diff --git a/nextflow.config b/nextflow.config index 133a7286..8a71d8fa 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,7 +1,7 @@ outputDir = 'results' params { input = null - outputDir = "${outputDir}" + outputDir = 'results' //"${outputDir}" tracedir = "${params.outputDir}/pipeline_info" genome = null // must be listed in conf/genomes.config @@ -42,7 +42,7 @@ params { deeptools_smooth_length = 75 deeptools_corr_method = "spearman" // correlation method for deeptools plotCorrelation: spearman or pearson deeptools_normalize_using = "RPGC" // set this to "None" if using a spike-in control - deeptools_normalize_samples = deeptools_normalize_using + deeptools_normalize_samples = params.deeptools_normalize_using deeptools_normalize_input = "RPGC" // this is separate from the above, only for input samples deeptools_excluded_chroms = "chrM chrX chrY"