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- Downloads
replace test files with small synthetic ones
- 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
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- .gitignore 1 addition, 0 deletions.gitignore
- .gitlab-ci.yml 2 additions, 0 deletions.gitlab-ci.yml
- images/workflow_dag.svg 181 additions, 139 deletionsimages/workflow_dag.svg
- tests/test_create_dag_chart/input_files/GSM1502498_1.fastq.gz 0 additions, 0 deletions...s/test_create_dag_chart/input_files/GSM1502498_1.fastq.gz
- tests/test_create_dag_chart/input_files/GSM1502498_2.fastq.gz 0 additions, 0 deletions...s/test_create_dag_chart/input_files/GSM1502498_2.fastq.gz
- tests/test_create_dag_chart/input_files/GSM1502500_1.fastq.gz 0 additions, 0 deletions...s/test_create_dag_chart/input_files/GSM1502500_1.fastq.gz
- tests/test_create_dag_chart/input_files/GSM1502500_2.fastq.gz 0 additions, 0 deletions...s/test_create_dag_chart/input_files/GSM1502500_2.fastq.gz
- tests/test_create_dag_chart/input_files/chr1-10000-20000.fa 168 additions, 0 deletionstests/test_create_dag_chart/input_files/chr1-10000-20000.fa
- tests/test_create_dag_chart/input_files/chr1-10000-20000.gtf 28 additions, 0 deletionstests/test_create_dag_chart/input_files/chr1-10000-20000.gtf
- tests/test_create_dag_chart/input_files/chr1-10000-20000.transcripts.fa 54 additions, 0 deletions...ate_dag_chart/input_files/chr1-10000-20000.transcripts.fa
- tests/test_create_dag_chart/input_files/synthetic.mate_1.fastq.gz 0 additions, 0 deletions...st_create_dag_chart/input_files/synthetic.mate_1.fastq.gz
- tests/test_create_dag_chart/input_files/synthetic.mate_2.fastq.gz 0 additions, 0 deletions...st_create_dag_chart/input_files/synthetic.mate_2.fastq.gz
- tests/test_create_dag_chart/samples.tsv 2 additions, 2 deletionstests/test_create_dag_chart/samples.tsv
- tests/test_integration_workflow/expected_output.files 132 additions, 0 deletionstests/test_integration_workflow/expected_output.files
- tests/test_integration_workflow/expected_output.md5 132 additions, 12 deletionstests/test_integration_workflow/expected_output.md5
- tests/test_integration_workflow/input_files/GSM1502498_1.fastq.gz 0 additions, 0 deletions...st_integration_workflow/input_files/GSM1502498_1.fastq.gz
- tests/test_integration_workflow/input_files/GSM1502498_2.fastq.gz 0 additions, 0 deletions...st_integration_workflow/input_files/GSM1502498_2.fastq.gz
- tests/test_integration_workflow/input_files/GSM1502500_1.fastq.gz 0 additions, 0 deletions...st_integration_workflow/input_files/GSM1502500_1.fastq.gz
- tests/test_integration_workflow/input_files/GSM1502500_2.fastq.gz 0 additions, 0 deletions...st_integration_workflow/input_files/GSM1502500_2.fastq.gz
- tests/test_integration_workflow/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf 0 additions, 62504 deletions...kflow/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf
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