Update gecco + migrate to nf-test

modules/nf-core/gecco/run/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::gecco=0.9.8
+  - bioconda::gecco=0.9.10

modules/nf-core/gecco/run/main.nf

@@ -4,8 +4,8 @@ process GECCO_RUN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gecco:0.9.8--pyhdfd78af_0':
-        'biocontainers/gecco:0.9.8--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/gecco:0.9.10--pyhdfd78af_0':
+        'biocontainers/gecco:0.9.10--pyhdfd78af_0' }"
 
     input:
     tuple val(meta), path(input), path(hmm)
@@ -44,4 +44,18 @@ process GECCO_RUN {
         gecco: \$(echo \$(gecco --version) | cut -f 2 -d ' ' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.genes.tsv
+    touch ${prefix}.features.tsv
+    touch ${prefix}.clusters.tsv
+    touch NC_018507.1_cluster_1.gbk
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gecco: \$(echo \$(gecco --version) | cut -f 2 -d ' ' )
+    END_VERSIONS
+    """
 }

modules/nf-core/gecco/run/tests/main.nf.test

@@ -0,0 +1,68 @@
+nextflow_process {
+
+    name "Test Process GECCO_RUN"
+    script "../main.nf"
+    process "GECCO_RUN"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "gecco"
+    tag "gecco/run"
+
+    test("gecco/run - candidatus_portiera_aleyrodidarum - genome_fasta") {
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta', checkIfExists: true),
+                    []
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    process.out.genes +
+                    process.out.features +
+                    process.out.clusters +
+                    process.out.versions
+                ) },
+                { assert path(process.out.gbk.get(0).get(1)).text.contains("MVKNDIDILILGGGCTGLSLAYYLSFLPNTVRIFLIENKFIYNND") }
+            )
+        }
+
+    }
+
+    test("gecco/run - candidatus_portiera_aleyrodidarum - genome_fasta - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/prokaryotes/candidatus_portiera_aleyrodidarum/genome/genome.fasta', checkIfExists: true),
+                    []
+                ]
+                input[1] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/gecco/run/tests/tags.yml

@@ -0,0 +1,2 @@
+gecco/run:
+  - "modules/nf-core/gecco/run/**"

tests/config/pytest_modules.yml

@@ -820,9 +820,6 @@ gatk4spark/baserecalibrator:
 gawk:
   - modules/nf-core/gawk/**
   - tests/modules/nf-core/gawk/**
-gecco/run:
-  - modules/nf-core/gecco/run/**
-  - tests/modules/nf-core/gecco/run/**
 gem2/gem2bedmappability:
   - modules/nf-core/gem2/gem2bedmappability/**
   - tests/modules/nf-core/gem2/gem2bedmappability/**