Updating Genome Nexus Subworkflow + Modules (for nucleovar nf-core lint check)

modules/msk/genomenexus/annotationpipeline/environment.yml

@@ -1,9 +1,6 @@
----
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "genomenexus_annotationpipeline"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "YOUR-TOOL-HERE"
+  - "genomenexus=version"

modules/msk/genomenexus/annotationpipeline/main.nf

@@ -4,14 +4,14 @@ process GENOMENEXUS_ANNOTATIONPIPELINE {
 
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'ghcr.io/msk-access/genomenexus_annotation-pipeline:1.0.5':
-        'ghcr.io/msk-access/genomenexus_annotation-pipeline:1.0.5' }"
+        'ghcr.io/msk-access/genomenexus_annotation-pipeline:1.0.4':
+        'ghcr.io/msk-access/genomenexus_annotation-pipeline:1.0.4' }"
 
     input:
     tuple val(meta), path(input_maf)
 
     output:
-    tuple val(meta), path("*.maf"), emit: annotated_maf
+    tuple val(meta), path("${meta.control_id}_${meta.case_id}_annotated.maf"), emit: annotated_maf
     path "versions.yml"           , emit: versions
 
     when:
@@ -22,11 +22,11 @@ process GENOMENEXUS_ANNOTATIONPIPELINE {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    java -Xms${task.memory.toMega()/4}m -Xmx${task.memory.toGiga()}g -jar /genome-nexus-annotation-pipeline/annotationPipeline/target/annotationPipeline.jar --filename ${input_maf} --output-filename ${meta.id}_annotated.maf
+    java -jar /genome-nexus-annotation-pipeline/annotationPipeline/target/annotationPipeline.jar --filename ${input_maf} --output-filename ${meta.id}_annotated.maf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        genomenexus: 'annotation pipeline version 1.0.5'
+        genomenexus: 'annotationpipeline version 1.0.4'
     END_VERSIONS
     """
 
@@ -35,11 +35,11 @@ process GENOMENEXUS_ANNOTATIONPIPELINE {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    touch ${meta.id}_annotated.maf
+    touch ${meta.control_id}_${meta.case_id}_annotated.maf
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        genomenexus: 'annotation pipeline version 1.0.5'
+        genomenexus: 'annotationpipeline version 1.0.4'
     END_VERSIONS
     """
 }

modules/msk/genomenexus/annotationpipeline/meta.yml

@@ -2,7 +2,7 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "genomenexus_annotationpipeline"
 
-description: Second module in genome nexus java pipeline to perform annotation of a MAF file type using the genomenexus suite of conversion and annotation tools. Genome Nexus is a comprehensive one-stop resource for fast, automated and high-throughput annotation and interpretation of genetic variants in cancer. Genome Nexus integrates information from a variety of existing resources, including databases that convert DNA changes to protein changes, predict the functional effects of protein mutations, and contain information about mutation frequencies, gene function, variant effects, and clinical actionability.
+description: DSL2 module to perform annotation of a MAF file type using the genomenexus suite of conversion and annotation tools.
 keywords:
   - annotate
   - vcf
@@ -11,7 +11,7 @@ keywords:
   - genomics
 tools:
   - "genomenexus":
-      description: "Second module in genome nexus java pipeline to perform an annotation of MAF file type using the genomenexus suite of conversion and annotation tools. Genome Nexus is a comprehensive one-stop resource for fast, automated and high-throughput annotation and interpretation of genetic variants in cancer. Genome Nexus integrates information from a variety of existing resources, including databases that convert DNA changes to protein changes, predict the functional effects of protein mutations, and contain information about mutation frequencies, gene function, variant effects, and clinical actionability."
+      description: "DSL2 module to perform an annotation of MAF file type using the genomenexus suite of conversion and annotation tools."
       homepage: "https://github.com/genome-nexus/genome-nexus-annotation-pipeline/"
       documentation: "https://github.com/genome-nexus/.github/blob/main/profile/README.md"
 

modules/msk/genomenexus/annotationpipeline/tests/main.nf.test

@@ -12,17 +12,17 @@ nextflow_process {
     tag "genomenexus"
     tag "genomenexus/annotationpipeline"
 
-    
+
     test("test normal ") {
 
 
         when {
             process {
                 """
-                
+
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.test_data_mskcc['genome_nexus']['test_maf'], checkIfExists: true)
+                    [ id:'test',case_id:'sample1',control_id:'sample2'], // meta map
+                    file(params.test_data_mskcc['genome_nexus']['sample2_sample1_annotated_maf'], checkIfExists: true)
                     ]
                 """
             }
@@ -32,25 +32,25 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-                
+
             )
         }
 
     }
 
-    
+
     test("test normal - stub") {
 
         options "-stub"
 
         when {
             process {
                 """
-                
-                
+
+
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.test_data_mskcc['genome_nexus']['test_maf'], checkIfExists: true)
+                    [ id:'test',case_id:'sample1',control_id:'sample2'], // meta map
+                    file(params.test_data_mskcc['genome_nexus']['sample2_sample1_annotated_maf'], checkIfExists: true)
                     ]
                 """
             }
@@ -59,7 +59,7 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success }
-                
+
             )
         }
 

modules/msk/genomenexus/annotationpipeline/tests/main.nf.test.snap

@@ -5,27 +5,35 @@
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": "test",
+                            "case_id": "sample1",
+                            "control_id": "sample2"
                         },
-                        "test_annotated.maf:md5,4547e768939e82f6d1f44e1c64b64c3a"
+                        "sample2_sample1_annotated.maf:md5,1a6973c12313853c23a7d99d84dc3167"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,faa1aee6ca139f0b49241579881c42e2"
+                    "versions.yml:md5,f0b525b535c5b271f5325cef7920e3ec"
                 ],
                 "annotated_maf": [
                     [
                         {
-                            "id": "test"
+                            "id": "test",
+                            "case_id": "sample1",
+                            "control_id": "sample2"
                         },
-                        "test_annotated.maf:md5,4547e768939e82f6d1f44e1c64b64c3a"
+                        "sample2_sample1_annotated.maf:md5,1a6973c12313853c23a7d99d84dc3167"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,faa1aee6ca139f0b49241579881c42e2"
+                    "versions.yml:md5,f0b525b535c5b271f5325cef7920e3ec"
                 ]
             }
         ],
-        "timestamp": "2024-07-25T11:12:27.03495"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-09T16:13:43.282868154"
     }
 }

modules/msk/genomenexus/vcf2maf/environment.yml

@@ -1,9 +1,7 @@
 ---
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
-name: "genomenexus_vcf2maf"
 channels:
   - conda-forge
   - bioconda
-  - defaults
 dependencies:
-  - "YOUR-TOOL-HERE"
+  - "genomenexus=version"

modules/msk/genomenexus/vcf2maf/main.nf

@@ -10,7 +10,7 @@ process GENOMENEXUS_VCF2MAF {
     tuple val(meta), path(vcf)
 
     output:
-    tuple val(meta), path("vcf2maf_output/${meta.id}.maf"), emit: maf
+    tuple val(meta), path("vcf2maf_output/${meta.control_id}_${meta.case_id}_annotated.maf"), emit: maf
     path "versions.yml"           , emit: versions
 
     when:
@@ -30,8 +30,8 @@ process GENOMENEXUS_VCF2MAF {
     """
 
     mkdir vcf2maf_output
-    touch ${meta.id}.maf
-    cp ${meta.id}.maf vcf2maf_output/
+    touch ${meta.control_id}_${meta.case_id}_annotated.maf
+    cp ${meta.control_id}_${meta.case_id}_annotated.maf vcf2maf_output/
     echo '"${task.process}": vcf2maf_lite.py v.0.0.1' > versions.yml
     """
 }

modules/msk/genomenexus/vcf2maf/meta.yml

@@ -2,7 +2,7 @@
 # yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json
 name: "genomenexus_vcf2maf"
 
-description: First module in genome nexus java pipeline to perform a native conversion of VCF file type to MAF file type using the genomenexus suite of conversion and annotation tools. Genome Nexus is a comprehensive one-stop resource for fast, automated and high-throughput annotation and interpretation of genetic variants in cancer. Genome Nexus integrates information from a variety of existing resources, including databases that convert DNA changes to protein changes, predict the functional effects of protein mutations, and contain information about mutation frequencies, gene function, variant effects, and clinical actionability.
+description: DSL2 module to perform a native conversion of VCF file type to MAF file type using the genomenexus suite of conversion and annotation tools.
 keywords:
   - convert
   - vcf
@@ -11,7 +11,7 @@ keywords:
   - genomics
 tools:
   - "genomenexus":
-      description: "First module in genome nexus java pipeline to perform a native conversion of VCF file type to MAF file type using the genomenexus suite of conversion and annotation tools. Genome Nexus is a comprehensive one-stop resource for fast, automated and high-throughput annotation and interpretation of genetic variants in cancer. Genome Nexus integrates information from a variety of existing resources, including databases that convert DNA changes to protein changes, predict the functional effects of protein mutations, and contain information about mutation frequencies, gene function, variant effects, and clinical actionability."
+      description: "DSL2 module to perform a native conversion of VCF file type to MAF file type using the genomenexus suite of conversion and annotation tools."
       homepage: "https://github.com/genome-nexus"
       documentation: "https://github.com/genome-nexus/.github/blob/main/profile/README.md"
 

modules/msk/genomenexus/vcf2maf/tests/main.nf.test

@@ -5,25 +5,25 @@ nextflow_process {
     name "Test Process GENOMENEXUS_VCF2MAF"
     script "../main.nf"
     process "GENOMENEXUS_VCF2MAF"
-    
+
 
     tag "modules"
     tag "modules_nfcore"
     tag "modules_msk"
     tag "genomenexus"
     tag "genomenexus/vcf2maf"
 
-    
+
     test("vcf2maf - test") {
 
         when {
             process {
                 """
-                
-                
+
+
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+                    [ id:'test',case_id:'sample1',control_id:'sample2'], // meta map
+                    file(params.test_data_mskcc['genome_nexus']['sample2_sample1_annotated_vcf'], checkIfExists: true)
                     ]
                 """
             }
@@ -32,26 +32,26 @@ nextflow_process {
         then {
             assertAll(
                 { assert process.success }
-                
-                
+
+
             )
         }
 
     }
 
-    
+
     test("vcf2maf - test - stub") {
 
         options "-stub"
 
         when {
             process {
                 """
-               
-                
+
+
                 input[0] = [
-                    [ id:'test'], // meta map
-                    file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+                    [ id:'test',case_id:'sample1',control_id:'sample2'], // meta map
+                    file(params.test_data_mskcc['genome_nexus']['sample2_sample1_annotated_vcf'], checkIfExists: true)
                     ]
                 """
             }
@@ -61,7 +61,7 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() }
-                
+
             )
         }
 

modules/msk/genomenexus/vcf2maf/tests/main.nf.test.snap

@@ -5,9 +5,11 @@
                 "0": [
                     [
                         {
-                            "id": "test"
+                            "id": "test",
+                            "case_id": "sample1",
+                            "control_id": "sample2"
                         },
-                        "test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "sample2_sample1_annotated.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -16,16 +18,22 @@
                 "maf": [
                     [
                         {
-                            "id": "test"
+                            "id": "test",
+                            "case_id": "sample1",
+                            "control_id": "sample2"
                         },
-                        "test.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "sample2_sample1_annotated.maf:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "versions": [
                     "versions.yml:md5,c60e8688d2d8110c4621c279a710a890"
                 ]
             }
         ],
-        "timestamp": "2024-06-24T11:56:07.276674"
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.2"
+        },
+        "timestamp": "2024-09-06T15:02:51.827835038"
     }
 }

subworkflows/msk/genome_nexus/main.nf

@@ -17,7 +17,7 @@ workflow GENOME_NEXUS {
 
 
     emit:
-    maf      = GENOMENEXUS_VCF2MAF.out.maf           // channel: [ val(meta), [ maf ] ]
+    maf      = GENOMENEXUS_ANNOTATIONPIPELINE.out.annotated_maf           // channel: [ val(meta), [ maf ] ]
     versions = ch_versions                     // channel: [ versions.yml ]
 }
 

subworkflows/msk/genome_nexus/tests/main.nf.test

@@ -10,31 +10,33 @@ nextflow_workflow {
     tag "subworkflows_nfcore"
     tag "subworkflows/genome_nexus"
     tag "subworkflows_msk"
-    
+
     tag "genomenexus"
     tag "genomenexus/vcf2maf"
     tag "genomenexus/annotationpipeline"
 
 
-    
+
     test("test - vcf - normal") {
 
         when {
             workflow {
                 """
-                
-                input[0] = [ [ id:'test' ], // meta map
-                        file(params.test_data['sarscov2']['illumina']['test_vcf'], checkIfExists: true)
+
+                input[0] = [ [ id:'test',case_id:'sample1',control_id:'sample2'], // meta map
+                        file(params.test_data_mskcc['genome_nexus']['sample2_sample1_annotated_vcf'], checkIfExists: true)
                         ]
                 """
             }
         }
 
+
+
         then {
             assertAll(
                 { assert workflow.success}
-                
+
             )
         }
     }
-}
+}