RGI/main export versions as explicit emission strings (#1909)

* Export versions  as explicit emission strings in addition to versions.yml for compatibility with hAMRonization

* Update YML

modules/rgi/main/main.nf

@@ -13,6 +13,8 @@ process RGI_MAIN {
     output:
     tuple val(meta), path("*.json"), emit: json
     tuple val(meta), path("*.txt") , emit: tsv
+    env VER                        , emit: tool_version
+    env DBVER                      , emit: db_version
     path "versions.yml"            , emit: versions
 
     when:
@@ -29,10 +31,13 @@ process RGI_MAIN {
         --output_file $prefix \\
         --input_sequence $fasta
 
+    VER=\$(rgi main --version)
+    DBVER=\$(rgi database --version)
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        rgi: \$(rgi main --version)
-        rgi-database: \$(rgi database --version)
+        rgi: \$(echo \$VER)
+        rgi-database: \$(echo \$DBVER)
     END_VERSIONS
     """
 }

modules/rgi/main/meta.yml

@@ -42,6 +42,12 @@ output:
       type: file
       description: Tab-delimited file with RGI results
       pattern: "*.{txt}"
-
+  - tool_version:
+      type: string
+      description: The version of the tool in string format (useful for downstream tools such as hAMRronization)
+  - db_version:
+      type: string
+      description: The version of the used database in string format (useful for downstream tools such as hAMRronization)
 authors:
   - "@rpetit3"
+  - "@jfy133"