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generate Snakemake inputs from LabKey data table
Adds script `scripts/labkey_to_snakemake.py` which - maps LabKey table fields to Snakemake parameters - assembles required parameters from the table data - infers required parameters from the input data - produces files `config.yaml` and `samples.tsv` required by the Snakemake pipeline A self-contained integration test for the script is located at `tests/test_scripts_labkey_to_snakemake` (execute script `test.sh`) and was added to the CI/CD pipeline. Note that intermittent changes to the `master` branch were merged into this branch to forego conflicts during merging. Closes #39
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- .gitlab-ci.yml 8 additions, 3 deletions.gitlab-ci.yml
- scripts/labkey_to_snakemake.py 248 additions, 0 deletionsscripts/labkey_to_snakemake.py
- tests/RNA_Seq_data_template_test.tsv 0 additions, 3 deletionstests/RNA_Seq_data_template_test.tsv
- tests/test_scripts_labkey_to_snakemake/expected_output.md5 2 additions, 0 deletionstests/test_scripts_labkey_to_snakemake/expected_output.md5
- tests/test_scripts_labkey_to_snakemake/input_dict.tsv 51 additions, 0 deletionstests/test_scripts_labkey_to_snakemake/input_dict.tsv
- tests/test_scripts_labkey_to_snakemake/input_lib_1.mate_1.fastq.gz 0 additions, 0 deletions...t_scripts_labkey_to_snakemake/input_lib_1.mate_1.fastq.gz
- tests/test_scripts_labkey_to_snakemake/input_lib_1.mate_2.fastq.gz 0 additions, 0 deletions...t_scripts_labkey_to_snakemake/input_lib_1.mate_2.fastq.gz
- tests/test_scripts_labkey_to_snakemake/input_lib_2.mate_1.fastq.gz 0 additions, 0 deletions...t_scripts_labkey_to_snakemake/input_lib_2.mate_1.fastq.gz
- tests/test_scripts_labkey_to_snakemake/input_lib_2.mate_2.fastq.gz 0 additions, 0 deletions...t_scripts_labkey_to_snakemake/input_lib_2.mate_2.fastq.gz
- tests/test_scripts_labkey_to_snakemake/input_table.tsv 3 additions, 0 deletionstests/test_scripts_labkey_to_snakemake/input_table.tsv
- tests/test_scripts_labkey_to_snakemake/test.sh 22 additions, 0 deletionstests/test_scripts_labkey_to_snakemake/test.sh
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