diff --git a/modules/local/multiqc.nf b/modules/local/multiqc.nf index d0695b40..38fc5391 100644 --- a/modules/local/multiqc.nf +++ b/modules/local/multiqc.nf @@ -10,45 +10,54 @@ process MULTIQC { path multiqc_config path mqc_custom_config path logo + path 'fastqc/*' path 'trimgalore/fastqc/*' path 'trimgalore/*' + path 'alignment/library/*' path 'alignment/library/*' path 'alignment/library/*' + path 'alignment/merged_library/unfiltered/*' path 'alignment/merged_library/unfiltered/*' path 'alignment/merged_library/unfiltered/*' path 'alignment/merged_library/unfiltered/picard_metrics/*' + path 'alignment/merged_library/filtered/*' path 'alignment/merged_library/filtered/*' path 'alignment/merged_library/filtered/*' path 'alignment/merged_library/filtered/picard_metrics/*' + path 'preseq/*' + path 'deeptools/*' path 'deeptools/*' + path 'phantompeakqualtools/*' path 'phantompeakqualtools/*' path 'phantompeakqualtools/*' path 'phantompeakqualtools/*' + path 'macs3/peaks/*' path 'macs3/peaks/*' path 'macs3/annotation/*' path 'macs3/featurecounts/*' + path 'deseq2/*' path 'deseq2/*' output: path "*multiqc_report.html", emit: report - path "*_data", emit: data - path "*_plots", optional: true, emit: plots - path "versions.yml", emit: versions + path "*_data" , emit: data + path "*_plots" , optional: true, emit: plots + path "versions.yml" , emit: versions when: task.ext.when == null || task.ext.when script: - def args = task.ext.args ?: '' + def args = task.ext.args ?: '' def custom_config = params.multiqc_config ? "--config ${mqc_custom_config}" : '' """ multiqc \\