Added the rtgtools/vcfeval module

modules/rtgtools/vcfeval/main.nf

@@ -1,46 +1,18 @@
-// TODO nf-core: If in doubt look at other nf-core/modules to see how we are doing things! :)
-//               https://github.com/nf-core/modules/tree/master/modules
-//               You can also ask for help via your pull request or on the #modules channel on the nf-core Slack workspace:
-//               https://nf-co.re/join
-// TODO nf-core: A module file SHOULD only define input and output files as command-line parameters.
-//               All other parameters MUST be provided using the "task.ext" directive, see here:
-//               https://www.nextflow.io/docs/latest/process.html#ext
-//               where "task.ext" is a string.
-//               Any parameters that need to be evaluated in the context of a particular sample
-//               e.g. single-end/paired-end data MUST also be defined and evaluated appropriately.
-// TODO nf-core: Software that can be piped together SHOULD be added to separate module files
-//               unless there is a run-time, storage advantage in implementing in this way
-//               e.g. it's ok to have a single module for bwa to output BAM instead of SAM:
-//                 bwa mem | samtools view -B -T ref.fasta
-// TODO nf-core: Optional inputs are not currently supported by Nextflow. However, using an empty
-//               list (`[]`) instead of a file can be used to work around this issue.
-
 process RTGTOOLS_VCFEVAL {
     tag "$meta.id"
     label 'process_medium'
 
-    // TODO nf-core: List required Conda package(s).
-    //               Software MUST be pinned to channel (i.e. "bioconda"), version (i.e. "1.10").
-    //               For Conda, the build (i.e. "h9402c20_2") must be EXCLUDED to support installation on different operating systems.
-    // TODO nf-core: See section in main README for further information regarding finding and adding container addresses to the section below.
     conda (params.enable_conda ? "bioconda::rtg-tools=3.12.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/rtg-tools:3.12.1--hdfd78af_0':
         'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
 
     input:
-    // TODO nf-core: Where applicable all sample-specific information e.g. "id", "single_end", "read_group"
+    tuple val(meta), path(truth_vcf), path(truth_vcf_tbi), path(query_vcf), path(query_vcf_tbi), path(bed)
-    //               MUST be provided as an input via a Groovy Map called "meta".
+    path(sdf)
-    //               This information may not be required in some instances e.g. indexing reference genome files:
-    //               https://github.com/nf-core/modules/blob/master/modules/bwa/index/main.nf
-    // TODO nf-core: Where applicable please provide/convert compressed files as input/output
-    //               e.g. "*.fastq.gz" and NOT "*.fastq", "*.bam" and NOT "*.sam" etc.
-    tuple val(meta), path(bam)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
+    tuple val(meta), path("*.txt"), emit: results
-    tuple val(meta), path("*.bam"), emit: bam
-    // TODO nf-core: List additional required output channels/values here
     path "versions.yml"           , emit: versions
 
     when:
@@ -49,19 +21,35 @@ process RTGTOOLS_VCFEVAL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    // TODO nf-core: Where possible, a command MUST be provided to obtain the version number of the software e.g. 1.10
+    def regions = bed ? "--bed-regions=$bed" : ""
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
+    def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
-    //               Each software used MUST provide the software name and version number in the YAML version file (versions.yml)
+    
-    // TODO nf-core: It MUST be possible to pass additional parameters to the tool as a command-line string via the "task.ext.args" directive
+    sdf_basename = sdf.getBaseName().replace(".tar","")
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    tar_decomp = ""
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    if((sdf =~ /.tar.gz\b/).find() == true) {
-    // TODO nf-core: Please replace the example samtools command below with your module's command
+        tar_decomp = "tar -xzf $sdf"  
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    }
+
     """
+    $tar_decomp
+
+    $truth_index
+    $query_index
+
+    rtg vcfeval \\
+        $args \\
+        --baseline=$truth_vcf \\
+        $regions \\
+        --calls=$query_vcf \\
+        --output=$prefix \\
+        --template=$sdf_basename \\
+        --threads=$task.cpus \\
+        > ${prefix}_results.txt
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        rtgtools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}'))
+        rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}'))
     END_VERSIONS
     """
 }

modules/rtgtools/vcfeval/meta.yml

@@ -1,51 +1,63 @@
 name: "rtgtools_vcfeval"
-## TODO nf-core: Add a description of the module and list keywords
+description: The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set
-description: write your description here
 keywords:
-  - sort
+  - benchmarking
+  - vcf
+  - rtg-tools
 tools:
   - "rtgtools":
-      ## TODO nf-core: Add a description and other details for the software below
       description: "RealTimeGenomics Tools -- Utilities for accurate VCF comparison and manipulation"
-      homepage: "None"
+      homepage: "https://www.realtimegenomics.com/products/rtg-tools"
-      documentation: "None"
+      documentation: "https://github.com/RealTimeGenomics/rtg-tools"
-      tool_dev_url: "None"
+      tool_dev_url: "https://github.com/RealTimeGenomics/rtg-tools"
       doi: ""
       licence: "['BSD']"
 
-## TODO nf-core: Add a description of all of the variables used as input
 input:
-  # Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
+  - truth_vcf:
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
       type: file
-      description: BAM/CRAM/SAM file
+      description: A standard VCF to compare against
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.{vcf,vcf.gz}"
+  - truth_vcf_index:
+      type: file
+      description: The index of the standard VCF (optional)
+      pattern: "*.tbi"
+  - 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"
+  - bed:
+      type: file
+      description: The BED file of the called VCF
+      pattern: "*.bed"
+  - sdf:
+      type: folder/file
+      description: The SDF (RTG Sequence Data File) of the reference genome. Can be a folder or a tar-zipped folder.
+      pattern: "*.{,tar.gz}"
 
-## TODO nf-core: Add a description of all of the variables used as output
 output:
-  #Only when we have meta
   - meta:
       type: map
       description: |
         Groovy Map containing sample information
         e.g. [ id:'test', single_end:false ]
-  # 
   - versions:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  ## TODO nf-core: Delete / customise this example output
+  - results:
-  - bam:
       type: file
-      description: Sorted BAM/CRAM/SAM file
+      description: A text file containing the results of the benchmark
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.txt"
 
 authors:
   - "@nvnieuwk"

tests/config/test_data.config

@@ -132,6 +132,7 @@ params {
                 transcriptome_fasta                            = "${test_data_dir}/genomics/homo_sapiens/genome/transcriptome.fasta"
                 genome2_fasta                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome2.fasta"
                 genome_chain_gz                                = "${test_data_dir}/genomics/homo_sapiens/genome/genome.chain.gz"
+                genome_21_sdf                                  = "${test_data_dir}/genomics/homo_sapiens/genome/genome_sdf.tar.gz"
                 genome_21_fasta                                = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta"
                 genome_21_fasta_fai                            = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.fasta.fai"
                 genome_21_dict                                 = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome.dict"
@@ -263,6 +264,9 @@ params {
                 test2_haplotc_ann_vcf_gz                       = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz"
                 test2_haplotc_ann_vcf_gz_tbi                   = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.ann.vcf.gz.tbi"
 
+                test2_haplotc_vcf_gz                           = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz"
+                test2_haplotc_vcf_gz_tbi                       = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/haplotypecaller_calls/test2_haplotc.vcf.gz.tbi"
+
                 test2_recal                                    = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal"
                 test2_recal_idx                                = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.recal.idx"
                 test2_tranches                                 = "${test_data_dir}/genomics/homo_sapiens/illumina/gatk/variantrecalibrator/test2.tranches"

tests/modules/rtgtools/vcfeval/main.nf

@@ -7,9 +7,35 @@ include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf'
 workflow test_rtgtools_vcfeval {
     
     input = [
-        [ id:'test', single_end:false ], // meta map
+        [ id:'test' ], // meta map
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)        
     ]
 
-    RTGTOOLS_VCFEVAL ( input )
+    sdf = Channel.value(
+        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
+    )
+
+    RTGTOOLS_VCFEVAL ( input, sdf )
+}
+
+workflow test_rtgtools_vcfeval_no_index {
+    
+    input = [
+        [ id:'test' ], // meta map
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+        [],
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz'], checkIfExists: true),
+        [],
+        file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)        
+    ]
+
+    sdf = Channel.value(
+        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
+    )
+
+    RTGTOOLS_VCFEVAL ( input, sdf )
 }

tests/modules/rtgtools/vcfeval/test.yml

@@ -1,14 +1,21 @@
-## TODO nf-core: Please run the following command to build this file:
+- name: rtgtools vcfeval test_rtgtools_vcfeval
-#                nf-core modules create-test-yml rtgtools/vcfeval
+  command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c tests/config/nextflow.config
-- name: "rtgtools vcfeval"
-  command: nextflow run ./tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c ./tests/config/nextflow.config -c ./tests/modules/rtgtools/vcfeval/nextflow.config
   tags:
-    - "rtgtools"
+    - rtgtools
-    #
+    - rtgtools/vcfeval
-    - "rtgtools/vcfeval"
-    #
   files:
-    - path: "output/rtgtools/test.bam"
+    - path: output/rtgtools/test_results.txt
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+      md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
     - path: output/rtgtools/versions.yml
-      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b
+      md5sum: 270ed7a5a8e347b251eb4aa2198f98e8
+
+- name: rtgtools vcfeval test_rtgtools_vcfeval_no_index
+  command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_index -c tests/config/nextflow.config
+  tags:
+    - rtgtools
+    - rtgtools/vcfeval
+  files:
+    - path: output/rtgtools/test_results.txt
+      md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
+    - path: output/rtgtools/versions.yml
+      md5sum: 8d0407000988c78fa43fe5cfe3d4449d