Updated samplesheet to include 'address' column

phac-nml · May 6, 2024 · 1e554dd · 1e554dd
1 parent f249833
commit 1e554dd
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Showing 5 changed files with 25 additions and 27 deletions.
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,4 +1,5 @@
-sample,fastq_1,fastq_2
-SAMPLE1,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R2.fastq.gz
-SAMPLE2,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R1.fastq.gz,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample2_R2.fastq.gz
-SAMPLE3,https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/illumina/amplicon/sample1_R1.fastq.gz,
+sample,mlst_alleles,address
+sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json,
+sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1
+sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1
+sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2
diff --git a/assets/schema_input.json b/assets/schema_input.json
@@ -14,19 +14,20 @@
                 "unique": true,
                 "errorMessage": "Sample name must be provided and cannot contain spaces"
             },
-            "profile_type": {
-                "meta": ["profile_type"],
-                "description": "Determines has already been clustered (True) or if it is new, and requiring nomenclature assignment (False)",
-                "errorMessage": "Please specify if the mlst profile has already been clustered (True) or if it is new and requires nomenclature assignment (False)",
-                "type": "boolean"
-            },
             "mlst_alleles": {
                 "type": "string",
                 "format": "file-path",
                 "pattern": "^\\S+\\.mlst\\.json(\\.gz)?$",
                 "errorMessage": "MLST JSON file from locidex report, cannot contain spaces and must have the extension: '.mlst.json' or '.mlst.json.gz'"
+            },
+            "address": {
+                "type": "string",
+                "pattern": "^\\d+(\\.\\d+)*$",
+                "meta": ["address"],
+                "description": "The loci-based typing identifier (address) of the sample",
+                "error_message": "Invalid loci-based typing identifier. Please ensure that the address follows the correct format, consisting of one or more digits separated by periods. Example of a valid identifier: '1.1.1'. Please review and correct the entry"
             }
         },
-        "required": ["sample", "profile_type", "mlst_alleles"]
+        "required": ["sample", "mlst_alleles"]
     }
 }
diff --git a/conf/test.config b/conf/test.config
@@ -20,7 +20,7 @@ params {
     max_time   = '1.h'
 
     // Input data
-    input  = 'https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/samplesheets/samplesheet1.csv'
+    input  = "${projectDir}/tests/data/samplesheets/samplesheet1.csv"
     ref_clusters = 'https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/clusters/expected_clusters.txt'
 }
 

diff --git a/tests/data/samplesheets/samplesheet1.csv b/tests/data/samplesheets/samplesheet1.csv
@@ -1,5 +1,5 @@
-sample,profile_type,mlst_alleles
-sampleQ,false,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json
-sample1,true,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json
-sample2,true,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json
-sample3,true,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json
+sample,mlst_alleles,address
+sampleQ,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleQ.mlst.json,
+sample1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1
+sample2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample2.mlst.json,1.1.1
+sample3,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample3.mlst.json,1.1.2
diff --git a/workflows/gas_nomenclature.nf b/workflows/gas_nomenclature.nf
@@ -22,10 +22,10 @@ include { paramsSummaryLog; paramsSummaryMap; fromSamplesheet  } from 'plugin/nf
 // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules
 //
 
-include { GENERATE_SAMPLE_JSON } from '../modules/local/generatesamplejson/main'
-include { SIMPLIFY_IRIDA_JSON  } from '../modules/local/simplifyiridajson/main'
-include { IRIDA_NEXT_OUTPUT    } from '../modules/local/iridanextoutput/main'
-include { GENERATE_SUMMARY     } from '../modules/local/generatesummary/main'
+include { LOCIDEX_MERGE as LOCIDEX_MERGE_REF    } from "../modules/local/locidex/merge/main"
+include { LOCIDEX_MERGE as LOCIDEX_MERGE_QUERY  } from "../modules/local/locidex/merge/main"
+include { PROFILE_DISTS                         } from "../modules/local/profile_dists/main"
+include { GAS_CALL                              } from "../modules/local/gas/call/main"
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -37,10 +37,6 @@ include { GENERATE_SUMMARY     } from '../modules/local/generatesummary/main'
 // MODULE: Installed directly from nf-core/modules
 //
 include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main'
-include { LOCIDEX_MERGE as LOCIDEX_MERGE_REF } from "../modules/local/locidex/merge/main"
-include { LOCIDEX_MERGE as LOCIDEX_MERGE_QUERY } from "../modules/local/locidex/merge/main"
-include { GAS_CALL } from "../modules/local/gas/call/main"
-include { PROFILE_DISTS } from "../modules/local/profile_dists/main"
 
 /*
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
@@ -73,8 +69,8 @@ workflow GAS_NOMENCLATURE {
     // NB: `input` corresponds to `params.input` and associated sample sheet schema
     input = Channel.fromSamplesheet("input");
     profiles = input.branch{
-        ref: it[0].profile_type
-        query: !it[0].profile_type
+        ref: it[0].address
+        query: !it[0].address
         errors: true // To discuss, add in check on file for erroneous values, may not be needed as nf-validation is working
     }