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- .gitignore 1 addition, 0 deletions.gitignore
- README.md 8 additions, 8 deletionsREADME.md
- Snakefile 643 additions, 711 deletionsSnakefile
- images/dag_test_workflow.svg 994 additions, 538 deletionsimages/dag_test_workflow.svg
- images/rule_graph.svg 463 additions, 353 deletionsimages/rule_graph.svg
- pipeline_documentation.md 41 additions, 48 deletionspipeline_documentation.md
- scripts/labkey_to_snakemake.py 618 additions, 281 deletionsscripts/labkey_to_snakemake.py
- tests/input_files/config.yaml 10 additions, 7 deletionstests/input_files/config.yaml
- tests/input_files/config_alfa.yaml 3 additions, 0 deletionstests/input_files/config_alfa.yaml
- tests/input_files/samples.tsv 3 additions, 3 deletionstests/input_files/samples.tsv
- tests/input_files/samples_alfa.tsv 5 additions, 5 deletionstests/input_files/samples_alfa.tsv
- tests/test_alfa/expected_output.md5 40 additions, 40 deletionstests/test_alfa/expected_output.md5
- tests/test_alfa/results/samples/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense.pe.Aligned.sortedByCoord.out.bam 0 additions, 0 deletions...nd_R1_on_minus_antisense.pe.Aligned.sortedByCoord.out.bam
- tests/test_alfa/results/samples/paired_end_R1_on_minus_antisense/map_genome/paired_end_R1_on_minus_antisense.pe.Aligned.sortedByCoord.out.bam.bai 0 additions, 0 deletions...1_on_minus_antisense.pe.Aligned.sortedByCoord.out.bam.bai
- tests/test_alfa/results/samples/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense.pe.Aligned.sortedByCoord.out.bam 0 additions, 0 deletions...ed_end_R1_on_minus_sense.pe.Aligned.sortedByCoord.out.bam
- tests/test_alfa/results/samples/paired_end_R1_on_minus_sense/map_genome/paired_end_R1_on_minus_sense.pe.Aligned.sortedByCoord.out.bam.bai 0 additions, 0 deletions...nd_R1_on_minus_sense.pe.Aligned.sortedByCoord.out.bam.bai
- tests/test_alfa/results/samples/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense.pe.Aligned.sortedByCoord.out.bam 0 additions, 0 deletions...end_R1_on_plus_antisense.pe.Aligned.sortedByCoord.out.bam
- tests/test_alfa/results/samples/paired_end_R1_on_plus_antisense/map_genome/paired_end_R1_on_plus_antisense.pe.Aligned.sortedByCoord.out.bam.bai 0 additions, 0 deletions...R1_on_plus_antisense.pe.Aligned.sortedByCoord.out.bam.bai
- tests/test_alfa/results/samples/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense.pe.Aligned.sortedByCoord.out.bam 0 additions, 0 deletions...red_end_R1_on_plus_sense.pe.Aligned.sortedByCoord.out.bam
- tests/test_alfa/results/samples/paired_end_R1_on_plus_sense/map_genome/paired_end_R1_on_plus_sense.pe.Aligned.sortedByCoord.out.bam.bai 0 additions, 0 deletions...end_R1_on_plus_sense.pe.Aligned.sortedByCoord.out.bam.bai
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