Update genomescope2 module and add nf-tests

modules/nf-core/genomescope2/main.nf

@@ -4,20 +4,22 @@ process GENOMESCOPE2 {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py310r41hdfd78af_5':
-        'biocontainers/genomescope2:2.0--py310r41hdfd78af_5' }"
+        'https://depot.galaxyproject.org/singularity/genomescope2:2.0--py311r42hdfd78af_6':
+        'biocontainers/genomescope2:2.0--py311r42hdfd78af_6' }"
 
     input:
     tuple val(meta), path(histogram)
 
     output:
-    tuple val(meta), path("*_linear_plot.png")            , emit: linear_plot_png
-    tuple val(meta), path("*_transformed_linear_plot.png"), emit: transformed_linear_plot_png
-    tuple val(meta), path("*_log_plot.png")               , emit: log_plot_png
-    tuple val(meta), path("*_transformed_log_plot.png")   , emit: transformed_log_plot_png
-    tuple val(meta), path("*_model.txt")                  , emit: model
-    tuple val(meta), path("*_summary.txt")                , emit: summary
-    path "versions.yml"                                   , emit: versions
+    tuple val(meta), path("${prefix}_linear_plot.png")            , emit: linear_plot_png
+    tuple val(meta), path("${prefix}_transformed_linear_plot.png"), emit: transformed_linear_plot_png
+    tuple val(meta), path("${prefix}_log_plot.png")               , emit: log_plot_png
+    tuple val(meta), path("${prefix}_transformed_log_plot.png")   , emit: transformed_log_plot_png
+    tuple val(meta), path("${prefix}_model.txt")                  , emit: model
+    tuple val(meta), path("${prefix}_summary.txt")                , emit: summary
+    tuple val(meta), path("${prefix}_lookup_table.txt")           , emit: lookup_table, optional: true
+    tuple val(meta), path("${prefix}_fitted_hist.png")            , emit: fitted_histogram_png, optional: true
+    path "versions.yml"                                           , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -32,6 +34,28 @@ process GENOMESCOPE2 {
         --output . \\
         --name_prefix $prefix
 
+    test -f "fitted_hist.png" && mv fitted_hist.png ${prefix}_fitted_hist.png
+    test -f "lookup_table.txt" && mv lookup_table.txt ${prefix}_lookup_table.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    '${task.process}':
+        genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' )
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}_linear_plot.png
+    touch ${prefix}_transformed_linear_plot.png
+    touch ${prefix}_log_plot.png
+    touch ${prefix}_transformed_log_plot.png
+    touch ${prefix}_model.txt
+    touch ${prefix}_summary.txt
+    touch ${prefix}_fitted_hist.png
+    touch ${prefix}_lookup_table.txt
+
     cat <<-END_VERSIONS > versions.yml
     '${task.process}':
         genomescope2: \$( genomescope2 -v | sed 's/GenomeScope //' )

modules/nf-core/genomescope2/meta.yml

@@ -11,7 +11,7 @@ tools:
       documentation: "https://github.com/tbenavi1/genomescope2.0/blob/master/README.md"
       tool_dev_url: "https://github.com/tbenavi1/genomescope2.0"
       doi: "10.1038/s41467-020-14998-3"
-      licence: "['Apache License, Version 2.0 (Apache-2.0)']"
+      licence: ["Apache-2.0"]
 input:
   - meta:
       type: map
@@ -60,6 +60,14 @@ output:
       type: file
       description: Genomescope2 histogram summary
       pattern: "*_summary.txt"
+  - lookup_table:
+      type: file
+      description: Fitted histogram lookup table
+      pattern: "*_lookup_table.txt"
+  - fitted_histogram_png:
+      type: file
+      description: A genomescope2 fitted histogram plot in PNG format
+      pattern: "*_fitted_hist.png"
 authors:
   - "@mahesh-panchal"
 maintainers:

modules/nf-core/genomescope2/tests/main.nf.test

@@ -0,0 +1,84 @@
+nextflow_process {
+
+    name "Test Process GENOMESCOPE2"
+    script "../main.nf"
+    config "./nextflow.config"
+    process "GENOMESCOPE2"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "genomescope2"
+    tag "meryl/count"
+    tag "meryl/histogram"
+
+    setup {
+        run('MERYL_COUNT'){
+            script "../../../../modules/nf-core/meryl/count/main.nf"
+            process {
+                """
+                input[0] = Channel.value([
+                    [ id: 'test', single_end: true ], // meta map
+                    file( params.modules_testdata_base_path + "/genomics/prokaryotes/bacteroides_fragilis/illumina/fastq/test1_1.fastq.gz", checkIfExists: true )
+                ])
+                """
+            }
+        }
+        run('MERYL_HISTOGRAM'){
+            script "../../../../modules/nf-core/meryl/histogram/main.nf"
+            process {
+                """
+                input[0] = MERYL_COUNT.out.meryl_db
+                """
+            }
+        }
+    }
+
+    test("bacteroides_fragilis - fastq") {
+
+        when {
+            process {
+                """
+                input[0] = MERYL_HISTOGRAM.out.hist
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert file(process.out.linear_plot_png[0][1]).exists() }, // PNG md5sum mismatches using conda
+                { assert file(process.out.transformed_linear_plot_png[0][1]).exists() }, // PNG md5sum mismatches using conda
+                { assert file(process.out.log_plot_png[0][1]).exists() }, // PNG md5sum mismatches using conda
+                { assert file(process.out.transformed_log_plot_png[0][1]).exists() }, // PNG md5sum mismatches using conda
+                { assert snapshot(process.out.model).match("model") },
+                { assert snapshot(process.out.summary).match("summary") },
+                { assert snapshot(process.out.lookup_table).match("lookup_table") },
+                { assert file(process.out.fitted_histogram_png[0][1]).exists() }, // PNG md5sum mismatches using conda
+                { assert snapshot(process.out.versions).match("versions") }
+            )
+        }
+
+    }
+
+    test("bacteroides_fragilis - fastq - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = MERYL_HISTOGRAM.out.hist
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}