pangolin v1.1.10

Updates:

• Better handling of path joining. Trusting os.path.join() to do its job.

pangolin v1.1.9

Minor changes:

• pandas dependency more flexible in setup.py now
• iqtree<2 specified in the conda environment instead

pangolin v1.1.8

Updates in this release include --panGUIlin header compatibility with new lineages metadata headers inherited from grapevine. Also more cores now passed to prep pipeline mafft and iqtree step.

pangolin v1.1.7

Updates in this release include:

• Outfile name now can be specified with an optional --outfile argument
• Bug fix Now won't max out bash args as instead of passing hashed taxon names through the cmd line, write to a temp config.yaml file with query_sequences specified as a config key. The sub workflow accepts this with the --configfile argument. This then loads tax names into the new snakemake without having to be passed through the shell command or then parsed. Could in theory pass everything through this config file, but I think it's probably useful to have the other things printed as part of the snakemake command call.
• Quite a lot of dev to the prep-pipeline in anticipation of the new data release tomorrow. Added in quite a lot of annotation and tomorrow will make it a flag in the pangolin command to prep your own pipeline, which will be fun.

pangolin v1.1.6

Updates in this release include:

• Bug fix: outdir when explicitly called was appending to cwd, which is now the temp dir for much of the running to write the .snakemake dir away from actual cwd. Have now fixed this and pangolin gets the absolute path of the old cwd and appends outdir to that before calling the snakemake pipeline. Convoluted, but it's fixed now.

pangolin v1.1.5

Updates in this release include:

• Bug fix if query was identical (or near identical with only ambiguous sequences differentiating it) to the outgroup, the resulting polytomy was collapsing to the root node, which didn't have a bootstrap or alrt value. The lineage was being assigned but with incorrect support values of 0,0. This is now fixed and the support for being assigned the base of lineage A is now 100 - (100 - alternative lineage 1) - (100-alternative lineage 2) etc... Which is a more satisfying solution.

• A new flag (--write-tree) that optionally writes a tree showing the placement of each query sequence in the guide tree.

• Branches that are now non-zero but very very short are being collapsed, which should overall increase accuracy of calls.

pangolin v1.1.4

Updates in this release include:

• Updated --directory of snakemake run to the tempdir so will now write .snakemake to temp.
• Updated tempdir to be an instance of tempfile.TemporaryDirectory, which handles the deletion of the tempdir.
• mafft command updated to mafft --addprofile {new_seq} {guide_aln} > {output} instead of mafft-profile.

pangolin v1.1.2

Panguilin good to go!

pangolin v1.1.1

pan-GUI-lin with appropriate bug fixes.

Now with optional --verbose flag.

pangolin v1.1: pan-GUI-lin

pangolin master now has optional --panGUIlin flag that will run the web app version of pangolin.