Amrfinderplus add tool and db version as output (#1912)

* not yet working: add db version to versions.yml

* next try: db version number not in versions.yml

* Fix amrfinderplus versioning

* Update main.nf

* Apply suggestions from code review

* Update main.nf

* Dump version for syncrony with run

* Update test.yml

* Apply suggestions from code review

* add tool and db version to output

* Apply suggestions from code review

Co-authored-by: James A. Fellows Yates <jfy133@gmail.com>

* Update meta.yml

Co-authored-by: James Fellows Yates <jfy133@gmail.com>

modules/amrfinderplus/run/main.nf

@@ -15,6 +15,8 @@ process AMRFINDERPLUS_RUN {
     tuple val(meta), path("${prefix}.tsv")          , emit: report
     tuple val(meta), path("${prefix}-mutations.tsv"), emit: mutation_report, optional: true
     path "versions.yml"                             , emit: versions
+    env VER                                         , emit: tool_version
+    env DBVER                                       , emit: db_version
 
     when:
     task.ext.when == null || task.ext.when
@@ -46,6 +48,8 @@ process AMRFINDERPLUS_RUN {
         --database amrfinderdb \\
         --threads $task.cpus > ${prefix}.tsv
 
+    VER=\$(amrfinder --version)
+    DBVER=\$(echo \$(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev)
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/amrfinderplus/run/meta.yml

@@ -46,6 +46,14 @@ output:
       type: file
       description: Report of organism-specific point-mutations
       pattern: "*-mutations.tsv"
+  - 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"
+  - "@louperelo"
+  - "@jfy133"