Amrfinderplus: add db-version to versions.yml (#1899)

* 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

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

modules/amrfinderplus/run/main.nf

@@ -2,10 +2,10 @@ process AMRFINDERPLUS_RUN {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
+    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
-        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
+        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -50,6 +50,7 @@ process AMRFINDERPLUS_RUN {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         amrfinderplus: \$(amrfinder --version)
+        amrfinderplus-database: \$(echo \$(echo \$(amrfinder --database amrfinderdb --database_version 2> stdout) | rev | cut -f 1 -d ' ' | rev))
     END_VERSIONS
     """
 }

modules/amrfinderplus/update/main.nf

@@ -2,10 +2,10 @@ process AMRFINDERPLUS_UPDATE {
     tag "update"
     label 'process_low'
 
-    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.23" : null)
+    conda (params.enable_conda ? "bioconda::ncbi-amrfinderplus=3.10.30" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus%3A3.10.23--h17dc2d4_0':
-        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.23--h17dc2d4_0' }"
+        'https://depot.galaxyproject.org/singularity/ncbi-amrfinderplus:3.10.30--h6e70893_0':
+        'quay.io/biocontainers/ncbi-amrfinderplus:3.10.30--h6e70893_0' }"
 
     output:
     path "amrfinderdb.tar.gz", emit: db

tests/modules/amrfinderplus/run/test.yml

@@ -1,11 +1,8 @@
 - name: amrfinderplus run test_amrfinderplus_run
-  command: nextflow run tests/modules/amrfinderplus/run -entry test_amrfinderplus_run -c tests/config/nextflow.config
+  command: nextflow run ./tests/modules/amrfinderplus/run -entry test_amrfinderplus_run -c ./tests/config/nextflow.config  -c ./tests/modules/amrfinderplus/run/nextflow.config
   tags:
-    - amrfinderplus/run
     - amrfinderplus
+    - amrfinderplus/run
   files:
-    - path: output/amrfinderplus/amrfinderdb.tar.gz
     - path: output/amrfinderplus/test.tsv
       md5sum: b4d261ace9be7d013c19d1f5c0005bfe
-    - path: output/amrfinderplus/versions.yml
-      md5sum: 642ca04a07d79fe4c4d02348562e3961

tests/modules/amrfinderplus/update/test.yml

@@ -5,5 +5,3 @@
     - amrfinderplus/update
   files:
     - path: output/amrfinderplus/amrfinderdb.tar.gz
-    - path: output/amrfinderplus/versions.yml
-      md5sum: 4db18fa509309db4da0920a7eeaba86c