Hard link figures in the top-level manuscript directory

Simplifies eLife upload and manuscript PDF building by placing all figures in the top-level manuscript directory. This commit also updates the rule used to link these figures from their more human-readable names to use hard links.
blab · huddlej · Aug 17, 2020 · Jul 20, 2020 · Jul 20, 2020 · Jul 21, 2020
commit bd08ea659ee3dd35ada4a14b3279e5ead543362f
diff --git a/Snakefile b/Snakefile
@@ -481,20 +481,20 @@ rule figures:
         rules.figure_for_vaccine_comparison.output,
         figure_names="manuscript/figures/figure_names.tsv"
     output:
-        "figures/Figure_1.pdf"
+        "manuscript/Figure_1.pdf"
     shell:
         """
         while read original_name new_name
         do
-            ln -s manuscript/figures/$original_name manuscript/figures/$new_name"
+            ln manuscript/figures/$original_name manuscript/$new_name
         done < {input.figure_names}
         """
 
 # Compile the manuscript after creating all figures and tables.
 rule manuscript:
     input:
         # Tables and figures
-        "figures/Figure_1.pdf",
+        "manuscript/Figure_1.pdf",
         rules.table_of_mutations_by_trunk_status_for_simulated_populations.output,
         rules.table_of_mutations_by_trunk_status_for_natural_populations.output,
 

diff --git a/manuscript/Figure_1.pdf b/manuscript/Figure_1.pdf
diff --git a/manuscript/Figure_10.png b/manuscript/Figure_10.png
diff --git a/manuscript/Figure_11.pdf b/manuscript/Figure_11.pdf
diff --git a/manuscript/Figure_12.png b/manuscript/Figure_12.png
diff --git a/manuscript/Figure_13.pdf b/manuscript/Figure_13.pdf
diff --git a/manuscript/Figure_14.pdf b/manuscript/Figure_14.pdf
diff --git a/manuscript/Figure_15.pdf b/manuscript/Figure_15.pdf
diff --git a/manuscript/Figure_2.pdf b/manuscript/Figure_2.pdf
diff --git a/manuscript/Figure_3-Figure_supplement_1.pdf b/manuscript/Figure_3-Figure_supplement_1.pdf
diff --git a/manuscript/Figure_3.pdf b/manuscript/Figure_3.pdf
diff --git a/manuscript/Figure_4-Figure_supplement_1.pdf b/manuscript/Figure_4-Figure_supplement_1.pdf
diff --git a/manuscript/Figure_4-Figure_supplement_2.pdf b/manuscript/Figure_4-Figure_supplement_2.pdf
diff --git a/manuscript/Figure_4-Figure_supplement_3.pdf b/manuscript/Figure_4-Figure_supplement_3.pdf
diff --git a/manuscript/Figure_4.pdf b/manuscript/Figure_4.pdf
diff --git a/manuscript/Figure_5-Figure_supplement_1.pdf b/manuscript/Figure_5-Figure_supplement_1.pdf
diff --git a/manuscript/Figure_5.pdf b/manuscript/Figure_5.pdf
diff --git a/manuscript/Figure_6-Figure_supplement_1.pdf b/manuscript/Figure_6-Figure_supplement_1.pdf
diff --git a/manuscript/Figure_6.pdf b/manuscript/Figure_6.pdf
diff --git a/manuscript/Figure_7-Figure_supplement_1.pdf b/manuscript/Figure_7-Figure_supplement_1.pdf
diff --git a/manuscript/Figure_7-Figure_supplement_2.pdf b/manuscript/Figure_7-Figure_supplement_2.pdf
diff --git a/manuscript/Figure_7-Figure_supplement_3.pdf b/manuscript/Figure_7-Figure_supplement_3.pdf
diff --git a/manuscript/Figure_7.pdf b/manuscript/Figure_7.pdf
diff --git a/manuscript/Figure_8-Figure_supplement_1.pdf b/manuscript/Figure_8-Figure_supplement_1.pdf
diff --git a/manuscript/Figure_8.pdf b/manuscript/Figure_8.pdf
diff --git a/manuscript/Figure_9.png b/manuscript/Figure_9.png
diff --git a/manuscript/flu_forecasting.tex b/manuscript/flu_forecasting.tex