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}" -- GitLab