Update hamronization/abricate (#4851)

* abricate --migrate_pytest

* Complete nf-test + add stub

* Fix linting

* Fix linting

* Update test names

* Update stub test

* Stage proper input files for stub tests

* Remove `echo <command>` from main.nf

modules/nf-core/hamronization/abricate/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::hamronization=1.1.1
+  - bioconda::hamronization=1.1.4

modules/nf-core/hamronization/abricate/main.nf

@@ -4,8 +4,8 @@ process HAMRONIZATION_ABRICATE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/hamronization:1.1.1--pyhdfd78af_0':
-        'biocontainers/hamronization:1.1.1--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/hamronization:1.1.4--pyhdfd78af_0':
+        'biocontainers/hamronization:1.1.4--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(report)
@@ -34,6 +34,16 @@ process HAMRONIZATION_ABRICATE {
         --reference_database_version ${reference_db_version} \\
         > ${prefix}.${format}
 
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        hamronization: \$(echo \$(hamronize --version 2>&1) | cut -f 2 -d ' ' )
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.${format}
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/hamronization/abricate/meta.yml

@@ -11,7 +11,7 @@ tools:
       homepage: "https://github.com/pha4ge/hAMRonization/"
       documentation: "https://github.com/pha4ge/hAMRonization/"
       tool_dev_url: "https://github.com/pha4ge/hAMRonization"
-      licence: "['GNU Lesser General Public v3 (LGPL v3)']"
+      licence: ["GNU Lesser General Public v3 (LGPL v3)"]
 input:
   - meta:
       type: map
@@ -23,15 +23,15 @@ input:
       description: Output TSV or CSV file from ABRicate
       pattern: "*.{csv,tsv}"
   - format:
-      type: value
+      type: string
       description: Type of report file to be produced
       pattern: "tsv|json"
   - software_version:
-      type: value
+      type: string
       description: Version of ABRicate used
       pattern: "[0-9].[0-9].[0-9]"
   - reference_db_version:
-      type: value
+      type: string
       description: Database version of ABRicate used
       pattern: "[0-9][0-9][0-9][0-9]-[A-Z][a-z][a-z]-[0-9][0-9]"
 output:

modules/nf-core/hamronization/abricate/tests/main.nf.test

@@ -0,0 +1,55 @@
+nextflow_process {
+
+    name "Test Process HAMRONIZATION_ABRICATE"
+    script "../main.nf"
+    process "HAMRONIZATION_ABRICATE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "hamronization"
+    tag "hamronization/abricate"
+
+    test("hamronization/abricate - bacteroides_fragilis - genome_abricate_tsv") {
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:"test" ], file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true) ]
+                input[1] = 'tsv'
+                input[2] = '1.0.1'
+                input[3] = '2021-Mar-27'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("hamronization/abricate - bacteroides_fragilis - genome_abricate_tsv - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [ [ id:"test" ], file(params.test_data['bacteroides_fragilis']['hamronization']['genome_abricate_tsv'], checkIfExists: true) ]
+                input[1] = 'tsv'
+                input[2] = '1.0.1'
+                input[3] = '2021-Mar-27'
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/hamronization/abricate/tests/tags.yml

@@ -0,0 +1,2 @@
+hamronization/abricate:
+  - "modules/nf-core/hamronization/abricate/**"

tests/config/pytest_modules.yml

@@ -1032,9 +1032,6 @@ gunc/run:
 gvcftools/extractvariants:
   - modules/nf-core/gvcftools/extractvariants/**
   - tests/modules/nf-core/gvcftools/extractvariants/**
-hamronization/abricate:
-  - modules/nf-core/hamronization/abricate/**
-  - tests/modules/nf-core/hamronization/abricate/**
 hamronization/amrfinderplus:
   - modules/nf-core/hamronization/amrfinderplus/**
   - tests/modules/nf-core/hamronization/amrfinderplus/**