Commit d7e0ddfe authored by khalid's avatar khalid
Browse files

Fastqc now declared output is only a logfile

parent f2c99462
......@@ -36,7 +36,7 @@ if config["SeOrPe"] == "PE":
"--complexity_threshold {params.complexity_threshold} "
"--html {output.report_html} "
"--json {output.report_json} "
"--report_title {params.report_title} "
"--report_title '{params.report_title} : {sample}' "
"{params.detect_adapter_for_pe} "
"{params.adapter_sequence} "
"{params.adapter_sequence_R2} "
......
......@@ -4,9 +4,10 @@ if config["SeOrPe"] == "SE":
input:
**<step_name>__fastqc_SE_inputs()
output:
html = config["results_dir"]+'/'+config["<step_name>__fastqc_SE_output_dir"]+'/{sample}'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
zip = config["results_dir"]+'/'+config["<step_name>__fastqc_SE_output_dir"]+'/{sample}'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
log: config["results_dir"]+'/logs/' + config["<step_name>__fastqc_SE_output_dir"] + '/{sample}_fastqc_log.txt'
#html = config["results_dir"]+'/'+config["<step_name>__fastqc_SE_output_dir"]+'/{sample}'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
#zip = config["results_dir"]+'/'+config["<step_name>__fastqc_SE_output_dir"]+'/{sample}'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
logFile = config["results_dir"]+'/'+config["<step_name>__fastqc_SE_output_dir"] + '/{sample}_fastqc_log.txt'
#log: config["results_dir"]+'/logs/' + config["<step_name>__fastqc_SE_output_dir"] + '/{sample}_fastqc_log.txt'
threads: 2
params:
command = config["<step_name>__fastqc_SE_command"],
......@@ -26,11 +27,12 @@ elif config["SeOrPe"] == "PE":
**<step_name>__fastqc_PE_inputs()
output:
#PE_Mark is "_" or "_R" see raw_reads
html1 = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"]+'/{sample}'+PE_Mark +'1'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
zip1 = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"]+'/{sample}'+PE_Mark +'1'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
html2 = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"]+'/{sample}'+PE_Mark +'2'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
zip2 = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"]+'/{sample}'+PE_Mark +'2'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
log: config["results_dir"]+'/logs/' + config["<step_name>__fastqc_PE_output_dir"] + '/{sample}_fastqc_log.txt'
#html1 = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"]+'/{sample}'+PE_Mark +'1'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
#zip1 = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"]+'/{sample}'+PE_Mark +'1'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
#html2 = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"]+'/{sample}'+PE_Mark +'2'+config["sample_suffix"].split(".")[0]+'_fastqc.html',
#zip2 = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"]+'/{sample}'+PE_Mark +'2'+config["sample_suffix"].split(".")[0]+'_fastqc.zip',
logFile = config["results_dir"]+'/'+config["<step_name>__fastqc_PE_output_dir"] + '/{sample}_fastqc_log.txt'
#log: config["results_dir"]+'/logs/' + config["<step_name>__fastqc_PE_output_dir"] + '/{sample}_fastqc_log.txt'
threads: 4
params:
command = config["<step_name>__fastqc_PE_command"],
......@@ -42,4 +44,4 @@ elif config["SeOrPe"] == "PE":
"-t {threads} "
"-o {params.output_dir} "
"--quiet "
"|& tee {log}"
"|& tee {output.logFile}"
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