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Set parameter organism as required wihtout an default value
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renewiegandt committed Dec 20, 2018
1 parent 1a7a812 commit 4844609
Showing 1 changed file with 3 additions and 3 deletions.
6 changes: 3 additions & 3 deletions pipeline.nf
Original file line number Diff line number Diff line change
Expand Up @@ -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]
Expand All @@ -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:
Expand Down Expand Up @@ -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
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