Kaiju version bump- nf-test -add stub (nf-core#4781)

* kaiju modules patch

* add kaiju nf-test and stub

* adding test & stub 4 kaiju2krona

* undo raven change

* kaiju2table & kaijumkfmi

* Add taxonomic profiling as a keyword in meta.yml

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

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kaiju=1.8.2
+  - bioconda::kaiju=1.10.0

modules/nf-core/kaiju/kaiju/main.nf

@@ -4,8 +4,8 @@ process KAIJU_KAIJU {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
-        'biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+        'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+        'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
 
     input:
     tuple val(meta), path(reads)
@@ -38,4 +38,18 @@ process KAIJU_KAIJU {
         kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def input = meta.single_end ? "-i ${reads}" : "-i ${reads[0]} -j ${reads[1]}"
+    """
+    touch ${prefix}.tsv
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
+
 }

modules/nf-core/kaiju/kaiju/meta.yml

@@ -26,7 +26,7 @@ input:
         respectively.
       pattern: "*.{fastq,fq,fasta,fa,fsa,fas,fna,fastq.gz,fq.gz,fasta.gz,fa.gz,fsa.gz,fas.gz,fna.gz}"
   - db:
-      type: files
+      type: directory
       description: |
         List containing the database and nodes files for Kaiju
         e.g. [ 'database.fmi', 'nodes.dmp' ]

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

@@ -0,0 +1,117 @@
+nextflow_process {
+
+    name "Test Process KAIJU_KAIJU"
+    script "../main.nf"
+    process "KAIJU_KAIJU"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "kaiju"
+    tag "kaiju/kaiju"
+    tag "untar"
+
+    test("sarscov2 - fastq - single-end") {
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] =  [
+                        [ 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] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.results[0][1]).getText().contains("C\tERR5069949.2257580\t2697049") }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fastq - paired-end") {
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    [ 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] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert path(process.out.results[0][1]).getText().contains("C\tERR5069949.2257580\t2697049") }
+            )
+        }
+    }
+
+    test("sarscov2 - fastq - stub") {
+
+        options '-stub'
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ],
+                    [ 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] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.results[0][1]).name).match() }
+            )
+        }
+    }
+
+}

modules/nf-core/kaiju/kaiju/tests/tags.yml

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

modules/nf-core/kaiju/kaiju2krona/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kaiju=1.8.2
+  - bioconda::kaiju=1.10.0

modules/nf-core/kaiju/kaiju2krona/main.nf

@@ -4,8 +4,8 @@ process KAIJU_KAIJU2KRONA {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/kaiju:1.8.2--h5b5514e_1':
-        'biocontainers/kaiju:1.8.2--h5b5514e_1' }"
+        'https://depot.galaxyproject.org/singularity/kaiju:1.10.0--h43eeafb_0':
+        'biocontainers/kaiju:1.10.0--h43eeafb_0' }"
 
     input:
     tuple val(meta), path(tsv)
@@ -36,4 +36,17 @@ process KAIJU_KAIJU2KRONA {
         kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
     END_VERSIONS
     """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.txt
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        kaiju: \$(echo \$( kaiju -h 2>&1 | sed -n 1p | sed 's/^.*Kaiju //' ))
+    END_VERSIONS
+    """
 }
+

modules/nf-core/kaiju/kaiju2krona/tests/main.nf.test

@@ -0,0 +1,105 @@
+nextflow_process {
+
+    name "Test Process KAIJU_KAIJU2KRONA"
+    script "../main.nf"
+    process "KAIJU_KAIJU2KRONA"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "kaiju"
+    tag "kaiju/kaiju2krona"
+    tag "kaiju/kaiju"
+    tag "untar"
+
+    test("sarscov2 - fastq - single-end") {
+
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+
+            run("KAIJU_KAIJU") {
+                script "../../kaiju/main.nf"
+                process {
+                    """
+                    input[0] =  [
+                            [ 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] = UNTAR.out.untar.map{ it[1] }
+                    """
+                }
+            }
+        }
+
+            when {
+                process {
+                    """
+                    input[0] = KAIJU_KAIJU.out.results
+                    input[1] = UNTAR.out.untar.map{ it[1] }
+                    """
+                }
+            }
+
+            then {
+                assertAll(
+                    { assert process.success },
+                    { assert snapshot(process.out).match() }
+                )
+            }
+
+    }
+
+    test("sarscov2 - fastq - stub") {
+
+        options "-stub"
+
+        setup {
+            run ("UNTAR"){
+                script "../../../untar/main.nf"
+                process {
+                    """
+                    input[0] = [ [], file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/db/kaiju.tar.gz', checkIfExists: true) ]
+                    """
+                }
+            }
+
+            run("KAIJU_KAIJU") {
+                script "../../kaiju/main.nf"
+                process {
+                    """
+                    input[0] =  [
+                            [ 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] = UNTAR.out.untar.map{ it[1] }
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = KAIJU_KAIJU.out.results
+                input[1] = UNTAR.out.untar.map{ it[1] }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(file(process.out.txt[0][1]).name).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/kaiju/kaiju2krona/tests/tags.yml

@@ -0,0 +1,2 @@
+kaiju/kaiju2krona:
+  - "modules/nf-core/kaiju/kaiju2krona/**"

modules/nf-core/kaiju/kaiju2table/environment.yml

@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::kaiju=1.8.2
+  - bioconda::kaiju=1.10.0