From fee59f2ea5a4e544d03265a2e6fb60220dd11f8b Mon Sep 17 00:00:00 2001 From: aineniamh Date: Sun, 5 Nov 2023 17:37:21 +0000 Subject: [PATCH 1/2] updating readme --- README.md | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/README.md b/README.md index 70513d1..4f00d98 100644 --- a/README.md +++ b/README.md @@ -396,6 +396,12 @@ The phylogenetic pipeline is activated by running with the flag `-rp/--run-phylo If you supply a path to the `-sd,--supplementary-datadir` for the phylogenetics module, you have the option of updating this data directory with the new consesnsus sequences generated during the piranaha analysis. If you run with the `-ud,--update-local-database` flag, piranha will write out the new sequences and any accompanying metadata supplied into the directory provided. +The files written out will be in the format `runname.today.fasta` and `runname.today.csv`. For example, if your runname supplied is `MIN001` and today's date is `2023-11-05`, the files written will be: +- `MIN001.2023-11-05.fasta` +- `MIN001.2023-11-05.csv` +with the newly generated consensus sequences and accompanying metadata from that run. + +> *Note:* if supplying the supplementary directory to piranha on a subsequent run, your updated local database will be included in the phylogenetics. However, piranha will ignore any files with identical `runname.today` patterns to the active run. So, if your current run would produce files called `MIN001.2023-11-05.fasta` and `MIN001.2023-11-05.csv`, if those files already exist in the supplementary data directory, they will be ignored. This is to avoid conflicts if piranha is run multiple times on the same data. ## Output options From d73b3cf81e2153dbe9e586406c7f3e7fa13c28f9 Mon Sep 17 00:00:00 2001 From: aineniamh Date: Sun, 5 Nov 2023 17:38:39 +0000 Subject: [PATCH 2/2] updating minor versioning for phylo update --- piranha/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/piranha/__init__.py b/piranha/__init__.py index a363eb6..b561cf3 100644 --- a/piranha/__init__.py +++ b/piranha/__init__.py @@ -1,5 +1,5 @@ _program = "piranha" -__version__ = "1.1.1" +__version__ = "1.2" __all__ = [ "input_parsing",