fixed typo and metagenomic QCSummary message

CHANGELOG.md

@@ -7,10 +7,14 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Updated`
 
+- Added QCMessage and QCSummary fields for metagenomic sequencing runs. See [PR 103](https://github.com/phac-nml/mikrokondo/pull/103)
+
 - Updated TSeemann's MLST default container to use version 2.23.0 of `mlst`. See [PR 97](https://github.com/phac-nml/mikrokondo/pull/97)
 
 ### `Fixed`
 
+- Fixed typo in metagenomic QC message. See [PR 103](https://github.com/phac-nml/mikrokondo/pull/103)
+
 - Fixed spelling issues issues in config values. See [PR 95](https://github.com/phac-nml/mikrokondo/pull/95)
 
 - Fixed the headers specified in the nextflow.config file for Kraken2. See [PR 96](https://github.com/phac-nml/mikrokondo/pull/96)

modules/local/report.nf

@@ -245,18 +245,21 @@ def create_action_call(sample_data, species_tag){
                 // nothing to do here
                 if(params.metagenomic_run){
                     final_message = "No QC Summary is provided for metagenomic samples."
+                    qc_summary = "No quality control criteria is applied for metagenomic samples."
                     sample_status = "NA"
                 }else{
-                    final_message = "[FAILED] Sample was determined to be metagenomic, and this was not specied as" +
+                    qc_summary = "[FAILED] Sample was determined to be metagenomic and this was not specified as a metagenomic run indicating contamination."
+                    final_message = "[FAILED] Sample was determined to be metagenomic and this was not specified as" +
                     " a metagenomic run indicating contamination REISOLATION AND RESEQUENCING RECOMMENDED." +
                     "There is additionally a possibility that your sample could not be identified as it is novel and " +
                     "not included in the program used to taxonomically classify your pipeline (however this is an unlikely culprit)."
                 }
                 sample_data[val.key]["QCStatus"] = sample_status
-                sample_data[val.key]["QCSummary"] = final_message
+                sample_data[val.key]["QCSummary"] = qc_summary
+                sample_data[val.key]["QCMessage"] = final_message
                 continue
             }
-            //def terminal_message = populate_qual_message(qual_data)
+
             def qual_message = []
             def failed_p = false
             def checks_failed = 0