zavolanlab / SCUREL

Method to detect 3'UTR changes from scRNA-seq

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Test workflow execution with a test data

dominikburri opened this issue · comments

Add some small samples to run the full workflow. As input the mapped reads can be used and the outputs are two list of genes and some visualisations. The test data should not exceed 20 MB.

This helps to

  • test the workflow and if all steps are running properly
  • configure and set-up own samples based on the provided test samples

The following should be added:

  • at least two samples with mapped reads in BAM format; the same genomic region should be used in all samples
  • cell type annotations for at least two cell types from the samples
  • the relevant subset of the genome annotation
  • the samples table samples.tsv
  • the configuration file config.yaml

see commit 2b88016 for inclusion of two samples and a corresponding github actions CI test.
Should the test data be described in the readme as an example?