/tree/scrnaseq

If you download the pipeline (nf-core download nf-core/scrnaseq) and view the conf/test.conf, you'll see the following:

    // Input data
    input        = 'https://github.com/nf-core/test-datasets/raw/scrnaseq/samplesheet-2-0.csv'

    // Genome references
    fasta        = 'https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/GRCm38.p6.genome.chr19.fa'
    gtf          = 'https://github.com/nf-core/test-datasets/raw/scrnaseq/reference/gencode.vM19.annotation.chr19.gtf'
    aligner      = 'star'
    protocol     = '10XV2'

I believe we can use the same here, right? For the full-test profile, you can see the content in conf/test_full.config:

input        = 'https://raw.githubusercontent.com/nf-core/test-datasets/scrnaseq/samplesheet_2.0_full.csv'