wittyer input fix and version update (#5844)

modules/nf-core/wittyer/Dockerfile

@@ -0,0 +1,12 @@
+FROM mcr.microsoft.com/dotnet/sdk:6.0 as builder
+WORKDIR /src
+COPY . /src
+RUN cd Wittyer \
+    && dotnet publish -f net6.0 -r linux-x64 -c Release -o /output \
+    && chmod +x /output/Wittyer
+
+FROM mcr.microsoft.com/dotnet/runtime:6.0
+LABEL git_repository=https://git.illumina.com/DASTE/Ilmn.Das.App.Wittyer.git
+WORKDIR /opt/Wittyer
+RUN apt-get -y update && apt-get -y install tabix libunwind8 openssl procps
+COPY --from=builder /output /opt/Wittyer

modules/nf-core/wittyer/README.md

@@ -1,6 +1,7 @@
 # Updating the docker container and making a new module release
 
 witty.er is a commercial tool from Illumina. The container provided for the witty.er nf-core module is not provided nor supported by Illumina. Updating the witty.er versions in the container and pushing the update to Dockerhub needs to be done manually.
+NOTE: an updated version of Dockerfile than the official one in github is used to build nf-core/wittyer:0.5.2, which is inserted here ./Dockerfile.
 
 1. Navigate to the witty.er github repository. - [witty.er](https://github.com/Illumina/witty.er)
 2. Download the latest release.

modules/nf-core/wittyer/main.nf

@@ -2,15 +2,15 @@ process WITTYER {
     tag "$meta.id"
     label 'process_single'
 
-    container "nf-core/wittyer:0.3.3.0"
+    container "nf-core/wittyer:0.5.2.0"
 
     // Exit if running this module with -profile conda / -profile mamba
     if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) {
         error "WITTYER module does not support Conda. Please use Docker / Singularity / Podman instead."
     }
 
     input:
-    tuple val(meta), path(query_vcf), path(query_vcf_index), path(truth_vcf), path(truth_vcf_index), path(bed)
+    tuple val(meta), path(query_vcf), path(truth_vcf), path(bed)
 
     output:
     tuple val(meta),    path("*.json")         , emit: report
@@ -24,20 +24,18 @@ process WITTYER {
     script:
     def args  = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def regions = bed ? "--includeBed=$bed" : ""
-    if ("$truth_vcf" == "${prefix}.vcf.gz")         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
-    if ("$query_vcf" == "${prefix}.vcf.gz")         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
-    if ("$query_vcf_index" == "${prefix}.vcf.gz.tbi") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
-    if ("$query_vcf_index" == "${prefix}.vcf.gz.tbi") error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    def regions = bed ? "-b $bed" : ""
+    if ("$truth_vcf" == "${prefix}.vcf")         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    if ("$query_vcf" == "${prefix}.vcf")         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
 
     // dotnet /opt/Wittyer/Wittyer.dll might need to be replaced with new docker image
     """
     mkdir bench
 
     dotnet /opt/Wittyer/Wittyer.dll \\
-        --truthVcf=${truth_vcf} \\
-        --inputVcf=${query_vcf} \\
-        --outputDirectory=bench \\
+        -t ${truth_vcf} \\
+        -i ${query_vcf} \\
+        -o bench \\
         ${regions} \\
         ${args}
 
@@ -56,6 +54,9 @@ process WITTYER {
     stub:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    if ("$truth_vcf" == "${prefix}.vcf")         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+    if ("$query_vcf" == "${prefix}.vcf")         error "Input and output names are the same, set prefix in module configuration to disambiguate!"
+
     """
     touch ${prefix}.json
     echo "" | gzip > ${prefix}.vcf.gz

modules/nf-core/wittyer/meta.yml

@@ -21,19 +21,13 @@ input:
   - query_vcf:
       type: file
       description: A VCF with called variants to benchmark against the standard
-      pattern: "*.{vcf,vcf.gz}"
-  - query_vcf_index:
-      type: file
-      description: The index of the called VCF (optional)
-      pattern: "*.tbi"
+      pattern: "*.{vcf}"
+
   - truth_vcf:
       type: file
       description: A standard VCF to compare against
-      pattern: "*.{vcf,vcf.gz}"
-  - truth_vcf_index:
-      type: file
-      description: The index of the standard VCF (optional)
-      pattern: "*.tbi"
+      pattern: "*.{vcf}"
+
   - bed:
       type: file
       description: A BED file specifying regions to be included in the analysis (optional)

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

@@ -7,20 +7,42 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "wittyer"
+    tag "tabix/bgzip"
 
     test("human - simulatedSV - vcf_gz") {
+        config "./test.config"
 
+        setup {
+            run('TABIX_BGZIP', alias: 'TABIX_BGZIP_1') {
+                script "../../../nf-core/tabix/bgzip"
+
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.test_data['homo_sapiens']['illumina']['simulated_sv'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+
+            run('TABIX_BGZIP', alias: 'TABIX_BGZIP_2') {
+                script "../../../nf-core/tabix/bgzip"
+
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.test_data['homo_sapiens']['illumina']['simulated_sv2'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
         when {
             process {
                 """
-                input[0] = [
-                    [ id:'test', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv2'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv2_tbi'], checkIfExists: true),
-                    []
-                    ]
+                input[0] = TABIX_BGZIP_1.out.output.join(TABIX_BGZIP_2.out.output).map{meta, vcf1, vcf2 -> tuple(meta, vcf1, vcf2, [])}
                 """
             }
         }
@@ -37,20 +59,45 @@ nextflow_process {
         }
 
     }
+        test("human - simulatedSV - vcf_gz - bed") {
+        config "./test.config"
+
+        setup {
+            run('TABIX_BGZIP', alias: 'TABIX_BGZIP_1') {
+                script "../../../nf-core/tabix/bgzip"
+
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.test_data['homo_sapiens']['illumina']['simulated_sv'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
 
-    test("human - simulatedSV - vcf_gz - bed") {
+            run('TABIX_BGZIP', alias: 'TABIX_BGZIP_2') {
+                script "../../../nf-core/tabix/bgzip"
 
+                process {
+                    """
+                    input[0] = [
+                        [ id:'test' ], // meta map
+                        file(params.test_data['homo_sapiens']['illumina']['simulated_sv2'], checkIfExists: true)
+                    ]
+                    """
+                }
+            }
+        }
         when {
             process {
                 """
-                input[0] = [
-                    [ id:'test_bed', single_end:false ], // meta map
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv2'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv2_tbi'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
-                    ]
+                input[0] = TABIX_BGZIP_1.out.output
+                    .join(TABIX_BGZIP_2.out.output)
+                    .map{meta, vcf1, vcf2 ->
+                        tuple(meta, vcf1, vcf2,
+                            [file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)])
+                        }
                 """
             }
         }
@@ -59,10 +106,10 @@ nextflow_process {
             assertAll(
                 { assert process.success },
                 { assert snapshot(process.out).match() },
-                { assert snapshot(process.out.bench_vcf).match("bed_bench_vcf") },
-                { assert snapshot(process.out.bench_vcf_tbi).match("bed_bench_vcf_tbi") },
-                { assert snapshot(process.out.report).match("bed_report") },
-                { assert snapshot(process.out.version).match("bed_version") }
+                { assert snapshot(process.out.bench_vcf).match("bench2_vcf") },
+                { assert snapshot(process.out.bench_vcf_tbi).match("bench2_vcf_tbi") },
+                { assert snapshot(process.out.report).match("report2") },
+                { assert snapshot(process.out.version).match("version2") }
             )
         }
 
@@ -74,13 +121,11 @@ nextflow_process {
 
         when {
             process {
-                """             
+                """
                 input[0] = [
                     [ id:'test_stub', single_end:false ], // meta map
                     file(params.test_data['homo_sapiens']['illumina']['simulated_sv'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv_tbi'], checkIfExists: true),
                     file(params.test_data['homo_sapiens']['illumina']['simulated_sv2'], checkIfExists: true),
-                    file(params.test_data['homo_sapiens']['illumina']['simulated_sv2_tbi'], checkIfExists: true),
                     []
                     ]
                 """