updated parameters for allele schema (#104)

* updated parameters for allele schema * updated changelog * fixed error in parameter updates * fixed misspelled param * updated test config * updated CLI argument * dropped allele scheme used from the irida-next config * updated tests to pass * updated container default settings * updated changelog and version
phac-nml · Sep 4, 2024 · 7093f01 · 7093f01
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -3,8 +3,7 @@
 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).
 
-## Unreleased
-
+## [0.4.0] - 2024-09-04
 
 ### `Changed`
 
@@ -16,6 +15,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 - 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)
 
+- Moved allele schema parameters under one option in the nextflow_schema.json. See [PR 104](https://github.com/phac-nml/mikrokondo/pull/104)
+
 
 ### `Fixed`
 
@@ -142,6 +143,7 @@ Initial release of phac-nml/mikrokondo. Mikrokondo currently supports: read trim
 
 - Added integration testing using [nf-test](https://www.nf-test.com/).
 
+[0.4.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.4.0
 [0.3.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.3.0
 [0.2.1]: https://github.com/phac-nml/mikrokondo/releases/tag/0.2.1
 [0.2.0]: https://github.com/phac-nml/mikrokondo/releases/tag/0.2.0

diff --git a/conf/irida_next.config b/conf/irida_next.config
@@ -152,7 +152,6 @@ iridanext {
                     "IdentificationMethod",
                     "meta.downsampled",
                     "SpeciesTopHit",
-                    "AlleleSchemeUsed",
                     "LocidexDatabaseInformation.db_name",
                     "LocidexDatabaseInformation.db_date",
                     "LocidexDatabaseInformation.db_version",

diff --git a/modules/local/locidex_select.nf b/modules/local/locidex_select.nf
@@ -53,21 +53,21 @@ process LOCIDEX_SELECT {
     def report_name = "${meta.id}_${params.locidex.db_config_output_name}"
     output_config = task.workDir.resolve(report_name)
 
-    if(params.allele_scheme == null && params.locidex.allele_database == null){
+    if(params.override_allele_scheme == null && params.locidex.allele_database == null){
         error("Allele calling is enabled but there is no allele scheme or locidex allele database location present.")
     }
 
     if(config){ // non null channel should evaluate to true
         if(manifest){
-            log.warn "A database manifest file was passed along with a config file. Using the allele database specified by '--allele_scheme' "
+            log.warn "A database manifest file was passed along with a config file. Using the allele database specified by '--override_allele_scheme' "
         }
         // Create output summary data for a locidex allele database if an allele scheme is passed in directly
         def jsonSlurper = new JsonSlurper()
         String json_data = config.text
         def locidex_config_data = jsonSlurper.parseText(json_data)
-        validate_locidex_db(locidex_config_data, params.allele_scheme)
+        validate_locidex_db(locidex_config_data, params.override_allele_scheme)
         write_config_data(locidex_config_data, output_config)
-        scheme = params.allele_scheme // reset the schem path to the passed allele scheme
+        scheme = params.override_allele_scheme // reset the schem path to the passed allele scheme
         paired_p = true
 
     }else{

diff --git a/nextflow.config b/nextflow.config
@@ -111,6 +111,10 @@ params {
     // SISTR parameters
     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
+    lx_allele_database = null // A path to the locidex manifest.json file needed for allele calling.
+
     // Locidex Options
     lx_min_evalue = 0.0001
     lx_min_dna_len = 1
@@ -127,10 +131,6 @@ params {
     lx_report_prop = "locus_name"
     lx_report_max_ambig = 0
     lx_report_max_stop = 0
-    lx_allele_database = null
-
-    // Overide an allele calling scheme, this will be applied globally if auto selection is not opted for
-    allele_scheme = null
 
 
     // Boilerplate options
@@ -1044,58 +1044,64 @@ profiles {
         cleanup                = false
     }
     docker {
-        docker.enabled         = true
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        docker.enabled          = true
+        conda.enabled           = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
+        docker.runOptions       = '-u $(id -u):$(id -g)'
     }
     arm {
         docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64'
     }
     singularity {
-        singularity.enabled    = true
-        singularity.autoMounts = true
-        docker.enabled         = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        singularity.enabled     = true
+        singularity.autoMounts  = true
+        conda.enabled           = false
+        docker.enabled          = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     podman {
-        podman.enabled         = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        podman.enabled          = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     shifter {
-        shifter.enabled        = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        charliecloud.enabled   = false
-        apptainer.enabled      = false
+        shifter.enabled         = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        charliecloud.enabled    = false
+        apptainer.enabled       = false
     }
     charliecloud {
-        charliecloud.enabled   = true
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        apptainer.enabled      = false
+        charliecloud.enabled    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        apptainer.enabled       = false
     }
     apptainer {
-        apptainer.enabled      = true
-        apptainer.autoMounts   = true
-        conda.enabled          = false
-        docker.enabled         = false
-        singularity.enabled    = false
-        podman.enabled         = false
-        shifter.enabled        = false
-        charliecloud.enabled   = false
+        apptainer.enabled       = true
+        apptainer.autoMounts    = true
+        conda.enabled           = false
+        docker.enabled          = false
+        singularity.enabled     = false
+        podman.enabled          = false
+        shifter.enabled         = false
+        charliecloud.enabled    = false
     }
     gitpod {
         executor.name          = 'local'
@@ -1188,7 +1194,7 @@ manifest {
     description     = """Mikrokondo"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '0.3.0'
+    version         = '0.4.0'
     defaultBranch   = 'main'
     doi             = ''
 }

diff --git a/nextflow_schema.json b/nextflow_schema.json
@@ -110,13 +110,6 @@
                     "exists": true,
                     "format": "directory-path",
                     "hidden": true
-                },
-                "allele_scheme": {
-                    "type": "string",
-                    "pattern": "^\\S+$",
-                    "exists": true,
-                    "format": "directory-path",
-                    "description": "An allele scheme to to use for Locidex"
                 }
             },
             "required": [
@@ -126,6 +119,28 @@
             ],
             "description": "The location of databases used by mikrokondo"
         },
+        "allele_schema_options": {
+            "title": "Allele Schema Options",
+            "type": "object",
+            "description": "Specify an allele calling schema.",
+            "default": "",
+            "properties": {
+                "lx_allele_database": {
+                    "type": "string",
+                    "description": "The path to a folder containing a collection of locidex databases to allow for automatic allele database selection. The folder should contain a 'manifest.json' file created by locidex. If you wish to force a certain allele scheme to be used you can specify an option for the `override_allele_scheme` argument which will perform allele calling with the specified scheme.",
+                    "pattern": "^\\S+$",
+                    "exists": true,
+                    "format": "directory-path"
+                },
+                "override_allele_scheme": {
+                    "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+$",
+                    "format": "directory-path"
+                }
+            }
+        },
         "institutional_config_options": {
             "title": "Institutional config options",
             "type": "object",
@@ -664,13 +679,6 @@
                     "default": 0,
                     "description": "Maximum number of internal stop codons allowed in a sequence.",
                     "minimum": 0
-                },
-                "lx_allele_database": {
-                    "type": "string",
-                    "description": "Folder of locidex databases. The folder should contain a 'manifest.json' file created by locidex",
-                    "pattern": "^\\S+$",
-                    "exists": true,
-                    "format": "directory-path"
                 }
             }
         },
@@ -743,6 +751,9 @@
         {
             "$ref": "#/definitions/databases_and_pre_computed_files"
         },
+        {
+            "$ref": "#/definitions/allele_schema_options"
+        },
         {
             "$ref": "#/definitions/institutional_config_options"
         },

diff --git a/subworkflows/local/locidex.nf b/subworkflows/local/locidex.nf
@@ -16,16 +16,16 @@ workflow LOCIDEX {
     paired_species = top_hit.join(contigs)
     paired_dbs = Channel.empty()
 
-    if(params.allele_scheme == null && params.locidex.allele_database == null && !params.skip_allele_calling){
+    if(params.override_allele_scheme == null && 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.allele_scheme != null){
+    if(params.override_allele_scheme != null){
         // allele scheme over rides the the manifest file
-        def config_file_in = [params.allele_scheme, params.locidex.config_data_file].join(File.separator)
+        def config_file_in = [params.override_allele_scheme, params.locidex.config_data_file].join(File.separator)
         config_file = file(config_file_in, checkIfExists: true)
     }else{
         def manifest_file_in = [params.locidex.allele_database, params.locidex.manifest_name].join(File.separator)

diff --git a/tests/modules/local/locidex_select/locidex_select.nf.test b/tests/modules/local/locidex_select/locidex_select.nf.test
@@ -241,7 +241,7 @@ nextflow_process {
             params {
                 outdir = "locidex_select"
                 lx_allele_database = null
-                allele_scheme = null
+                override_allele_scheme = null
             }
 
         }
@@ -351,7 +351,7 @@ nextflow_process {
 
             params {
                 outdir = "locidex_select"
-                allele_scheme = "${projectDir}/tests/data/databases/locidex_dbs/locidex_vc"
+                override_allele_scheme = "${projectDir}/tests/data/databases/locidex_dbs/locidex_vc"
                 lx_allele_database = "${projectDir}/tests/data/databases/locidex_dbs"
             }
 

diff --git a/tests/pipelines/main.from_assemblies.nf.test b/tests/pipelines/main.from_assemblies.nf.test
@@ -341,7 +341,7 @@ nextflow_pipeline {
                 skip_subtyping = false
                 skip_allele_calling = false
 
-                allele_scheme = "$baseDir/tests/data/databases/locidex_dbs/locidex_salm"
+                override_allele_scheme = "$baseDir/tests/data/databases/locidex_dbs/locidex_salm"
 
                 max_memory = "2.GB"
                 max_cpus = 1
@@ -707,7 +707,6 @@ nextflow_pipeline {
             assert iridanext_samples.st_120.findAll { it.path == "Assembly/Subtyping/Locidex/Report/st_120.locidex.report.profile.mlst.subtyping.json.gz" }.size() == 1
             assert iridanext_samples.st_120.findAll { it.path == "Assembly/Subtyping/Locidex/Summary/st_120.locidex.summary.json" }.size() == 1
 
-            assert vibrio_metadata.AlleleSchemeUsed.contains("locidex_dbs/locidex_vc")
             assert vibrio_metadata.locidex_db_name == "Vibrio cholerae"
             assert vibrio_metadata.locidex_db_date == "2024-07-30"
             assert vibrio_metadata.locidex_db_version == "1.0.0"
@@ -740,7 +739,7 @@ nextflow_pipeline {
                 mash_sketch = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/mash.msh"
                 dehosting_idx = "https://github.com/phac-nml/mikrokondo/raw/dev/tests/data/databases/campy.mmi"
                 kraken2_db = "$baseDir/tests/data/kraken2/test"
-                allele_scheme= "$baseDir/tests/data/databases/locidex_dbs/locidex_vc"
+                override_allele_scheme= "$baseDir/tests/data/databases/locidex_dbs/locidex_vc"
                 qt_min_contig_length = 1
 
                 skip_bakta = true
@@ -780,7 +779,6 @@ nextflow_pipeline {
             assert iridanext_samples.st_120.findAll { it.path == "Assembly/Subtyping/Locidex/Report/st_120.locidex.report.profile.mlst.subtyping.json.gz" }.size() == 1
             assert iridanext_samples.st_120.findAll { it.path == "Assembly/Subtyping/Locidex/Summary/st_120.locidex.summary.json" }.size() == 1
 
-            assert vibrio_metadata.AlleleSchemeUsed.contains("locidex_dbs/locidex_vc")
             assert vibrio_metadata.locidex_db_name == "Vibrio cholerae_1"
             assert vibrio_metadata.locidex_db_date == "2024-08-01"
             assert vibrio_metadata.locidex_db_version == "1.0.0"

diff --git a/workflows/PostAssembly.nf b/workflows/PostAssembly.nf
@@ -95,12 +95,12 @@ workflow POST_ASSEMBLY {
 
 
     if(!params.skip_allele_calling){
-        if (!params.skip_species_classification || params.allele_scheme){
+        if (!params.skip_species_classification || params.override_allele_scheme){
             LOCIDEX(ch_filtered_contigs, top_hit)
             ch_versions = ch_versions.mix(LOCIDEX.out.versions)
             ch_reports = ch_reports.mix(LOCIDEX.out.reports)
         }else{
-            log.info "Skipping locidex since there is no '--allele_scheme' set and '--skip_species_classification' is enabled"
+            log.info "Skipping locidex since there is no '--override_allele_scheme' set and '--skip_species_classification' is enabled"
         }
     }