Added nf-tests to geNomad modules (nf-core#4674)

* Added nf-tests to geNomad modules

* Fixed meta.yml linting

* Updated genomad version and removed empty files from snapshot

* Fixed Docker

* Updated genomad_download snapshot

* Changed docker options to bypass fixOwnership issues

modules/nf-core/genomad/download/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::genomad=1.5.2
+  - bioconda::genomad=1.7.4

modules/nf-core/genomad/download/main.nf

@@ -3,8 +3,8 @@ process GENOMAD_DOWNLOAD {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
-        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genomad:1.7.4--pyhdfd78af_0':
+        'biocontainers/genomad:1.7.4--pyhdfd78af_0' }"
 
     output:
     path "genomad_db/"  , emit: genomad_db

modules/nf-core/genomad/download/meta.yml

@@ -15,7 +15,7 @@ tools:
       documentation: https://portal.nersc.gov/genomad/
       tool_dev_url: https://github.com/apcamargo/genomad/
       doi: 10.1101/2023.03.05.531206
-      licence: "['Lawrence Berkeley National Labs BSD variant license']"
+      licence: ["Lawrence Berkeley National Labs BSD variant license"]
 output:
   - versions:
       type: file

modules/nf-core/genomad/download/tests/main.nf.test

@@ -0,0 +1,34 @@
+nextflow_process {
+
+    name "Test Process GENOMAD_DOWNLOAD"
+    script "../main.nf"
+    process "GENOMAD_DOWNLOAD"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "genomad"
+    tag "genomad/download"
+
+    test("No input") {
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("No input - stub") {
+
+        options "-stub"
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}

modules/nf-core/genomad/download/tests/nextflow.config

@@ -0,0 +1,2 @@
+docker.fixOwnership = false
+docker.runOptions = '-u $(id -u):$(id -g)'

modules/nf-core/genomad/download/tests/tags.yml

@@ -0,0 +1,2 @@
+genomad/download:
+  - "modules/nf-core/genomad/download/**"

modules/nf-core/genomad/endtoend/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::genomad=1.5.2
+  - bioconda::genomad=1.7.4

modules/nf-core/genomad/endtoend/main.nf

@@ -4,26 +4,26 @@ process GENOMAD_ENDTOEND {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genomad:1.5.2--pyhdfd78af_0':
-        'biocontainers/genomad:1.5.2--pyhdfd78af_0' }"
+        'https://depot.galaxyproject.org/singularity/genomad:1.7.4--pyhdfd78af_0':
+        'biocontainers/genomad:1.7.4--pyhdfd78af_0' }"
 
     input:
     tuple val(meta) , path(fasta)
     path  genomad_db
 
     output:
-    tuple val(meta), path("*_aggregated_classification/*_aggregated_classification.tsv")    , emit: aggregated_classification
+    tuple val(meta), path("*_aggregated_classification/*_aggregated_classification.tsv")    , emit: aggregated_classification   , optional: true
     tuple val(meta), path("*_annotate/*_taxonomy.tsv")                                      , emit: taxonomy
     tuple val(meta), path("*_find_proviruses/*_provirus.tsv")                               , emit: provirus
     tuple val(meta), path("*_score_calibration/*_compositions.tsv")                         , emit: compositions                , optional: true
     tuple val(meta), path("*_score_calibration/*_calibrated_aggregated_classification.tsv") , emit: calibrated_classification   , optional: true
-    tuple val(meta), path("*_summary/*_plasmid.fna")                                        , emit: plasmid_fasta
+    tuple val(meta), path("*_summary/*_plasmid.fna.gz")                                     , emit: plasmid_fasta
     tuple val(meta), path("*_summary/*_plasmid_genes.tsv")                                  , emit: plasmid_genes
-    tuple val(meta), path("*_summary/*_plasmid_proteins.faa")                               , emit: plasmid_proteins
+    tuple val(meta), path("*_summary/*_plasmid_proteins.faa.gz")                            , emit: plasmid_proteins
     tuple val(meta), path("*_summary/*_plasmid_summary.tsv")                                , emit: plasmid_summary
-    tuple val(meta), path("*_summary/*_virus.fna")                                          , emit: virus_fasta
+    tuple val(meta), path("*_summary/*_virus.fna.gz")                                       , emit: virus_fasta
     tuple val(meta), path("*_summary/*_virus_genes.tsv")                                    , emit: virus_genes
-    tuple val(meta), path("*_summary/*_virus_proteins.faa")                                 , emit: virus_proteins
+    tuple val(meta), path("*_summary/*_virus_proteins.faa.gz")                              , emit: virus_proteins
     tuple val(meta), path("*_summary/*_virus_summary.tsv")                                  , emit: virus_summary
     path "versions.yml"                                                                     , emit: versions
 
@@ -42,6 +42,9 @@ process GENOMAD_ENDTOEND {
         --threads $task.cpus \\
         $args
 
+    gzip ./**/*.fna
+    gzip ./**/*.faa
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         genomad: \$(echo \$(genomad --version 2>&1) | sed 's/^.*geNomad, version //; s/ .*\$//')
@@ -65,13 +68,13 @@ process GENOMAD_ENDTOEND {
     touch ${filename}_score_calibration/${filename}_calibrated_aggregated_classification.tsv
     touch ${filename}_score_calibration/${filename}_compositions.tsv
     mkdir ${filename}_summary
-    touch ${filename}_summary/${filename}_plasmid.fna
+    touch ${filename}_summary/${filename}_plasmid.fna.gz
     touch ${filename}_summary/${filename}_plasmid_genes.tsv
-    touch ${filename}_summary/${filename}_plasmid_proteins.faa
+    touch ${filename}_summary/${filename}_plasmid_proteins.faa.gz
     touch ${filename}_summary/${filename}_plasmid_summary.tsv
-    touch ${filename}_summary/${filename}_virus.fna
+    touch ${filename}_summary/${filename}_virus.fna.gz
     touch ${filename}_summary/${filename}_virus_genes.tsv
-    touch ${filename}_summary/${filename}_virus_proteins.faa
+    touch ${filename}_summary/${filename}_virus_proteins.faa.gz
     touch ${filename}_summary/${filename}_virus_summary.tsv
 
     cat <<-END_VERSIONS > versions.yml

modules/nf-core/genomad/endtoend/meta.yml

@@ -15,7 +15,7 @@ tools:
       documentation: https://portal.nersc.gov/genomad/
       tool_dev_url: https://github.com/apcamargo/genomad/
       doi: 10.1101/2023.03.05.531206
-      licence: "['Lawrence Berkeley National Labs BSD variant license']"
+      licence: ["Lawrence Berkeley National Labs BSD variant license"]
 input:
   - meta:
       type: map