From dd67d851f3df511b2c70d60dfc9074080eaf72ee Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Wed, 1 Dec 2021 17:15:09 +0100
Subject: [PATCH] debug accel_align
---
tools/accel_align/accel_align.rule.snakefile | 4 ++--
1 file changed, 2 insertions(+), 2 deletions(-)
diff --git a/tools/accel_align/accel_align.rule.snakefile b/tools/accel_align/accel_align.rule.snakefile
index 235d1d64..1ac570d8 100755
--- a/tools/accel_align/accel_align.rule.snakefile
+++ b/tools/accel_align/accel_align.rule.snakefile
@@ -14,7 +14,7 @@ if config["SeOrPe"] == "PE":
output_dir = config["results_dir"]+"/"+config["<step_name>__accel_align_PE_output_dir"],
#indexPrefix = config["<step_name>__accel_align_index_output_dir"]+"/index",
#/patho_index/indexName.fna.hash
- indexPrefix = lambda w, input: os.path.splitext(input.index[0])[0],
+ indexPrefix = lambda w, input: os.path.splitext([x for x in input.index if 'hash' in x][0])[0],
accel_align_seed_length = config["<step_name>__accel_align_seed_length"],
accel_align_insert_size = config["<step_name>__accel_align_insert_size"],
accel_align_softclipping = "-s" if config["<step_name>__accel_align_softclipping"] else "",
@@ -52,7 +52,7 @@ elif config["SeOrPe"] == "SE":
accel_align_softclipping = "-s" if config["<step_name>__accel_align_softclipping"] else "",
accel_align_alignment_free = "-x" if config["<step_name>__accel_align_alignment_free"] else "",
#indexPrefix = config["<step_name>__accel_align_index_output_dir"]+"/index",
- indexPrefix = lambda w, input: os.path.splitext([x for x in input.index])[0],
+ indexPrefix = lambda w, input: os.path.splitext([x for x in input.index if 'hash' in x][0])[0],
shell:
"{params.command} "
"-t {threads} "
--
GitLab