Merge pull request #842 from nf-core/metascreen-message

Improve error message for metagenomic classification incorrect parameters

Author: jfy133

CHANGELOG.md

@@ -9,10 +9,11 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ### `Fixed`
 
+- [#828](https://github.com/nf-core/eager/issues/828) Improved error message if required metagenomic screening parameters not set correctly
 - [#836](https://github.com/nf-core/eager/issues/836) Remove deprecated parameters from test profiles
 - [#838](https://github.com/nf-core/eager/issues/836) Fix --snpcapture_bed files not being picked up by Nextflow
 - Fix PMDtools reference mask not being picked up by Nextflow, and it's use being evaluated against --snpcapture_bed rather than --pmdtools_reference_mask
-- Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly. 
+- Renamed a range of MultiQC general stats table headers to improve clarity, documentation has been updated accordingly.
 
 ### `Dependencies`
 

main.nf

@@ -107,12 +107,13 @@ if (params.run_multivcfanalyzer) {
 }
 
 if (params.run_metagenomic_screening) {
-  if ( params.bam_unmapped_type == "discard" ) {
-  exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --bam_unmapped_type 'fastq'. Supplied: --bam_unmapped_type '${params.bam_unmapped_type}'."
+
+  if ( !params.run_bam_filtering ) {
+  exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --run_bam_filtering --bam_unmapped_type 'fastq'."
   }
 
-  if (params.bam_unmapped_type != 'fastq' ) {
-  exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads in FASTQ format. Please supply --bam_unmapped_type 'fastq'. Found parameter: --bam_unmapped_type '${params.bam_unmapped_type}'."
+  if ( params.bam_unmapped_type != "fastq" ) {
+  exit 1, "[nf-core/eager] error: metagenomic classification can only run on unmapped reads. Please supply --bam_unmapped_type 'fastq'. Supplied: --bam_unmapped_type '${params.bam_unmapped_type}'."
   }
 
   if (!params.database) {