Update dragmap + add nf-test

modules/nf-core/dragmap/align/environment.yml

@@ -4,7 +4,7 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - dragmap=1.2.1
+  - dragmap=1.3.0
   # renovate: datasource=conda depName=bioconda/samtools
-  - samtools=1.15.1
+  - samtools=1.16
   - pigz=2.3.4

modules/nf-core/dragmap/align/main.nf

@@ -4,8 +4,8 @@ process DRAGMAP_ALIGN {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0':
-        'biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:5ebebbc128cd624282eaa37d2c7fe01505a91a69-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0':
+        'biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:bb7e33c2ede38421063b8379a5fb3453645bb047-0' }"
 
     input:
     tuple val(meta) , path(reads)

modules/nf-core/dragmap/align/tests/main.nf.test

@@ -0,0 +1,185 @@
+nextflow_process {
+
+    name "Test Process DRAGMAP_ALIGN"
+    script "../main.nf"
+    process "DRAGMAP_ALIGN"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "dragmap"
+    tag "dragmap/align"
+
+    test("sarscov2 - fastq, hashtable, false") {
+
+        setup {
+            run("DRAGMAP_HASHTABLE") {
+                script "../../hashtable/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id:'test'],
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = DRAGMAP_HASHTABLE.out.hashmap
+                input[2] = false //sort
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    file(process.out.log[0][1]).readLines()[2..4],
+                    file(process.out.versions[0]).name
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - fastq, hashtable, true") {
+
+        setup {
+            run("DRAGMAP_HASHTABLE") {
+                script "../../hashtable/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id:'test'],
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:true ], // meta map
+                    file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true)
+                ]
+                input[1] = DRAGMAP_HASHTABLE.out.hashmap
+                input[2] = true //sort
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    file(process.out.log[0][1]).readLines()[2..4],
+                    file(process.out.versions[0]).name
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [fastq1, fastq2], hashtable, false") {
+
+        setup {
+            run("DRAGMAP_HASHTABLE") {
+                script "../../hashtable/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id:'test'],
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                input[1] = DRAGMAP_HASHTABLE.out.hashmap
+                input[2] = false //sort
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    file(process.out.log[0][1]).readLines()[2..4],
+                    file(process.out.versions[0]).name
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [fastq1, fastq2], hashtable, true") {
+
+        setup {
+            run("DRAGMAP_HASHTABLE") {
+                script "../../hashtable/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id:'test'],
+                        file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.test_data['sarscov2']['illumina']['test_2_fastq_gz'], checkIfExists: true)
+                    ]
+                ]
+                input[1] = DRAGMAP_HASHTABLE.out.hashmap
+                input[2] = true //sort
+                """
+            }
+        }
+
+        then {
+            assertAll (
+                { assert process.success },
+                { assert snapshot(
+                    file(process.out.bam[0][1]).name,
+                    file(process.out.log[0][1]).readLines()[2..4],
+                    file(process.out.versions[0]).name
+                ).match() }
+            )
+        }
+
+    }
+
+}

modules/nf-core/dragmap/align/tests/tags.yml

@@ -0,0 +1,2 @@
+dragmap/align:
+  - modules/nf-core/dragmap/align/**

modules/nf-core/dragmap/hashtable/main.nf

@@ -4,8 +4,8 @@ process DRAGMAP_HASHTABLE {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/dragmap:1.3.0--h72d16da_1':
-        'biocontainers/dragmap:1.3.0--h72d16da_1' }"
+        'https://depot.galaxyproject.org/singularity/1.3.0--h91baf5a_3':
+        'biocontainers/dragmap:1.3.0--h91baf5a_3' }"
 
     input:
     tuple val(meta), path(fasta)

modules/nf-core/dragmap/hashtable/tests/main.nf.test

@@ -0,0 +1,41 @@
+nextflow_process {
+
+    name "Test Process DRAGMAP_HASHTABLE"
+    script "../main.nf"
+    process "DRAGMAP_HASHTABLE"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "dragmap"
+    tag "dragmap/hashtable"
+
+    test("sarscov2 - fasta") {
+
+        when {
+
+            process {
+                """
+                input[0] = [
+                    [id:'test'],
+                    file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                        file(process.out.hashmap[0][1]).name,
+                        file(process.out.versions[0]).name
+                    ).match() 
+                }
+            )
+        }
+
+    }
+
+    // TODO Add test using alt-masked bed file
+    // https://github.com/Illumina/dragmap#build-hash-table-using-an-alt-masked-bed-file
+
+}

modules/nf-core/dragmap/hashtable/tests/tags.yml

@@ -0,0 +1,2 @@
+dragmap/hashtable:
+  - modules/nf-core/dragmap/hashtable/**

tests/config/pytest_modules.yml

@@ -924,14 +924,6 @@ deseq2/differential:
   - modules/nf-core/deseq2/differential/**
   - tests/modules/nf-core/deseq2/differential/**
 
-dragmap/align:
-  - modules/nf-core/dragmap/align/**
-  - tests/modules/nf-core/dragmap/align/**
-
-dragmap/hashtable:
-  - modules/nf-core/dragmap/hashtable/**
-  - tests/modules/nf-core/dragmap/hashtable/**
-
 dshbio/exportsegments:
   - modules/nf-core/dshbio/exportsegments/**
   - tests/modules/nf-core/dshbio/exportsegments/**