From ee8cb8b6edd53a925e0469b6305ac4a976391f63 Mon Sep 17 00:00:00 2001
From: Floreal Cabanettes <floreal.cabanettes@inra.fr>
Date: Wed, 22 Aug 2018 17:49:24 +0200
Subject: [PATCH] Easy dry run if only 1 batch
---
snakecnv/mergebatches.snk | 7 +++++++
1 file changed, 7 insertions(+)
diff --git a/snakecnv/mergebatches.snk b/snakecnv/mergebatches.snk
index 9855e09..16a8331 100644
--- a/snakecnv/mergebatches.snk
+++ b/snakecnv/mergebatches.snk
@@ -2,6 +2,7 @@ import sys
import re
import os
from glob import glob
+import shutil
from os.path import join, isfile
@@ -83,6 +84,12 @@ shell.prefix("export PATH=%s/bin:\"$PATH\";" % ROOTPATH)
batches, chromosomes, variant_types = get_batches(WDIR)
+if len(batches) == 1:
+ b_filtered = os.path.join(WDIR, "batch001", "filtered")
+ f_filtered = os.path.join(WDIR, "filtered")
+ shutil.move(b_filtered, f_filtered)
+ os.symlink(f_filtered, b_filtered)
+
include: "tools/threads.snk"
localrules: all, bamlist
--
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