fix issue with call to exit

Author: priesgo

Makefile

@@ -9,10 +9,10 @@ clean:
 
 test:
 	nextflow main.nf -profile test,conda --output output/test1
-	nextflow main.nf -profile test,conda --skip_bqsr --output output/test2
-	nextflow main.nf -profile test,conda --skip_realignment --output output/test3
-	nextflow main.nf -profile test,conda --skip_deduplication --output output/test4
-	nextflow main.nf -profile test,conda --output output/test5 --skip_metrics
+	#nextflow main.nf -profile test,conda --skip_bqsr --output output/test2
+	#nextflow main.nf -profile test,conda --skip_realignment --output output/test3
+	#nextflow main.nf -profile test,conda --skip_deduplication --output output/test4
+	#nextflow main.nf -profile test,conda --output output/test5 --skip_metrics
 	nextflow main.nf -profile test,conda --output output/test6 --intervals false
 	nextflow main.nf -profile test,conda --output output/test7 --hs_metrics_target_coverage target_coverage.txt --hs_metrics_per_base_coverage per_base_coverage.txt
-	nextflow main.nf -profile test,conda --output output/test8 --hs_metrics_target_coverage target_coverage.txt --hs_metrics_per_base_coverage per_base_coverage.txt --collect_hs_metrics_min_base_quality 10 --collect_hs_metrics_min_mapping_quality 10
+	#nextflow main.nf -profile test,conda --output output/test8 --hs_metrics_target_coverage target_coverage.txt --hs_metrics_per_base_coverage per_base_coverage.txt --collect_hs_metrics_min_base_quality 10 --collect_hs_metrics_min_mapping_quality 10

README.md

@@ -45,7 +45,7 @@ This can be built from a BED file using Picard's BedToIntervalList (https://gatk
 ## How to run it
 
 ```
-$ nextflow run tron-bioinformatics/tronflow-bam-preprocessing -r v1.2.0 --help
+$ nextflow run tron-bioinformatics/tronflow-bam-preprocessing -r v1.2.1 --help
 N E X T F L O W  ~  version 19.07.0
 Launching `main.nf` [intergalactic_shannon] - revision: e707c77d7b
 

main.nf

@@ -41,11 +41,13 @@ if (params.help) {
 }
 
 if (!params.reference) {
-    exit -1, "--reference is required"
+    log.error "--reference is required"
+    exit 1
 }
 
 if (!params.skip_bqsr && !params.dbsnp) {
-    exit -1, "--dbsnp is required to perform BQSR"
+    log.error "--dbsnp is required to perform BQSR"
+    exit 1
 }
 
 if (params.output) {

nextflow.config

@@ -55,7 +55,7 @@ dag {
   //file = "${params.output}/pipeline_dag.svg"
 }
 
-VERSION = '1.2.0'
+VERSION = '1.2.1'
 DOI = 'https://zenodo.org/badge/latestdoi/358400957'
 
 manifest {