- renaming bedgraph
- creating ALFA qc plots

removed conda dependence, moved import statement.

included ALFA in finish rule, corrected annotation.gtf and config.yaml, created new .svg

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

- separate organism genome architecture (different input folder)
- change MD5 checksums to match the new output

CJHerrmann authored 5 years ago and Alex Kanitz committed 5 years ago

- add script `tests/test_rule_graph/test.sh` to generate a rule graph in `images/rule_graph.svg`
- display rule graph created in `README.md` instead of specific workflow DAG
- add test script to GitLab CI config
- renamed test to create workflow DAG from `test_create_dag_chart` to `test_create_dag_image` (also output file is renamed from `images/workflow_dag.svg` to `images/dag_test_workflow.svg`

- 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