From 29a281b5bb1ecfc9f4c87fde485561699a18c7da Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Fri, 3 Dec 2021 16:49:13 +0100
Subject: [PATCH] Debug snap
---
tools/snap/snap.rule.snakefile | 4 +---
1 file changed, 1 insertion(+), 3 deletions(-)
diff --git a/tools/snap/snap.rule.snakefile b/tools/snap/snap.rule.snakefile
index 212ea916..ae8a8a49 100755
--- a/tools/snap/snap.rule.snakefile
+++ b/tools/snap/snap.rule.snakefile
@@ -11,8 +11,6 @@ if config["SeOrPe"] == "PE":
config["<step_name>__snap_threads"]
params:
command = config["<step_name>__snap_PE_command"],
- #indexPrefix = config["<step_name>__snap_index_output_dir"]+"/index",
- #/patho_index/indexName.fna.hash
indexDir = lambda w, input: os.path.dirname([x for x in input.index if 'GenomeIndexHash' in x]),
snap_seed_number = config["<step_name>__snap_seed_number"],
snap_min_insert_size = config["<step_name>__snap_min_insert_size"],
@@ -47,7 +45,7 @@ elif config["SeOrPe"] == "SE":
command = config["<step_name>__snap_PE_command"],
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"]
+ 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]),
shell:
"{params.command} "
--
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