From 84d1f6451b12352eba5a8bfefcfcce8b2d98c5aa Mon Sep 17 00:00:00 2001
From: Don Freed <DonFreed@users.noreply.github.com>
Date: Thu, 21 Oct 2021 05:29:56 -0700
Subject: [PATCH] fix: run dependencies with non-existent ancient files before
 the consuming job (#1202)
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Fixes #946

Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
---
 snakemake/dag.py                              |  2 +-
 tests/test_ancient_dag/Snakefile              | 39 +++++++++++++++++++
 .../expected-results/.gitkeep                 |  0
 tests/tests.py                                |  4 ++
 4 files changed, 44 insertions(+), 1 deletion(-)
 create mode 100644 tests/test_ancient_dag/Snakefile
 create mode 100644 tests/test_ancient_dag/expected-results/.gitkeep

diff --git a/snakemake/dag.py b/snakemake/dag.py
index f6ef9b69d..e60eaa7c0 100755
--- a/snakemake/dag.py
+++ b/snakemake/dag.py
@@ -1040,7 +1040,7 @@ def update_needrun(job):
                     if job_ not in visited:
                         # TODO may it happen that order determines whether
                         # _n_until_ready is incremented for this job?
-                        if all(f.is_ancient for f in files):
+                        if all(f.is_ancient and f.exists for f in files):
                             # No other reason to run job_.
                             # Since all files are ancient, we do not trigger it.
                             continue
diff --git a/tests/test_ancient_dag/Snakefile b/tests/test_ancient_dag/Snakefile
new file mode 100644
index 000000000..b74c6872d
--- /dev/null
+++ b/tests/test_ancient_dag/Snakefile
@@ -0,0 +1,39 @@
+shell.executable("bash")
+
+rule all:
+    input:
+        "d.out",
+
+rule A:
+    output:
+        "a.out",
+    shell:
+        "echo 'text' > {output}"
+
+rule B:
+    input:
+        ancient("a.out"),
+    output:
+        "b_{i}.out",
+    shell:
+        "cat {input} > {output}"
+
+# rule C is required for #946
+#  use `range(20)` so test will pass in < 5% of cases where issue is present
+rule C:
+    input:
+        expand("b_{i}.out", i=list(range(20))),
+    output:
+        "c.out",
+    shell:
+        "cat {input} > {output}"
+
+# For #946, 'a.out' is required as input, but does not need to be `ancient()`
+rule D:
+    input:
+        "a.out",
+        "c.out",
+    output:
+        "d.out",
+    shell:
+        "cat {input} > {output}"
diff --git a/tests/test_ancient_dag/expected-results/.gitkeep b/tests/test_ancient_dag/expected-results/.gitkeep
new file mode 100644
index 000000000..e69de29bb
diff --git a/tests/tests.py b/tests/tests.py
index 9511a63d2..0223c0bc2 100644
--- a/tests/tests.py
+++ b/tests/tests.py
@@ -1320,3 +1320,7 @@ def test_github_issue1158():
         dpath("test_github_issue1158"),
         cluster="./qsub.py",
     )
+
+
+def test_ancient_dag():
+    run(dpath("test_ancient_dag"))