Update Prokka to take compressed input && tidy module script

modules/nf-core/prokka/environment.yml

@@ -3,3 +3,4 @@ channels:
   - bioconda
 dependencies:
   - bioconda::prokka=1.14.6
+  - conda-forge::openjdk=8.0.412

modules/nf-core/prokka/main.nf

@@ -1,11 +1,11 @@
 process PROKKA {
-    tag "$meta.id"
+    tag "${meta.id}"
     label 'process_low'
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/prokka:1.14.6--pl5321hdfd78af_4' :
-        'biocontainers/prokka:1.14.6--pl5321hdfd78af_4' }"
+        'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/3a/3af46b047c8fe84112adeaecf300878217c629b97f111f923ecf327656ddd141/data' :
+        'community.wave.seqera.io/library/prokka_openjdk:10546cadeef11472' }"
 
     input:
     tuple val(meta), path(fasta)
@@ -31,18 +31,49 @@ process PROKKA {
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args   ?: ''
-    prefix   = task.ext.prefix ?: "${meta.id}"
-    def proteins_opt = proteins ? "--proteins ${proteins[0]}" : ""
-    def prodigal_tf = prodigal_tf ? "--prodigaltf ${prodigal_tf[0]}" : ""
+    def args             = task.ext.args   ?: ''
+    prefix               = task.ext.prefix ?: "${meta.id}"
+    def input            = fasta.toString() - ~/\.gz$/
+    def decompress       = fasta.getExtension() == "gz" ? "gunzip -c ${fasta} > ${input}" : ""
+    def cleanup          = fasta.getExtension() == "gz" ? "rm ${input}" : ""
+    def proteins_opt     = proteins ? "--proteins ${proteins}" : ""
+    def prodigal_tf_in   = prodigal_tf ? "--prodigaltf ${prodigal_tf}" : ""
     """
+    ${decompress}
+
     prokka \\
-        $args \\
-        --cpus $task.cpus \\
-        --prefix $prefix \\
-        $proteins_opt \\
-        $prodigal_tf \\
-        $fasta
+        ${args} \\
+        --cpus ${task.cpus} \\
+        --prefix ${prefix} \\
+        ${proteins_opt} \\
+        ${prodigal_tf_in} \\
+        ${input}
+
+    ${cleanup}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        prokka: \$(echo \$(prokka --version 2>&1) | sed 's/^.*prokka //')
+    END_VERSIONS
+    """
+
+    stub:
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    mkdir ${prefix}
+    touch ${prefix}/${prefix}.gff
+    touch ${prefix}/${prefix}.gbk
+    touch ${prefix}/${prefix}.fna
+    touch ${prefix}/${prefix}.faa
+    touch ${prefix}/${prefix}.ffn
+    touch ${prefix}/${prefix}.sqn
+    touch ${prefix}/${prefix}.fsa
+    touch ${prefix}/${prefix}.tbl
+    touch ${prefix}/${prefix}.err
+    touch ${prefix}/${prefix}.log
+    touch ${prefix}/${prefix}.txt
+    touch ${prefix}/${prefix}.tsv
+    touch ${prefix}/${prefix}.gff
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/nf-core/prokka/tests/main.nf.test

@@ -47,4 +47,69 @@ nextflow_process {
 
     }
 
+    test("Prokka - sarscov2 - genome.fasta.gz") {
+
+        when {
+            process {
+                """
+                input[0] =  Channel.fromList([
+                        tuple([ id:'test', single_end:false ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true))
+                    ])
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.gbk.get(0).get(1)).exists() },
+                { assert path(process.out.log.get(0).get(1)).exists() },
+                { assert path(process.out.sqn.get(0).get(1)).exists() },
+                { assert snapshot(
+                    process.out.gff,
+                    process.out.fna,
+                    process.out.faa,
+                    process.out.ffn,
+                    process.out.fsa,
+                    process.out.tbl,
+                    process.out.err,
+                    process.out.txt,
+                    process.out.tsv,
+                    process.out.versions
+                    ).match()
+                }
+            )
+        }
+
+    }
+
+    test("Prokka - sarscov2 - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] =  Channel.fromList([
+                        tuple([ id:'test', single_end:false ], // meta map
+                        file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta.gz', checkIfExists: true))
+                    ])
+                input[1] = []
+                input[2] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
 }