Don't use prophyle dir as output

fixes #24
karel-brinda · Aug 9, 2021 · d9b4084 · d9b4084
1 parent 8fd52c8
commit d9b4084
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Showing 2 changed files with 9 additions and 4 deletions.
diff --git a/workflow/rules/common.smk b/workflow/rules/common.smk
@@ -251,6 +251,10 @@ def fn_post_compr_summary(_batch):
     return fn_post_compr(_batch) + ".summary"
 
 
+def fn_prophyle_kmer_stats(_batch):
+    return f"results/post/{_batch}/index.fa.kmers.tsv"
+
+
 # def fn_prophyle_tree(_batch):
 #    return f"results/post/{_batch}/tree.nw"
 

diff --git a/workflow/rules/post.smk b/workflow/rules/post.smk
@@ -10,17 +10,18 @@ checkpoint prophyle_index:
         w_batch_asms,
         nw=fn_tree_sorted(_batch="{batch}"),
     output:
-        d1=directory(dir_prophyle(_batch="{batch}")),
-        d2=directory(dir_prophyle_propagation(_batch="{batch}")),
+        #d2=directory(dir_prophyle_propagation(_batch="{batch}")),
         #nw=fn_prophyle_tree(_batch="{batch}"),
+        s=fn_prophyle_kmer_stats(_batch="{batch}"),
     params:
         k=31,
+        pro_dir=directory(dir_prophyle(_batch="{batch}")),
         asm_dir=fn_asm_seq_dir("{batch}"),
     shell:
         """
         prophyle index  -T -A -S\\
             -k {params.k} -g {params.asm_dir}\\
-            {input.nw} {output.d1}
+            {input.nw} {params.pro_dir}
         """
 
 
@@ -61,7 +62,7 @@ rule post_list:
     input:
         list=fn_nodes_sorted(_batch="{batch}"),
         fa=w_batch_posts,
-        dpp=dir_prophyle_propagation(_batch="{batch}"),
+        s=fn_prophyle_kmer_stats(_batch="{batch}"),
     output:
         list=fn_post_list(_batch="{batch}"),
     run: