From 4629d1f3ddd52fec11a867f444fe329256150959 Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Mon, 6 Dec 2021 09:35:16 +0100
Subject: [PATCH] Debug snap align
---
tools/snap/snap.rule.snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/tools/snap/snap.rule.snakefile b/tools/snap/snap.rule.snakefile
index ae8a8a49..dd1fd1e9 100755
--- a/tools/snap/snap.rule.snakefile
+++ b/tools/snap/snap.rule.snakefile
@@ -11,7 +11,7 @@ if config["SeOrPe"] == "PE":
config["<step_name>__snap_threads"]
params:
command = config["<step_name>__snap_PE_command"],
- indexDir = lambda w, input: os.path.dirname([x for x in input.index if 'GenomeIndexHash' in x]),
+ indexDir = lambda w, input: os.path.dirname(input.index[0]),
snap_seed_number = config["<step_name>__snap_seed_number"],
snap_min_insert_size = config["<step_name>__snap_min_insert_size"],
snap_max_insert_size = config["<step_name>__snap_max_insert_size"],
@@ -46,7 +46,7 @@ elif config["SeOrPe"] == "SE":
snap_seed_number = config["<step_name>__snap_seed_number"],
snap_disable_alt_awareness = "-A-" if config["<step_name>__snap_disable_alt_awareness"] else "",
snap_max_score_gap = config["<step_name>__snap_max_score_gap"],
- indexDir = lambda w, input: os.path.dirname([x for x in input.index if 'GenomeIndexHash' in x]),
+ indexDir = lambda w, input: os.path.dirname( input.index[0]),
shell:
"{params.command} "
"{params.indexDir} "
--
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