Merge remote-tracking branch 'origin/master' into alfa_qc

.gitignore

.gitlab-ci.yml

scripts/labkey_api.md

scripts/labkey_api.py

snakemake/Snakefile

snakemake/paired_end.snakefile

snakemake/run_test.sh

snakemake/single_end.snakefile

tests/input_files/GSM1502498_1.fastq.gz

tests/input_files/GSM1502498_2.fastq.gz

tests/input_files/GSM1502500_1.fastq.gz

tests/input_files/GSM1502500_2.fastq.gz

tests/input_files/Homo_sapiens.GRCh38.99.chr.chrom_22.gtf

...s/Homo_sapiens.GRCh38.dna_sm.primary_assembly.chrom_22.fa

tests/input_files/transcripts_chrom_22.fa

tests/samples.tsv