diff --git a/main.nf b/main.nf index 9cc12203..f400b181 100644 --- a/main.nf +++ b/main.nf @@ -22,7 +22,7 @@ def helpMessage() { Mandatory arguments: --reads Path to input data (must be surrounded with quotes). NOTE! Paired-end data is NOT supported by this pipeline! For paired-end data, use Read 1 only - --genome Name of iGenomes reference. Not needed if the --mature, --hairpin, --mirtrace_species is giving. + --genome Name of iGenomes reference. Not needed if --mature, --hairpin, --mirtrace_species are provided. --protocol Library preparation protocol. Default: "illumina". Can be set as "illumina", "nextflex", "qiaseq" or "cats" @@ -187,8 +187,8 @@ if(params.readPaths){ // Header log info log.info nfcoreHeader() -if(workflow.revision) summary['Pipeline Release'] = workflow.revision def summary = [:] +if(workflow.revision) summary['Pipeline Release'] = workflow.revision summary['Run Name'] = custom_runName ?: workflow.runName summary['Reads'] = params.reads summary['Genome'] = params.genome @@ -211,7 +211,7 @@ summary['Current path'] = "$PWD" summary['Script dir'] = workflow.projectDir summary['Config Profile'] = (workflow.profile == 'standard' ? 'UPPMAX' : workflow.profile) summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job" -if(workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container" +if(workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container" summary['Script dir'] = workflow.projectDir summary['User'] = workflow.userName if(workflow.profile == 'awsbatch'){ @@ -223,8 +223,8 @@ if(params.config_profile_description) summary['Config Description'] = params.con if(params.config_profile_contact) summary['Config Contact'] = params.config_profile_contact if(params.config_profile_url) summary['Config URL'] = params.config_profile_url if(params.email) { - summary['E-mail Address'] = params.email - summary['MultiQC maxsize'] = params.maxMultiqcEmailFileSize + summary['E-mail Address'] = params.email + summary['MultiQC maxsize'] = params.maxMultiqcEmailFileSize } log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n") log.info "\033[2m----------------------------------------------------\033[0m"