- 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

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

- Rules now integrated include #7, #8, #9, #10, #11, #12, #13, #14, #15, #16, #17
- Applies both for single-end and paired-end subworkflows
- DAG image updated
- Test sample tables and outcomes updated
- Unused preprocessing subworkflow removed

Closes #48
Closes #6

- remove log files and add '.snakemake' directories to '.gitignore'
- update wrong link in 'README.md'
- delete superfluous script documentation 'scripts/labkey_api.md'
- add Snakemake-specific file extension '.smk' to subworkflows
- remove non-deterministic workflow output from md5 sums

`README.md` file describes
- aim and background of the project (including the workflow DAG representation)
- how to install requirements (including setting up a `conda` environment for the project)
- how to execute the workflow run integration test
- how to run the workflow on your own samples (including how to auto-generate required params from LabKey metadata)

Additional minor changes:
- minor changes in various test and related files, including updates of paths
- root directory now includes subdirectory `runs/` for a user's workflow runs (contents not version-controlled)

BIOPZ-Gypas Foivos authored 5 years ago and Alex Kanitz committed 5 years ago

- replace corrupt input files
- add script that runs locally named `run_test.sh` in the snakemake directory
- add script to CI/CD pipeline
- fix typo in `paired_end.snakefile`
- update samples.tsv with fake adapter `XXXXXXX` when we do not want to trim them