From 22e29eafa0b1303112b841be7295a38dd8d506df Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Wed, 1 Dec 2021 17:22:45 +0100
Subject: [PATCH] debug accel_align
---
tools/accel_align/accel_align.rule.snakefile | 18 ++++++++++--------
1 file changed, 10 insertions(+), 8 deletions(-)
diff --git a/tools/accel_align/accel_align.rule.snakefile b/tools/accel_align/accel_align.rule.snakefile
index 1ac570d8..e80bf361 100755
--- a/tools/accel_align/accel_align.rule.snakefile
+++ b/tools/accel_align/accel_align.rule.snakefile
@@ -11,7 +11,7 @@ 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_PE_output_dir"],
+ tmp_sam = config["results_dir"]+"/"+config["<step_name>__accel_align_PE_output_dir"]+"/{sample}.sam",
#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 if 'hash' in x][0])[0],
@@ -26,12 +26,13 @@ if config["SeOrPe"] == "PE":
"-p {params.accel_align_insert_size} "
"{params.accel_align_alignment_free} "
"{params.accel_align_alignment_free} "
- "-o {params.output_dir} "
+ "-o {params.tmp_sam} "
"{params.indexPrefix} "
"{input.read} {input.read2} 2> {log}; "
- "samtools view -b {params.output_dir} 2>> {log} "
+ "samtools view -b {params.tmp_sam}/ 2>> {log} "
"| samtools sort -@ {threads} > {output.bam} 2>> {log} && "
- "samtools index -@ {threads} {output.bam} 2>> {log}"
+ "samtools index -@ {threads} {output.bam} 2>> {log}; "
+ "rm -f {params.tmp_sam} "
elif config["SeOrPe"] == "SE":
@@ -46,7 +47,7 @@ elif config["SeOrPe"] == "SE":
threads:
config["<step_name>__accel_align_threads"]
params:
- output_dir = config["results_dir"]+"/"+config["<step_name>__accel_align_SE_output_dir"],
+ tmp_sam = config["results_dir"]+"/"+config["<step_name>__accel_align_PE_output_dir"]+"/{sample}.sam",
command = config["<step_name>__accel_align_PE_command"],
accel_align_seed_length = config["<step_name>__accel_align_seed_length"],
accel_align_softclipping = "-s" if config["<step_name>__accel_align_softclipping"] else "",
@@ -59,9 +60,10 @@ elif config["SeOrPe"] == "SE":
"-l {params.accel_align_seed_length} "
"{params.accel_align_alignment_free} "
"{params.accel_align_alignment_free} "
- "-o {params.output_dir} "
+ "-o {params.tmp_sam} "
"{params.indexPrefix} "
"{input.read} 2> {log}; "
- "| samtools view -b {params.output_dir} 2>> {log} "
+ "| samtools view -b {params.tmp_sam} 2>> {log} "
"| samtools sort -@ {threads} > {output.bam} 2>> {log} && "
- "samtools index -@ {threads} {output.bam} 2>> {log}"
+ "samtools index -@ {threads} {output.bam} 2>> {log}; "
+ "rm -f {params.tmp_sam} "
--
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