BIOPZ-Iborra de Toledo Paula authored 5 years ago and Alex Kanitz committed 5 years ago

-  Remove files with non-deterministic output from `tests/test_integration_workflow/expected_output.files`
-  Update MD5 sums in `tests/test_integration_workflow/expected_output.md5`
-  Update new workflow DAG and rule graph images

BIOPZ-Katsantoni Maria authored 5 years ago and Alex Kanitz committed 5 years ago

- add script that prepares Snakemake input files 'samples.tsv' and 'config.yaml' from LabKey table
- script either connects to API directly (with '--remote' and related options) or processes a tab-separated LabKey dump file
- add tests for both use cases
- common input files for tests now in 'tests/input_files'
- update all other tests to account for new file locations
- update documentation

- replaces existing larger libraries and annotations in test cases `test_create_dag_chart` and `test_integration_workflow`
- adds the following new test files:
  - `chr1-10000-20000.fa`: artificial chromosome of length 10'000 (based on human chromosome 1)
  - `chr1-10000-20000.gtf`: matching gene annotation file with two gene and three multi-exon transcripts entries
  - `chr1-10000-20000.transcripts.fa`: sequences of the transcripts listed in the gene annotation file
  - `synthetic.mate_?.fastq.gz`: 10 read pairs randomly sampled from the genic regions of the artificial chromosome
  - `synthetic.*.bed`: BED files with expected alignments for each read; names of overlapping genes are specified in a 7th column
- updates file paths in the relevant sample tables
- extends and updates checksum checking of result files in CI/CD pipeline