Add snakemake-file-targets script

1 files changed, 25 insertions, 0 deletions

diff --git a/snakemake-file-targets b/snakemake-file-targets
new file mode 100755
index 0000000..12dca78
--- /dev/null
+++ b/snakemake-file-targets
@@ -0,0 +1,25 @@
+#!/usr/bin/env python3
+"""Print all concrete file targets.
+
+Usage: snakemake-file-targets [SNAKEFILE]
+"""
+import sys
+from snakemake.workflow import Workflow
+
+if len(sys.argv) == 1:
+    snakefile = "Snakefile"
+elif len(sys.argv) == 2 and sys.argv[1] not in ["-h", "--help"]:
+    snakefile = sys.argv[1]
+else:
+    sys.exit(__doc__)
+
+workflow = Workflow(snakefile=snakefile, snakemakepath="snakemake")
+workflow.include(snakefile)
+
+for rule in workflow.rules:
+    for fname in rule.output:
+        if not callable(fname) and not fname.contains_wildcard():
+            try:
+                print(fname)
+            except BrokenPipeError:
+                sys.exit(0)