v1.0.1

• Fix input of augur refine (time tree process) from consensus tree (v1.0.0) to best ML tree (v1.0.1).

• Improve documentation for bootstrapping and usage with augur v31.1.0.

• Detailed Changelog

v1.0.0

• Visualize bootstrap support values in Nextstrain (with auspice view)
• Upgrade to augur v31.1.0 which requires different gff3 for concat sequences as input - see README & #16
• Add AUGUR_RECURSION_LIMIT env var to task environment to fix #17
• Remove conda environment yaml associated with fluflo release v0.4.0

v0.4.0

• Bundling as final release v0.4.0 so can safely release v1.0.0 which contains updated env (augur & auspice) without changing routine processes for users pulling from -r main.
• Note: while bootstrap supported trees may be generated in this release, visualization of them is NOT supported but will be in fluflo v1.0.0. This requires an update to environment (see #16) with breaking change (augur v31.1.0 requires different gff3 for concat sequences as input) so tagging this release to decouple from main.
• Add AUGUR_RECURSION_LIMIT env var to task environment
• Fix conda env by simplifying

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