From 1ac4ea2a8369d5a51376dbb84f807a8c9476fb90 Mon Sep 17 00:00:00 2001
From: khalid <khalid.belkhir@umontpellier.fr>
Date: Wed, 1 Dec 2021 15:56:20 +0100
Subject: [PATCH] debug accel_align

---
 tools/accel_align/accel_align.rule.snakefile | 15 ++++++++-------
 1 file changed, 8 insertions(+), 7 deletions(-)

diff --git a/tools/accel_align/accel_align.rule.snakefile b/tools/accel_align/accel_align.rule.snakefile
index fa041164..830180df 100755
--- a/tools/accel_align/accel_align.rule.snakefile
+++ b/tools/accel_align/accel_align.rule.snakefile
@@ -11,9 +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"],
             #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 ][0]),
+            indexPrefix = lambda w, input: os.path.splitext([x for x in input.index ][1]),
             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 "",
@@ -27,8 +28,8 @@ if config["SeOrPe"] == "PE":
             "{params.accel_align_alignment_free} "
             "-o {params.output_dir} "
             "{params.indexPrefix} "
-            "{input.read} {input.read2} 2> {log} "
-            "| samtools view -b 2>> {log} "
+            "{input.read} {input.read2} 2> {log}; "
+            "samtools view -b {params.output_dir} 2>> {log} "
             "| samtools sort -@ {threads} > {output.bam} 2>> {log} && "
             "samtools index -@ {threads} {output.bam} 2>> {log}"
 
@@ -45,13 +46,13 @@ 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"]
+            output_dir = config["results_dir"]+"/"+config["<step_name>__accel_align_SE_output_dir"],
             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 "",
             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][1]),
         shell:
             "{params.command} "
             "-t {threads} "
@@ -60,7 +61,7 @@ elif config["SeOrPe"] == "SE":
             "{params.accel_align_alignment_free} "
             "-o {params.output_dir} "
             "{params.indexPrefix} "
-            "{input.read} 2> {log} "
-            "| samtools view -b 2>> {log} "
+            "{input.read} 2> {log}; "
+            "| samtools view -b {params.output_dir} 2>> {log} "
             "| samtools sort -@ {threads} > {output.bam} 2>> {log} && "
             "samtools index -@ {threads} {output.bam} 2>> {log}"
-- 
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