Merge branch 'main' of github.com:soedinglab/phylo_grad

Author: benjamin-lieser

benchmark_test/Snakefile

@@ -1,13 +1,9 @@
-localrules: random_phylo, unroot, random_fasta, sim_phy, phy_to_fasta, collect_iqtree_benchmark
+localrules: random_phylo, random_fasta, sim_phy, phy_to_fasta, collect_iqtree_benchmark
 
 rule random_phylo:
-    output: "data/random/root_tree_{num_leafs}.nwk"
-    shell: "phylotree generate -t {wildcards.num_leafs} -b > {output}"
-
-rule unroot:
-    input: "data/random/root_tree_{num_leafs}.nwk"
-    output: "data/random/tree_{num_leafs}.nwk"
-    shell: "nw_reroot -d {input} > {output}"
+    output: ensure("data/random/tree_{num_leafs}.nwk", non_empty=True)
+    retries: 5
+    shell: "nw_reroot -d <(phylotree generate -t {wildcards.num_leafs} -b) > {output}"
 
 rule random_fasta:
     input: "data/random/tree_{num_leafs}.nwk"
@@ -60,4 +56,4 @@ rule collect_iqtree_benchmark:
     input: iqtree = expand("data/sim/alignment_{num_leafs}_{L}.fasta.iqtree.time", num_leafs=[2**n for n in [4,6,8,10,12]], L=[100,500]),
            phylograd = expand("data/sim/alignment_{num_leafs}_{L}.fasta.phylograd.time", num_leafs=[2**n for n in [4,6,8,10,12]], L=[100,500])
     output: "data/iqtree_benchmark.txt"
-    shell: "tail -n +1 {input.iqtree} {input.phylograd} > {output}"
+    shell: "tail -n +1 {input.iqtree} {input.phylograd} > {output}"