Update dragmap + add nf-test (#4379)

* new module picard/scatterintervalsbyns * update annotsv to 3.3.6 * update installannotations * update dragmap modules + add nf-test * fix singularity container * add human test + stubs * fix tests * update mulled containers + conda env * fix tests * chore: Remove pytest-workflow tests --------- Co-authored-by: Edmund Miller <[email protected]>
nf-core · Dec 7, 2023 · 8f0bec8 · 8f0bec8
1 parent 9b1b7a7
commit 8f0bec8
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Showing 16 changed files with 483 additions and 170 deletions.
diff --git a/modules/nf-core/dragmap/align/environment.yml b/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
-  - pigz=2.3.4
+  - samtools=1.18
+  - pigz=2.8
diff --git a/modules/nf-core/dragmap/align/main.nf b/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:7eed251370ac7f3537c3d9472cdb2f9f5d8da1c5-0':
+        'biocontainers/mulled-v2-580d344d9d4a496cd403932da8765f9e0187774d:7eed251370ac7f3537c3d9472cdb2f9f5d8da1c5-0' }"
 
     input:
     tuple val(meta) , path(reads)
@@ -43,4 +43,18 @@ process DRAGMAP_ALIGN {
         pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    touch ${prefix}.bam
+    touch ${prefix}.log
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        dragmap: \$(echo \$(dragen-os --version 2>&1))
+        samtools: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//')
+        pigz: \$( pigz --version 2>&1 | sed 's/pigz //g' )
+    END_VERSIONS
+    """
 }
diff --git a/modules/nf-core/dragmap/align/tests/main.nf.test b/modules/nf-core/dragmap/align/tests/main.nf.test
@@ -0,0 +1,276 @@
+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().findAll { it.startsWith("decompHash") },
+                    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().findAll { it.startsWith("decompHash") },
+                    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().findAll { it.startsWith("decompHash") },
+                    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().findAll { it.startsWith("decompHash") },
+                    file(process.out.versions[0]).name
+                ).match() }
+            )
+        }
+
+    }
+
+    test("homo_sapiens - [fastq1, fastq2], hashtable, true") {
+
+        setup {
+            run("DRAGMAP_HASHTABLE") {
+                script "../../hashtable/main.nf"
+                process {
+                    """
+                    input[0] = [
+                        [id:'test'],
+                        file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test', single_end:false ], // meta map
+                    [
+                        file(params.test_data['homo_sapiens']['illumina']['test_1_fastq_gz'], checkIfExists: true),
+                        file(params.test_data['homo_sapiens']['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().findAll { it.startsWith("decompHash") },
+                    file(process.out.versions[0]).name
+                ).match() }
+            )
+        }
+
+    }
+
+    test("sarscov2 - [fastq1, fastq2], hashtable, true - stub") {
+
+        options "-stub"
+        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]).name,
+                    file(process.out.versions[0]).name
+                ).match() }
+            )
+        }
+
+    }
+
+}