.gitignore

.DS_Store
data_preparation/
.snakemake*
template_slurm.sh
slurm_logs/*
# indexing and creating a sequence dictionary gets done within pipeline
data/zebraFinch/genome/*.sa
data/zebraFinch/genome/*.pac
data/zebraFinch/genome/*.bwt
data/zebraFinch/genome/*.ann
data/zebraFinch/genome/*.amb
data/zebraFinch/genome/*.fai
data/zebraFinch/genome/*.dict
rules/.snakemake
data/BHduck/genome/*.sa
data/BHduck/genome/*.pac
data/BHduck/genome/*.bwt
data/BHduck/genome/*.ann
data/BHduck/genome/*.amb
data/BHduck/genome/*.fai
data/BHduck/genome/*.dict
/data/
fastp.*
intervalFiles/
out
err
__pycache__
log/
fastq2bam/
intervalFiles/
freebayes/
gatk/
logs/
*_dryrun.txt
results/
tmp/
.test/ecoli/benchmarks/
.test/ecoli/logs/
.test/ecoli/results/
.test/ecoli/data/
*.lic
.test/ci/results
.test/ci/benchmarks
.test/ci/logs
.vscode
.test/trackhub/*.sizes
.test/trackhub/out.log