From 3caf9979ac25904b38c49d96b3901b54a0e6fb2a Mon Sep 17 00:00:00 2001
From: renewiegandt <rene.wiegandt@mpi-bn.mpg.de>
Date: Tue, 16 Apr 2019 10:21:47 +0200
Subject: [PATCH] Added error message for missing required parameters
---
pipeline.nf | 45 ++++++++++++++++++++++++---------------------
1 file changed, 24 insertions(+), 21 deletions(-)
diff --git a/pipeline.nf b/pipeline.nf
index c50ba2d..1c1230b 100644
--- a/pipeline.nf
+++ b/pipeline.nf
@@ -89,32 +89,19 @@ val_missing = false
send_help = false
missing_params = []
+//@TODO remove iteration over all parameter
params.each { key, value ->
if (req_params.contains(key)){
if (key == "gtf_annotation" && value == "" && params.gtf_merged == ""){
val_missing = true
+ missing_params.add("$key or gtf_merged")
} else {
if (value == ""){
val_missing = true
- missing_params + key
+ missing_params.add(key)
}
}
}
- if (!(all_params.contains(key))){
- println("Warning: Parameter $key is unknown. Please check for typos or the parameter list!")
- }
- if(int_params.contains(key)) {
- if (!("${value}" ==~ /\d+/ )){
- println("ERROR: $key needs to be an Integer")
- System.exit(2)
- }
- }
- if(file_params.contains(key) || (key == "gtf_merged" && value != "") ) {
- if(!file(value).exists()) {
- println("ERROR: $key not found. Please check the given path.")
- System.exit(2)
- }
- }
}
if (val_missing){
@@ -122,8 +109,8 @@ if (val_missing){
println("Error: Following required parameters are missing: $missing_params")
}
if (send_help || "${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]
+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]
Required arguments:
--bigwig Path to BigWig-file
@@ -185,8 +172,8 @@ if (send_help || "${params.help}" != "0") {
config
Evaluation:
--max_uropa_runs INT Maximum number UROPA runs running parallelized (Default: 10)
- All arguments can be set in the configuration files
- """
+All arguments can be set in the configuration files
+"""
System.exit(2)
} else {
Channel.fromPath(params.bigwig).map {it -> [it.simpleName, it]}.set {bigwig_input}
@@ -202,7 +189,23 @@ if (send_help || "${params.help}" != "0") {
}
}
-
+params.each { key, value ->
+ if (!(all_params.contains(key))){
+ println("Warning: Parameter $key is unknown. Please check for typos or the parameter list!")
+ }
+ if(int_params.contains(key)) {
+ if (!("${value}" ==~ /\d+/ )){
+ println("ERROR: $key needs to be an Integer")
+ System.exit(2)
+ }
+ }
+ if(file_params.contains(key) || (key == "gtf_merged" && value != "") ) {
+ if(!file(value).exists()) {
+ println("ERROR: $key not found. Please check the given path.")
+ System.exit(2)
+ }
+ }
+}
if (!("${params.identity}" ==~ /^0\.[8-9][[0-9]*]?|^1(\.0)?/ )){
println("ERROR: --identity needs to be float in range 0.8 to 1.0")