Should fix the remaining issues

Author: apeltzer

main.nf

@@ -1139,12 +1139,12 @@ process multiqc {
     file multiqc_config from ch_multiqc_config.collect().ifEmpty([])
     file ('fastqc_raw/*') from ch_fastqc_results.collect().ifEmpty([])
     file('fastqc/*') from ch_fastqc_after_clipping.collect().ifEmpty([])
-    file ('software_versions/*') from software_versions_yaml.collect().ifEmpty([])
+    file ('software_versions/software_versions_mqc*') from software_versions_yaml.collect().ifEmpty([])
     file ('adapter_removal/*') from ch_adapterremoval_logs.collect().ifEmpty([])
     file ('idxstats/*') from ch_idxstats_for_multiqc.collect().ifEmpty([])
     file ('preseq/*') from ch_preseq_results.collect().ifEmpty([])
-    file ('damageprofiler/*') from ch_damageprofiler_results.collect().ifEmpty([])
-    file ('qualimap/*') from ch_qualimap_results.collect().ifEmpty([])
+    file ('damageprofiler/dmgprof*') from ch_damageprofiler_results.collect().ifEmpty([])
+    file ('qualimap*') from ch_qualimap_results.collect().ifEmpty([])
     file ('markdup/*') from ch_markdup_results_for_multiqc.collect().ifEmpty([])
     file ('dedup*/*') from ch_dedup_results_for_multiqc.collect().ifEmpty([])
     file ('fastp/*') from ch_fastp_for_multiqc.collect().ifEmpty([])