create snakemake rule for clock_model

ktmeaton · Mar 3, 2021 · 4a53263 · 4a53263
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diff --git a/.gitignore b/.gitignore
@@ -24,6 +24,7 @@ results/snippy_pairwise/*
 # Phylogeny
 results/iqtree/*/*ckp.gz
 results/iqtree/*/*uniqueseq*
+results/iqtree/*/*filter50*
 
 # Snippy Multi Alignments
 results/snippy_multi/*/*.aln*

diff --git a/docs/notes/Notes_Development.md b/docs/notes/Notes_Development.md
@@ -7,7 +7,11 @@
     - iqtree
     - multiqc
 1. Decided not to upload qualimap, too many small files!
-1. Add parse_tree notebook to snakemake pipeline!
+1. Move log directory to within results.
+1. Add parse_tree notebook to snakemake pipeline.
+1. Add clock_model notebook to snakemake pipeline.
+1. Rename 'clock_model' output directory to 'clock'
+1. Remove xml tree output.
 
 ## TO-DO
 
@@ -16,5 +20,3 @@
 1. Check if multiqc still runs without eager output dir...
 1. Maybe write a function to condense exporting.
 1. Now that results are uploaded, shrink report file?
-1. Move log directory to within results.
-1. Rename 'clock_model' output directory to 'clock'
diff --git a/results/clock_model/clock_model.tsv b/results/clock_model/clock_model.tsv