Finished resolving merge conflicts. There were a lot.

.gitignore

ChipathlonMethodParameters.xlsx

chipathlon/conf.py

chipathlon/db.py

chipathlon/generators/align_generator.py

chipathlon/generators/idr_generator.py

chipathlon/generators/module_generator.py

chipathlon/generators/peak_call_generator.py

chipathlon/generators/remove_duplicates_generator.py

chipathlon/genome.py

chipathlon/jobs/modules/align.yaml

chipathlon/jobs/modules/idr.yaml

chipathlon/jobs/modules/peak_call.yaml

chipathlon/jobs/modules/remove_duplicates.yaml

chipathlon/jobs/params/bedtools_bam_to_bed.yaml

chipathlon/jobs/params/bowtie2_align_paired.yaml

chipathlon/jobs/params/bowtie2_align_single.yaml

chipathlon/jobs/params/bwa_align_paired.yaml

chipathlon/jobs/params/bwa_align_single.yaml

chipathlon/jobs/params/bwa_sai_to_sam.yaml