add log to report rule

ktmeaton · Apr 14, 2022 · 94fc942 · 94fc942
1 parent 861ffb1
commit 94fc942
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diff --git a/docs/notes/Notes_development.md b/docs/notes/Notes_development.md
@@ -16,8 +16,7 @@
 
 ## To Do
 
-1. Consolidate `summary` and `usher_metadata`.
+1. Summarize recombinants by parents and dates observed.
 1. Edit Auspice json to change default colorings,filters,and panels.
 1. Automate unit test update.
-1. Move `report` output to `reporting` directory.
 1. Test the `exclude_clades` param of Nextclade to make sure it isn't removing.
diff --git a/workflow/Snakefile b/workflow/Snakefile
@@ -678,9 +678,7 @@ rule report:
     """
     csvtk cut -t -f "{params.cols}" {input.summary} \
       | csvtk rename -t -f "{params.cols}" -n "{params.cols_rename}" \
-      | csvtk mutate2 -t -n "status" -e '""' \
-      | csvtk mutate2 -t -n "new_this_week" -e '""' \
-      > {output.report};
+      1> {output.report} 2> {log};
     """
 
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