merged with updated master

.gitignore

.gitlab-ci.yml

Snakefile

images/dag_test_workflow.svg

images/rule_graph.svg

scripts/labkey_to_snakemake.py

tests/input_files/config.yaml

tests/input_files/config_alfa.yaml

tests/input_files/homo_sapiens/annotation.gtf

tests/input_files/homo_sapiens/quick_start.gtf

tests/input_files/samples_alfa.tsv

tests/test_alfa/expected_output.md5

...d_end_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam

...d_R1_on_minus_antisense_Aligned.sortedByCoord.out.bam.bai

...aired_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam

...d_end_R1_on_minus_sense_Aligned.sortedByCoord.out.bam.bai

...ed_end_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam

...nd_R1_on_plus_antisense_Aligned.sortedByCoord.out.bam.bai

...paired_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam

...ed_end_R1_on_plus_sense_Aligned.sortedByCoord.out.bam.bai