Added irida-id to new_addresses output to be compatible with IRIDA-Next

conf/iridanext.config

@@ -4,14 +4,18 @@ iridanext {
         path = "${params.outdir}/iridanext.output.json.gz"
         overwrite = true
         files {
+            idkey = "irida_id"
             samples = ["**/input/*_error_report.csv"]
         }
         metadata {
-            idkey = "id_irida"
             samples {
+                keep = [
+                    "address"
+                ]
                 csv {
-                    path = "**/filter/new_addresses.csv"
-                    idcol = "id"
+                    path = "**/filter/new_addresses.tsv"
+                    sep = "\t"
+                    idcol = 'irida_id'
                 }
             }
         }

docs/output.md

@@ -93,7 +93,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d
 <summary>Output files</summary>
 
 - `filter/`
-  - `new_addresses.csv`
+  - `new_addresses.tsv`
 
 </details>
 

modules/local/filter_query/main.nf

@@ -13,7 +13,7 @@ process FILTER_QUERY {
     val out_format
 
     output:
-    path("new_addresses.*"),    emit: csv
+    path("new_addresses.*"),    emit: tsv
     path("versions.yml"),       emit: versions
 
     script:
@@ -24,13 +24,16 @@ process FILTER_QUERY {
 
     """
     # Filter the query samples only; keep only the 'id' and 'address' columns
+    csvtk cut -t -f 2 ${query_ids} > query_list.txt # Need to use the second column to pull meta.id because there is no header
+    csvtk add-header ${query_ids} -t -n irida_id,id > id.txt
     csvtk grep \\
         ${addresses} \\
         -f 1 \\
-        -P ${query_ids} \\
+        -P query_list.txt \\
         --delimiter "${delimiter}" \\
         --out-delimiter "${out_delimiter}" | \\
-    csvtk cut -f id,address > ${outputFile}.${out_extension}
+    csvtk cut -t -f id,address > tmp.tsv
+    csvtk join -t -f id id.txt tmp.tsv > ${outputFile}.${out_extension}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

tests/data/irida/sample_name_add_iridanext.output.json

@@ -1,30 +1,38 @@
 {
     "files": {
         "global": [
-            
+
         ],
         "samples": {
-            "sample_1": [
+            "sampleQ": [
                 {
                     "path": "input/sample_1_error_report.csv"
                 }
             ],
-            "sample_2_sample2": [
+            "sample1": [
+                {
+                    "path": "input/sample_2_error_report.csv"
+                }
+            ],
+            "sample2": [
                 {
                     "path": "input/sample_2_sample2_error_report.csv"
                 }
             ],
-            "sample_2": [
+            "sampleR": [
                 {
-                    "path": "input/sample_2_error_report.csv"
+                    "path": "input/sample4_error_report.csv"
                 }
             ]
         }
     },
     "metadata": {
         "samples": {
-            "sample_1": {
-                "address": "1.1.3"
+            "sampleQ": {
+                "address": "2.2.3"
+            },
+            "sampleR": {
+                "address": "2.2.3"
             }
         }
     }

tests/data/samplesheets/samplesheet-sample_name.csv

@@ -3,3 +3,4 @@ sampleQ,sample 1,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/
 sample1,sample#2,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sample1.mlst.json,1.1.1
 sample2,sample#2,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
+sampleR,sample4,https://raw.githubusercontent.com/phac-nml/gasnomenclature/dev/tests/data/reports/sampleF.mlst.json,

tests/pipelines/main.nf.test

@@ -221,9 +221,9 @@ nextflow_pipeline {
             assert lines.contains("sampleR,[\'sampleF\'],Query sampleR ID and JSON key in sampleF.mlst.json DO NOT MATCH. The 'sampleF' key in sampleF.mlst.json has been forcefully changed to 'sampleR': User should manually check input files to ensure correctness.")
 
             // Check filter_query csv file
-            lines = path("$launchDir/results/filter/new_addresses.csv").readLines()
-            assert lines.contains("sampleQ,2.2.3")
-            assert lines.contains("sampleR,2.2.3")
+            lines = path("$launchDir/results/filter/new_addresses.tsv").readLines()
+            assert lines.contains("sampleQ\tsampleQ\t2.2.3")
+            assert lines.contains("sampleR\tsampleR\t2.2.3")
 
             // Check IRIDA Next JSON output
             assert path("$launchDir/results/iridanext.output.json").json == path("$baseDir/tests/data/irida/mismatched_iridanext.output.json").json
@@ -271,8 +271,8 @@ nextflow_pipeline {
             assert lines.contains('sample3,"[\'extra_key\', \'sample3\']","MLST JSON file (sample3_multiplekeys.mlst.json) contains multiple keys: [\'extra_key\', \'sample3\']. The MLST JSON file has been modified to retain only the \'sample3\' entry"')
 
             // Check filtered query csv results
-            lines = path("$launchDir/results/filter/new_addresses.csv").readLines()
-            assert lines.contains("sampleQ,1.1.3")
+            lines = path("$launchDir/results/filter/new_addresses.tsv").readLines()
+            assert lines.contains("sampleQ\tsampleQ\t1.1.3")
 
             // Check IRIDA Next JSON output
             assert path("$launchDir/results/iridanext.output.json").json == path("$baseDir/tests/data/irida/multiplekeys_iridanext.output.json").json
@@ -320,8 +320,8 @@ nextflow_pipeline {
             assert lines.contains('sample3,"[\'extra_key\', \'sample4\']",No key in the MLST JSON file (sample3_multiplekeys_nomatch.mlst.json) matches the specified sample ID \'sample3\'. The first key \'extra_key\' has been forcefully changed to \'sample3\' and all other keys have been removed.')
 
             // Check filtered query csv results
-            lines = path("$launchDir/results/filter/new_addresses.csv").readLines()
-            assert lines.contains("sampleQ,1.1.3")
+            lines = path("$launchDir/results/filter/new_addresses.tsv").readLines()
+            assert lines.contains("sampleQ\tsampleQ\t1.1.3")
 
             // Check IRIDA Next JSON output
             assert path("$launchDir/results/iridanext.output.json").json == path("$baseDir/tests/data/irida/multiplekeys_iridanext.output.json").json
@@ -385,8 +385,9 @@ nextflow_pipeline {
             assert lines.contains("sample_2_sample2,[\'sample2\'],Reference sample_2_sample2 ID and JSON key in sample2.mlst.json DO NOT MATCH. The 'sample2' key in sample2.mlst.json has been forcefully changed to 'sample_2_sample2': User should manually check input files to ensure correctness.")
 
             // Check filter_query csv file
-            lines = path("$launchDir/results/filter/new_addresses.csv").readLines()
-            assert lines.contains("sample_1,1.1.3")
+            lines = path("$launchDir/results/filter/new_addresses.tsv").readLines()
+            assert lines.contains("sampleQ\tsample_1\t2.2.3")
+            assert lines.contains("sampleR\tsample4\t2.2.3")
 
             // Check IRIDA Next JSON output
             assert path("$launchDir/results/iridanext.output.json").json == path("$baseDir/tests/data/irida/sample_name_add_iridanext.output.json").json

workflows/gas_nomenclature.nf

@@ -106,6 +106,11 @@ workflow GAS_NOMENCLATURE {
     reference_values = input_assure.result.collect{ meta, mlst -> mlst}
     query_values = profiles.query.collect{ meta, mlst -> mlst }
 
+    // Query Map: Use to return meta.irida_id to output for mapping to IRIDA-Next JSON
+    query_map = profiles.query.map{ meta, mlst->
+        tuple(meta.id, meta.irida_id)
+    }.collect()
+
     // LOCIDEX modules
     ref_tag = Channel.value("ref")
     query_tag = Channel.value("value")
@@ -166,16 +171,19 @@ workflow GAS_NOMENCLATURE {
     called_data = GAS_CALL(expected_clusters.text, distances.results)
     ch_versions = ch_versions.mix(called_data.versions)
 
-    // Filter the new queried samples and addresses into a CSV/JSON file for the IRIDANext plug in
-    query_ids = profiles.query.collectFile { it[0].id + '\n' }
+    // Filter the new queried samples and addresses into a CSV/JSON file for the IRIDANext plug in and
+    // add a column with IRIDA ID to allow for IRIDANext plugin to include metadata
+    query_irida_ids = profiles.query.collectFile {  it[0].irida_id + '\t' + it[0].id + '\n'}
 
-    new_addresses = FILTER_QUERY(query_ids, called_data.distances, "tsv", "csv")
+    new_addresses = FILTER_QUERY(query_irida_ids, called_data.distances, "tsv", "tsv")
     ch_versions = ch_versions.mix(new_addresses.versions)
 
     CUSTOM_DUMPSOFTWAREVERSIONS (
         ch_versions.unique().collectFile(name: 'collated_versions.yml')
     )
 
+
+
 }
 
 /*