Migrate meryl unionsum nftest (#5404)

* Initial migration * Update tests, add mandatory value, lint * Bump version * Update snapshot
nf-core · Mar 27, 2024 · b7f584e · b7f584e
1 parent a3501bc
commit b7f584e
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Showing 10 changed files with 774 additions and 61 deletions.
diff --git a/modules/nf-core/meryl/unionsum/environment.yml b/modules/nf-core/meryl/unionsum/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::meryl=1.3
+  - bioconda::meryl=1.4.1
diff --git a/modules/nf-core/meryl/unionsum/main.nf b/modules/nf-core/meryl/unionsum/main.nf
@@ -4,11 +4,12 @@ process MERYL_UNIONSUM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/meryl:1.3--h87f3376_1':
-        'biocontainers/meryl:1.3--h87f3376_1' }"
+        'https://depot.galaxyproject.org/singularity/meryl:1.4.1--h4ac6f70_0':
+        'biocontainers/meryl:1.4.1--h4ac6f70_0' }"
 
     input:
     tuple val(meta), path(meryl_dbs)
+    val kvalue
 
     output:
     tuple val(meta), path("*.unionsum.meryldb"), emit: meryl_db
@@ -22,6 +23,7 @@ process MERYL_UNIONSUM {
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
     meryl union-sum \\
+        k=$kvalue \\
         threads=$task.cpus \\
         $args \\
         output ${prefix}.unionsum.meryldb \\
@@ -32,4 +34,16 @@ process MERYL_UNIONSUM {
         meryl: \$( meryl --version |& sed 's/meryl //' )
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.unionsum.meryldb
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        meryl: \$( meryl --version |& sed 's/meryl //' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/meryl/unionsum/meta.yml b/modules/nf-core/meryl/unionsum/meta.yml
@@ -3,13 +3,14 @@ description: A genomic k-mer counter (and sequence utility) with nice features.
 keywords:
   - k-mer
   - unionsum
+  - reference-free
 tools:
   - "meryl":
       description: "A genomic k-mer counter (and sequence utility) with nice features. "
       homepage: "https://github.com/marbl/meryl"
       documentation: "https://meryl.readthedocs.io/en/latest/quick-start.html"
       tool_dev_url: "https://github.com/marbl/meryl"
-      licence: "['GPL']"
+      licence: ["GPL"]
 input:
   - meta:
       type: map
@@ -19,6 +20,9 @@ input:
   - meryl_dbs:
       type: directory
       description: Meryl k-mer databases
+  - kvalue:
+      type: integer
+      description: An integer value of k to use as the k-mer value.
 output:
   - meta:
       type: map

diff --git a/modules/nf-core/meryl/unionsum/tests/main.nf.test b/modules/nf-core/meryl/unionsum/tests/main.nf.test
@@ -0,0 +1,123 @@
+nextflow_process {
+
+    name "Test Process MERYL_UNIONSUM"
+    script "../main.nf"
+    process "MERYL_UNIONSUM"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "meryl"
+    tag "meryl/unionsum"
+    tag "meryl/count"
+
+    test("sarscov2 - fastq - single_end") {
+
+        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/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true )
+                    ])
+                    input[1] = Channel.value(21)
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = MERYL_COUNT.out.meryl_db
+                input[1] = Channel.value(21)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fastq - paired_end") {
+
+        setup {
+            run('MERYL_COUNT'){
+                script "../../../../../modules/nf-core/meryl/count/main.nf"
+                process {
+                    """
+                    input[0] = Channel.value([
+                        [ id: 'test', single_end: false ], // meta map
+                        [
+                            file( params.modules_testdata_base_path + "/genomics/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true ),
+                            file( params.modules_testdata_base_path + "/genomics/sarscov2/illumina/fastq/test_2.fastq.gz", checkIfExists: true )
+                        ]
+                    ])
+                    input[1] = Channel.value(21)
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = MERYL_COUNT.out.meryl_db
+                input[1] = Channel.value(21)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fastq- stub") {
+
+        options "-stub"
+
+        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/sarscov2/illumina/fastq/test_1.fastq.gz", checkIfExists: true )
+                    ])
+                    input[1] = Channel.value(21)
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = MERYL_COUNT.out.meryl_db
+                input[1] = Channel.value(21)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}