Merge pull request #711 from maxibor/dev

Fix condition preventing to run multivcfanalyzer

Author: jfy133

CHANGELOG.md

@@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - [#707](https://github.com/nf-core/eager/pull/707) - Fix typo in UnifiedGenotyper IndelRealigner command
 - Fixed some Java tools not following process memory specifications
 - Updated template to nf-core/tools 1.13.2
+- [#711](https://github.com/nf-core/eager/pull/711) - Fix conditional execution preventing multivcfanalyze to run
 
 ### `Dependencies`
 

main.nf

@@ -2494,22 +2494,22 @@ process vcf2genome {
 // More complex consensus caller with additional filtering functionality (e.g. for heterozygous calls) to generate SNP tables and other things sometimes used in aDNA bacteria studies
 
 // Create input channel for MultiVCFAnalyzer, possibly mixing with pre-made VCFs.
-if (params.additional_vcf_files == '') {
-    ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it[7] }.collect()
+if (!params.additional_vcf_files) {
+    ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it[-1] }.collect()
 } else {
-    ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it [7] }.collect().mix(ch_extravcfs_for_multivcfanalyzer)
+    ch_vcfs_for_multivcfanalyzer = ch_ug_for_multivcfanalyzer.map{ it [-1] }.collect().mix(ch_extravcfs_for_multivcfanalyzer)
 }
 
 process multivcfanalyzer {
   label  'mc_small'
   publishDir "${params.outdir}/multivcfanalyzer", mode: params.publish_dir_mode
 
   when:
-  params.genotyping_tool == 'ug' && params.run_multivcfanalyzer && params.gatk_ploidy == '2'
+  params.genotyping_tool == 'ug' && params.run_multivcfanalyzer && params.gatk_ploidy.toString() == '2'
 
   input:
-  file vcf from ch_vcfs_for_multivcfanalyzer.collect()
-  file fasta from ch_fasta_for_multivcfanalyzer.collect()
+  file vcf from ch_vcfs_for_multivcfanalyzer
+  file fasta from ch_fasta_for_multivcfanalyzer
 
   output:
   file('fullAlignment.fasta.gz')