Merge pull request #114 from phac-nml/dev

Dev

CHANGELOG.md

@@ -3,6 +3,20 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+
+## [0.4.1] - 2024-09-16
+
+### `Fixed`
+
+- Fixed null species ID in QCMessage when no organism qc data available. [PR 111](https://github.com/phac-nml/mikrokondo/pull/111)
+
+### `Changed`
+
+- Removed missing alleles from final report fixing issue [112](https://github.com/phac-nml/mikrokondo/issues/112).
+
+- Changed default option for `override_allele_scheme` from `null` to "" (evaluates to false). [PR 109](https://github.com/phac-nml/mikrokondo/pull/109)
+
+
 ## [0.4.0] - 2024-09-04
 
 ### `Changed`

modules/local/locidex_select.nf

@@ -53,7 +53,7 @@ process LOCIDEX_SELECT {
     def report_name = "${meta.id}_${params.locidex.db_config_output_name}"
     output_config = task.workDir.resolve(report_name)
 
-    if(params.override_allele_scheme == null && params.locidex.allele_database == null){
+    if(!params.override_allele_scheme && params.locidex.allele_database == null){
         error("Allele calling is enabled but there is no allele scheme or locidex allele database location present.")
     }
 
@@ -67,7 +67,7 @@ process LOCIDEX_SELECT {
         def locidex_config_data = jsonSlurper.parseText(json_data)
         validate_locidex_db(locidex_config_data, params.override_allele_scheme)
         write_config_data(locidex_config_data, output_config)
-        scheme = params.override_allele_scheme // reset the schem path to the passed allele scheme
+        scheme = params.override_allele_scheme // reset the scheme path to the passed allele scheme
         paired_p = true
 
     }else{

modules/local/report.nf

@@ -373,7 +373,12 @@ def create_action_call(sample_data, species_tag){
             def tests_passed = "Passed Tests: ${checks - checks_failed - checks_ignored}/${checks}"
             qual_message.add(tests_passed)
 
-            def species_id = "Species ID: ${val.value[val.key][params.top_hit_species.report_tag]}"
+
+            def species_selected = val.value[val.key][params.top_hit_species.report_tag]
+            if(species_selected == null){
+                species_selected = organism_criteria
+            }
+            def species_id = "Species ID: ${species_selected}"
             qual_message.add(species_id)
 
             // Qual summary not final message

nextflow.config

@@ -112,7 +112,7 @@ params {
     sr_full_cgmlst = true // Use full set of cgMLST alleles which can include highly similar alleles
 
     // Allele Scheme Options
-    override_allele_scheme = null // Supply an allele scheme that will be used for allele calling of all samples
+    override_allele_scheme = "" // Supply an allele scheme that will be used for allele calling of all samples
     lx_allele_database = null // A path to the locidex manifest.json file needed for allele calling.
 
     // Locidex Options
@@ -257,6 +257,7 @@ params {
         data_sample_key = "sample_name"
         missing_allele_value = '-'
         reportable_alleles = []
+        report_exclude_fields = ["MissingAlleles"]
     }
 
     allele_scheme_selected {
@@ -1194,7 +1195,7 @@ manifest {
     description     = """Mikrokondo"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.4.0'
+    version         = '0.4.1'
     defaultBranch   = 'main'
     doi             = ''
 }

nextflow_schema.json

@@ -136,8 +136,10 @@
                     "type": "string",
                     "description": "Specify the path to an allele calling schema to be used. This schema will be used for allele calling of all samples.",
                     "exists": true,
-                    "pattern": "^\\S+$",
-                    "format": "directory-path"
+                    "pattern": "^\\S*$",
+                    "format": "directory-path",
+                    "default": "",
+                    "help_text": ""
                 }
             }
         },

subworkflows/local/locidex.nf

@@ -16,14 +16,14 @@ workflow LOCIDEX {
     paired_species = top_hit.join(contigs)
     paired_dbs = Channel.empty()
 
-    if(params.override_allele_scheme == null && params.locidex.allele_database == null && !params.skip_allele_calling){
+    if(!params.override_allele_scheme && params.locidex.allele_database == null && !params.skip_allele_calling){
         error("Allele calling is enabled, but no locidex database directory has been configured.")
     }
 
     def manifest_file = [] // Default empty values for entries
     def config_file = []
 
-    if(params.override_allele_scheme != null){
+    if(params.override_allele_scheme){
         // allele scheme over rides the the manifest file
         def config_file_in = [params.override_allele_scheme, params.locidex.config_data_file].join(File.separator)
         config_file = file(config_file_in, checkIfExists: true)

tests/main.nf.test

@@ -88,7 +88,7 @@ nextflow_pipeline {
             assert !iridanext_metadata.CSE.containsKey("Length Value")
             assert !iridanext_metadata.CSE.containsKey("nr contigs Status")
             assert !iridanext_metadata.CSE.containsKey("nr contigs Value")
-            assert iridanext_metadata.CSE."QC Summary" == "FAILED Species ID: null; Passed Tests: 0/6; Organism QC Criteria: No organism specific QC data available."
+            assert iridanext_metadata.CSE."QC Summary" == "FAILED Species ID: No organism specific QC data available.; Passed Tests: 0/6; Organism QC Criteria: No organism specific QC data available."
 
             assert iridanext_metadata.CSE."Downsampled" == false
             assert !iridanext_metadata.CSE.containsKey("predicted_identification_name")