v0.3.0

• Add pipeline parameter to specify tree root in augur refine process (see PR #9)
• Add profiles to specify memory usage from command line (ex. -profile conda,low_memory). low_memory = 8GB, medium_memory = 16GB, and high_memory = 64GB.

v0.2.0

• Ability to specify reference genome in the form of an a) GenBank file or b) FASTA file (also requires GFF file). The option to specify the FASTA format originated from the need to construct a more tailored reference genome than may be available (ex. concatenated segments). This feature is added in PR #6.

v0.1.3

• Add ability to adjust the AUGUR_RECURSION_LIMIT environmental variable with the --recursion_limit flag. Default is 10000. This fixes "FATAL: Maximum recursion depth reached" error.

v0.1.2

• Fixed iqtree process cpu usage issue to be specified in config file instead of auto-detected

v0.1.1

• initial release
• generate msa from multifasta
• generate ML tree
• augur suite
• visualization in Nextstrain
• author: JMC
• version: 0.1.1
• language: Nextflow