Port gget/gget to nf-test and update

modules/nf-core/gget/gget/environment.yml

@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::gget=0.27.2
+- conda-forge::gget=0.29.1

modules/nf-core/gget/gget/main.nf

@@ -4,15 +4,15 @@ process GGET_GGET {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/gget:0.27.2--pyh4a94de4_2':
-        'biocontainers/gget:0.27.2--pyh4a94de4_2' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/7c/7ca1a63d986bc5b68d0543ce326a703265d4a3645be7e05f9af94f2992aa8352/data':
+        'community.wave.seqera.io/library/gget:0.29.1--3b5a50589bc0feb3' }"
 
     input:
     tuple val(meta), path(files)
 
     output:
-    tuple val(meta), path("*[!versions.yml][!${prefix}.${extension}]*"), emit: files, optional: true
-    tuple val(meta), path("${prefix}.${extension}")                   , emit: output, optional: true
+    tuple val(meta), path("*[!versions.yml][!${prefix}.${extension}]*"), emit: files , optional: true
+    tuple val(meta), path("${prefix}.${extension}")                    , emit: output, optional: true
     path "versions.yml", emit: versions
 
     when:
@@ -26,6 +26,7 @@ process GGET_GGET {
                 args.contains("-csv")   ? "csv" :
                 "json"
     """
+    export MPLCONFIGDIR=\$PWD/.tmp
     gget \\
         $args \\
         -o ${prefix}.${extension} \\
@@ -36,4 +37,20 @@ process GGET_GGET {
         gget: \$(echo \$(gget --version 2>&1 | sed 's/gget version: //g'))
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    extension = args.startsWith("pdb")  ? "pdb" :
+                args.contains("-csv")   ? "csv" :
+                "json"
+    """
+    export MPLCONFIGDIR=\$PWD/.tmp    #included in stub to stop errors in the version string
+    touch ${prefix}.${extension}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gget: \$(echo \$(gget --version 2>&1 | sed 's/gget version: //g'))
+    END_VERSIONS
+    """
 }