Update stranger (#5717)

* everything but snapshot * fix gz snap * update testdata paths * Update main.nf.test * update test --------- Co-authored-by: Simon Pearce <[email protected]>
nf-core · Jun 24, 2024 · c48824e · c48824e
1 parent 0a92fa8
commit c48824e
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Showing 10 changed files with 161 additions and 74 deletions.
diff --git a/modules/nf-core/stranger/environment.yml b/modules/nf-core/stranger/environment.yml
@@ -4,4 +4,4 @@ channels:
   - bioconda
   - defaults
 dependencies:
-  - bioconda::stranger=0.8.1
+  - bioconda::stranger=0.9.0
diff --git a/modules/nf-core/stranger/main.nf b/modules/nf-core/stranger/main.nf
@@ -4,8 +4,8 @@ process STRANGER {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/stranger:0.8.1--pyh5e36f6f_0':
-        'biocontainers/stranger:0.8.1--pyh5e36f6f_0' }"
+        'https://depot.galaxyproject.org/singularity/stranger:0.9.0--pyh7cba7a3_0':
+        'biocontainers/stranger:0.9.0--pyh7cba7a3_0' }"
 
     input:
     tuple val(meta), path(vcf)
@@ -37,7 +37,7 @@ process STRANGER {
     stub:
     def prefix = task.ext.prefix ?: "${meta.id}"
     """
-    touch ${prefix}.vcf.gz
+    echo "" | gzip > ${prefix}.vcf.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

diff --git a/modules/nf-core/stranger/tests/main.nf.test b/modules/nf-core/stranger/tests/main.nf.test
@@ -0,0 +1,82 @@
+nextflow_process {
+
+    name "Test Process STRANGER"
+    script "../main.nf"
+    process "STRANGER"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "stranger"
+    tag "expansionhunter"
+
+    setup {
+        run("EXPANSIONHUNTER") {
+            script "../../expansionhunter/main.nf"
+            process {
+                """
+                 input[0] = [
+                    [ id:'test' ], // meta map
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true),
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/illumina/bam/test.paired_end.sorted.bam.bai', checkIfExists: true)
+                ]
+                input[1] = [
+                    [id:'fasta'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[2] = [
+                    [id:'fai'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/genome.fasta.fai', checkIfExists: true)
+                ]
+                input[3] = [
+                    [id:'catalogue'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/loci/repeat_expansions.json', checkIfExists: true)
+                ]
+                """
+            }
+        }
+    }
+
+    test("homo_sapiens - vcf, repeat_catalogue") {
+
+        when {
+            process {
+                """
+                input[0] = EXPANSIONHUNTER.out.vcf
+                input[1] = [
+                    [id:'catalogue'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/loci/repeat_expansions.json', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+
+    }
+
+    test("homo_sapiens - vcf, repeat_catalogue - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = EXPANSIONHUNTER.out.vcf
+                input[1] = [
+                    [id:'catalogue'],
+                    file(params.modules_testdata_base_path + 'genomics/homo_sapiens/genome/loci/repeat_expansions.json', checkIfExists: true)
+                ]
+                """
+            }
+        }
+
+        then {
+            assert process.success
+            assert snapshot(process.out).match()
+        }
+    }
+}
diff --git a/modules/nf-core/stranger/tests/main.nf.test.snap b/modules/nf-core/stranger/tests/main.nf.test.snap
@@ -0,0 +1,68 @@
+{
+    "homo_sapiens - vcf, repeat_catalogue - stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "stranger.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,369e472eaaf24bf7d154b41bc731ac50"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "stranger.vcf.gz:md5,68b329da9893e34099c7d8ad5cb9c940"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,369e472eaaf24bf7d154b41bc731ac50"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-24T06:58:08.232701026"
+    },
+    "homo_sapiens - vcf, repeat_catalogue": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "stranger.vcf.gz:md5,bce108ecdcff045eebd6cf831be9b5a8"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,369e472eaaf24bf7d154b41bc731ac50"
+                ],
+                "vcf": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "stranger.vcf.gz:md5,bce108ecdcff045eebd6cf831be9b5a8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,369e472eaaf24bf7d154b41bc731ac50"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-06-24T06:57:54.749238699"
+    }
+}
diff --git a/modules/nf-core/stranger/tests/nextflow.config b/modules/nf-core/stranger/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+     withName: 'STRANGER' {
+         ext.prefix = "stranger"
+     }
+ }
diff --git a/modules/nf-core/stranger/tests/tags.yml b/modules/nf-core/stranger/tests/tags.yml
@@ -0,0 +1,2 @@
+stranger:
+  - "modules/nf-core/stranger/**"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
@@ -1642,9 +1642,6 @@ stecfinder:
 stitch:
   - modules/nf-core/stitch/**
   - tests/modules/nf-core/stitch/**
-stranger:
-  - modules/nf-core/stranger/**
-  - tests/modules/nf-core/stranger/**
 subworkflows/align_bowtie2:
   - subworkflows/nf-core/align_bowtie2/**
   - tests/subworkflows/nf-core/align_bowtie2/**

diff --git a/tests/modules/nf-core/stranger/main.nf b/tests/modules/nf-core/stranger/main.nf
diff --git a/tests/modules/nf-core/stranger/nextflow.config b/tests/modules/nf-core/stranger/nextflow.config
diff --git a/tests/modules/nf-core/stranger/test.yml b/tests/modules/nf-core/stranger/test.yml