epiGBS2 release with some bug fixes

src/rules/denovo.rules:

• library is now always directional
• to save space, six output files were made temporary

src/rules/reference.rules:

• library is now always directional
• to save space, six output files were made temporary
• added flag “—scaffolds” during methylation calling to allow compatibility with reference genome assemblies with contigs
• removed MQ parameter in rule SNP calling

src/env/bismark.yaml :

• fixed problems with the environment files

src/parameter_test/paramTest.tsv :

• improved default parameters

src/rules/paramTest.rules:

• fixed bugs