From 4844609d709c67e353c4727d0247ee0287bedf55 Mon Sep 17 00:00:00 2001 From: renewiegandt Date: Thu, 20 Dec 2018 13:14:41 +0100 Subject: [PATCH] Set parameter organism as required wihtout an default value --- pipeline.nf | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/pipeline.nf b/pipeline.nf index 55b7c26..3d51f1b 100644 --- a/pipeline.nf +++ b/pipeline.nf @@ -55,10 +55,10 @@ params.best_motif = 3 // Top n motifs per cluster //creating_gtf - params.organism="hg38" + params.organism="" params.tissue="" -if (params.bigwig == "" || params.bed == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || "${params.help}" != "0"){ +if (params.bigwig == "" || params.bed == "" || params.organism == "" || params.genome_fasta == "" || params.motif_db == "" || params.config == "" || "${params.help}" != "0"){ log.info """ Usage: nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --config [UROPA-config-file] @@ -70,6 +70,7 @@ Required arguments: --config Path to UROPA configuration file --create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored. Path can be set as tfbs_path in next run. (Default: './') + --organism Input organism [hg38 | hg19 | mm9 | mm10] --out Output Directory (Default: './out/') Optional arguments: @@ -115,7 +116,6 @@ Optional arguments: --motif_similarity_thresh FLOAT Threshold for motif similarity score (Default: 0.00001) Creating GTF: - --organism [hg38 | hg19 | mm9 | mm10] Input organism --tissues List/String List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON config All arguments can be set in the configuration files