From fe7395ddecadebcc4d9f727af38a0a595e89ed02 Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Wed, 1 Dec 2021 16:57:46 +0100
Subject: [PATCH] debug accel_align indexing
---
tools/accel_align/accel_align.rule.snakefile | 6 +++---
tools/accel_align_index/accel_align_index.rule.snakefile | 8 ++++++--
2 files changed, 9 insertions(+), 5 deletions(-)
diff --git a/tools/accel_align/accel_align.rule.snakefile b/tools/accel_align/accel_align.rule.snakefile
index 830180df..235d1d64 100755
--- a/tools/accel_align/accel_align.rule.snakefile
+++ b/tools/accel_align/accel_align.rule.snakefile
@@ -11,10 +11,10 @@ if config["SeOrPe"] == "PE":
config["<step_name>__accel_align_threads"]
params:
command = config["<step_name>__accel_align_PE_command"],
- output_dir = config["results_dir"]+"/"+config["<step_name>__accel_align_SE_output_dir"],
+ 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([x for x in input.index ][1]),
+ indexPrefix = lambda w, input: os.path.splitext(input.index[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][1]),
+ indexPrefix = lambda w, input: os.path.splitext([x for x in input.index])[0],
shell:
"{params.command} "
"-t {threads} "
diff --git a/tools/accel_align_index/accel_align_index.rule.snakefile b/tools/accel_align_index/accel_align_index.rule.snakefile
index 46e2bf17..d78aae48 100755
--- a/tools/accel_align_index/accel_align_index.rule.snakefile
+++ b/tools/accel_align_index/accel_align_index.rule.snakefile
@@ -2,6 +2,10 @@ rule <step_name>__accel_align_index:
input:
**<step_name>__accel_align_index_inputs()
output:
+ index = (
+ config["<step_name>__accel_align_index_output_dir"]+"/index",
+ config["<step_name>__accel_align_index_output_dir"]+"/index.hash",
+ )
index = config["<step_name>__accel_align_index_output_dir"]+"/index.hash",
log:
config["results_dir"]+"/logs/" + config["<step_name>__accel_align_index_output_dir"] + "/index.log"
@@ -14,5 +18,5 @@ rule <step_name>__accel_align_index:
"-l {params.accel_align_index_kmers_length} "
"{input.genome_fasta} "
"|& tee {log};"
- "cp {input.genome_fasta} {params.out_dir}/index "
- "cp {input.genome_fasta}.hash {params.out_dir}/index.hash "
+ "cp {input.genome_fasta} {params.out_dir}/index; "
+ "mv {input.genome_fasta}.hash {params.out_dir}/index.hash ;"
--
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