From 3c076024435704be6ed13a0fa715a4c11d1c8825 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Wed, 4 May 2022 16:51:09 +0200
Subject: [PATCH 01/29] Added the version.yml

---
 modules/rtgtools/vcfeval/main.nf              | 67 +++++++++++++++++++
 modules/rtgtools/vcfeval/meta.yml             | 51 ++++++++++++++
 tests/config/pytest_modules.yml               |  4 ++
 tests/modules/rtgtools/vcfeval/main.nf        | 15 +++++
 .../modules/rtgtools/vcfeval/nextflow.config  |  5 ++
 tests/modules/rtgtools/vcfeval/test.yml       | 14 ++++
 6 files changed, 156 insertions(+)
 create mode 100644 modules/rtgtools/vcfeval/main.nf
 create mode 100644 modules/rtgtools/vcfeval/meta.yml
 create mode 100644 tests/modules/rtgtools/vcfeval/main.nf
 create mode 100644 tests/modules/rtgtools/vcfeval/nextflow.config
 create mode 100644 tests/modules/rtgtools/vcfeval/test.yml

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
new file mode 100644
index 00000000..4fd8aa4b
--- /dev/null
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -0,0 +1,67 @@
+// 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"
+    //               MUST be provided as an input via a Groovy Map called "meta".
+    //               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("*.bam"), emit: bam
+    // TODO nf-core: List additional required output channels/values here
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    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
+    //               If the software is unable to output a version number on the command-line then it can be manually specified
+    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
+    //               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
+    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
+    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
+    // TODO nf-core: Please replace the example samtools command below with your module's command
+    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    """
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        rtgtools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}'))
+    END_VERSIONS
+    """
+}
diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
new file mode 100644
index 00000000..512a7734
--- /dev/null
+++ b/modules/rtgtools/vcfeval/meta.yml
@@ -0,0 +1,51 @@
+name: "rtgtools_vcfeval"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+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"
+      documentation: "None"
+      tool_dev_url: "None"
+      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 ]
+  # 
+  ## TODO nf-core: Delete / customise this example input
+  - bam:
+      type: file
+      description: BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+## 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
+  - bam:
+      type: file
+      description: Sorted BAM/CRAM/SAM file
+      pattern: "*.{bam,cram,sam}"
+
+authors:
+  - "@nvnieuwk"
diff --git a/tests/config/pytest_modules.yml b/tests/config/pytest_modules.yml
index 32a28477..f702deda 100644
--- a/tests/config/pytest_modules.yml
+++ b/tests/config/pytest_modules.yml
@@ -1591,6 +1591,10 @@ rseqc/tin:
   - modules/rseqc/tin/**
   - tests/modules/rseqc/tin/**
 
+rtgtools/vcfeval:
+  - modules/rtgtools/vcfeval/**
+  - tests/modules/rtgtools/vcfeval/**
+
 salmon/index:
   - modules/salmon/index/**
   - tests/modules/salmon/index/**
diff --git a/tests/modules/rtgtools/vcfeval/main.nf b/tests/modules/rtgtools/vcfeval/main.nf
new file mode 100644
index 00000000..1a4297fc
--- /dev/null
+++ b/tests/modules/rtgtools/vcfeval/main.nf
@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf'
+
+workflow test_rtgtools_vcfeval {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    RTGTOOLS_VCFEVAL ( input )
+}
diff --git a/tests/modules/rtgtools/vcfeval/nextflow.config b/tests/modules/rtgtools/vcfeval/nextflow.config
new file mode 100644
index 00000000..50f50a7a
--- /dev/null
+++ b/tests/modules/rtgtools/vcfeval/nextflow.config
@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}
\ No newline at end of file
diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
new file mode 100644
index 00000000..862f4acd
--- /dev/null
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -0,0 +1,14 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml rtgtools/vcfeval
+- 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/vcfeval"
+    #
+  files:
+    - path: "output/rtgtools/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/rtgtools/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b

From 84b354ab6a110861db68e0d3eb6b0e746d014845 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 6 May 2022 14:23:40 +0200
Subject: [PATCH 02/29] Added the rtgtools/vcfeval module

---
 modules/rtgtools/vcfeval/main.nf        | 70 ++++++++++---------------
 modules/rtgtools/vcfeval/meta.yml       | 54 +++++++++++--------
 tests/config/test_data.config           |  4 ++
 tests/modules/rtgtools/vcfeval/main.nf  | 32 +++++++++--
 tests/modules/rtgtools/vcfeval/test.yml | 29 ++++++----
 5 files changed, 113 insertions(+), 76 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 4fd8aa4b..0b927a22 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/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"
-    //               MUST be provided as an input via a Groovy Map called "meta".
-    //               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)
+    tuple val(meta), path(truth_vcf), path(truth_vcf_tbi), path(query_vcf), path(query_vcf_tbi), path(bed)
+    path(sdf)
 
     output:
-    // TODO nf-core: Named file extensions MUST be emitted for ALL output channels
-    tuple val(meta), path("*.bam"), emit: bam
-    // TODO nf-core: List additional required output channels/values here
+    tuple val(meta), path("*.txt"), emit: results
     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
-    //               If the software is unable to output a version number on the command-line then it can be manually specified
-    //               e.g. https://github.com/nf-core/modules/blob/master/modules/homer/annotatepeaks/main.nf
-    //               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
-    // TODO nf-core: If the tool supports multi-threading then you MUST provide the appropriate parameter
-    //               using the Nextflow "task" variable e.g. "--threads $task.cpus"
-    // TODO nf-core: Please replace the example samtools command below with your module's command
-    // TODO nf-core: Please indent the command appropriately (4 spaces!!) to help with readability ;)
+    def regions = bed ? "--bed-regions=$bed" : ""
+    def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
+    def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
+    
+    sdf_basename = sdf.getBaseName().replace(".tar","")
+    tar_decomp = ""
+    if((sdf =~ /.tar.gz\b/).find() == true) {
+        tar_decomp = "tar -xzf $sdf"  
+    }
+
     """
+    $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
     """
 }
diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
index 512a7734..061ea876 100644
--- a/modules/rtgtools/vcfeval/meta.yml
+++ b/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: write your description here
+description: The VCFeval tool of RTG tools. It is used to evaluate called variants for agreement with a baseline variant set
 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"
-      documentation: "None"
-      tool_dev_url: "None"
+      homepage: "https://www.realtimegenomics.com/products/rtg-tools"
+      documentation: "https://github.com/RealTimeGenomics/rtg-tools"
+      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 ]
-  # 
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
+  - truth_vcf:
       type: file
-      description: BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      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"
+  - 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
-  - bam:
+  - results:
       type: file
-      description: Sorted BAM/CRAM/SAM file
-      pattern: "*.{bam,cram,sam}"
+      description: A text file containing the results of the benchmark
+      pattern: "*.txt"
 
 authors:
   - "@nvnieuwk"
diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 62e38c4d..5a204ae1 100644
--- a/tests/config/test_data.config
+++ b/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"
diff --git a/tests/modules/rtgtools/vcfeval/main.nf b/tests/modules/rtgtools/vcfeval/main.nf
index 1a4297fc..baf3c54d 100644
--- a/tests/modules/rtgtools/vcfeval/main.nf
+++ b/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
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+        [ 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_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 )
 }
diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index 862f4acd..73ed8cc6 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -1,14 +1,21 @@
-## TODO nf-core: Please run the following command to build this file:
-#                nf-core modules create-test-yml rtgtools/vcfeval
-- 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
+- name: rtgtools vcfeval test_rtgtools_vcfeval
+  command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval -c tests/config/nextflow.config
   tags:
-    - "rtgtools"
-    #
-    - "rtgtools/vcfeval"
-    #
+    - rtgtools
+    - rtgtools/vcfeval
   files:
-    - path: "output/rtgtools/test.bam"
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/rtgtools/test_results.txt
+      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

From 8c857dee3a3ea50a41e212ac2e8dda24b50c90f6 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 6 May 2022 16:16:57 +0200
Subject: [PATCH 03/29] Fixed the sdf folder fetching

---
 tests/config/test_data.config | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index 5a204ae1..f8d6b948 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -132,7 +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_sdf                                  = "${test_data_dir}/genomics/homo_sapiens/genome/chr21/sequence/genome_sdf.tar.gz"
                 genome_21_fasta                                = "${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"

From e271410017c52b6ada3008db313a702c8e005263 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Fri, 6 May 2022 16:21:32 +0200
Subject: [PATCH 04/29] Removed some whitespaces

---
 modules/rtgtools/vcfeval/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 0b927a22..9daadd05 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -24,11 +24,11 @@ process RTGTOOLS_VCFEVAL {
     def regions = bed ? "--bed-regions=$bed" : ""
     def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
     def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
-    
+
     sdf_basename = sdf.getBaseName().replace(".tar","")
     tar_decomp = ""
     if((sdf =~ /.tar.gz\b/).find() == true) {
-        tar_decomp = "tar -xzf $sdf"  
+        tar_decomp = "tar -xzf $sdf"
     }
 
     """

From 6fd9246aef346ba9975db049fcdbc9de7d6074f9 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Mon, 9 May 2022 08:07:33 +0200
Subject: [PATCH 05/29] Update modules/rtgtools/vcfeval/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
---
 modules/rtgtools/vcfeval/main.nf | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 9daadd05..97d96d89 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -8,7 +8,8 @@ process RTGTOOLS_VCFEVAL {
         'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(truth_vcf), path(truth_vcf_tbi), path(query_vcf), path(query_vcf_tbi), path(bed)
+    tuple val(meta),  path(query_vcf), path(query_vcf_tbi), path(bed)
+    tuple path(truth_vcf), path(truth_vcf_tbi),
     path(sdf)
 
     output:

From d18af7358a7b3cebb59a81a5b71414e40fc39256 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 9 May 2022 09:20:42 +0200
Subject: [PATCH 06/29] Moved untarring the genome sdf folder to the test
 itself

---
 modules/rtgtools/vcfeval/main.nf       | 14 ++------
 tests/modules/rtgtools/vcfeval/main.nf | 46 +++++++++++++++++++-------
 2 files changed, 37 insertions(+), 23 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 97d96d89..83895b64 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -8,8 +8,8 @@ process RTGTOOLS_VCFEVAL {
         'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta),  path(query_vcf), path(query_vcf_tbi), path(bed)
-    tuple path(truth_vcf), path(truth_vcf_tbi),
+    tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(bed)
+    tuple path(truth_vcf), path(truth_vcf_tbi)
     path(sdf)
 
     output:
@@ -26,15 +26,7 @@ process RTGTOOLS_VCFEVAL {
     def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
     def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
 
-    sdf_basename = sdf.getBaseName().replace(".tar","")
-    tar_decomp = ""
-    if((sdf =~ /.tar.gz\b/).find() == true) {
-        tar_decomp = "tar -xzf $sdf"
-    }
-
     """
-    $tar_decomp
-
     $truth_index
     $query_index
 
@@ -44,7 +36,7 @@ process RTGTOOLS_VCFEVAL {
         $regions \\
         --calls=$query_vcf \\
         --output=$prefix \\
-        --template=$sdf_basename \\
+        --template=$sdf \\
         --threads=$task.cpus \\
         > ${prefix}_results.txt
 
diff --git a/tests/modules/rtgtools/vcfeval/main.nf b/tests/modules/rtgtools/vcfeval/main.nf
index baf3c54d..35a2206b 100644
--- a/tests/modules/rtgtools/vcfeval/main.nf
+++ b/tests/modules/rtgtools/vcfeval/main.nf
@@ -3,39 +3,61 @@
 nextflow.enable.dsl = 2
 
 include { RTGTOOLS_VCFEVAL } from '../../../../modules/rtgtools/vcfeval/main.nf'
+include { UNTAR } from '../../../modules/untar/main.nf'
 
 workflow test_rtgtools_vcfeval {
     
     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_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)        
     ]
 
-    sdf = Channel.value(
-        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
-    )
+    truth = [
+        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)
+    ]
 
-    RTGTOOLS_VCFEVAL ( input, sdf )
+    compressed_sdf = [
+        [],
+        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
+    ]
+
+    sdf = UNTAR( compressed_sdf ).untar
+        .map({
+            meta, folder ->
+                folder
+        })
+    
+
+    RTGTOOLS_VCFEVAL ( input, truth, 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'])
-    )
+    truth = [
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
+        []
+    ]
 
-    RTGTOOLS_VCFEVAL ( input, sdf )
+    compressed_sdf = [
+        [],
+        file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
+    ]
+
+    sdf = UNTAR( compressed_sdf ).untar
+        .map({
+            meta, folder ->
+                [folder]
+        })
+
+    RTGTOOLS_VCFEVAL ( input, truth, sdf )
 }

From bf91f9dd9b62c98175d962bd51dbe2d0b7f91d4c Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Mon, 9 May 2022 14:54:52 +0200
Subject: [PATCH 07/29] update arriba module

---
 modules/arriba/main.nf  | 32 ++++++++++++++++++++++++++++----
 modules/arriba/meta.yml | 22 +++++++++++++++++++++-
 2 files changed, 49 insertions(+), 5 deletions(-)

diff --git a/modules/arriba/main.nf b/modules/arriba/main.nf
index e0d30b45..b7883acd 100644
--- a/modules/arriba/main.nf
+++ b/modules/arriba/main.nf
@@ -2,15 +2,20 @@ process ARRIBA {
     tag "$meta.id"
     label 'process_medium'
 
-    conda (params.enable_conda ? "bioconda::arriba=2.1.0" : null)
+    conda (params.enable_conda ? "bioconda::arriba=2.2.1" : null)
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/arriba:2.1.0--h3198e80_1' :
-        'quay.io/biocontainers/arriba:2.1.0--h3198e80_1' }"
+        'https://depot.galaxyproject.org/singularity/arriba:2.2.1--hecb563c_2' :
+        'quay.io/biocontainers/arriba:2.2.1--hecb563c_2' }"
 
     input:
     tuple val(meta), path(bam)
     path fasta
     path gtf
+    path blacklist
+    path known_fusions
+    path structural_variants
+    path tags
+    path protein_domains
 
     output:
     tuple val(meta), path("*.fusions.tsv")          , emit: fusions
@@ -23,7 +28,12 @@ process ARRIBA {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def blacklist = (args.contains('-b')) ? '' : '-f blacklist'
+    def blacklist = blacklist ? "-b $blacklist" : "-f blacklist"
+    def known_fusions = known_fusions ? "-k $known_fusions" : ""
+    def structural_variants = structural_variants ? "-d $structual_variants" : ""
+    def tags = tags ? "-t $tags" : ""
+    def protein_domains = protein_domains ? "-p $protein_domains" : ""
+
     """
     arriba \\
         -x $bam \\
@@ -32,6 +42,10 @@ process ARRIBA {
         -o ${prefix}.fusions.tsv \\
         -O ${prefix}.fusions.discarded.tsv \\
         $blacklist \\
+        $known_fusions \\
+        $structural_variants \\
+        $tags \\
+        $protein_domains \\
         $args
 
     cat <<-END_VERSIONS > versions.yml
@@ -39,4 +53,14 @@ process ARRIBA {
         arriba: \$(arriba -h | grep 'Version:' 2>&1 |  sed 's/Version:\s//')
     END_VERSIONS
     """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    echo stub > ${prefix}.fusions.tsv
+    echo stub > ${prefix}.fusions.discarded.tsv
+
+    echo "${task.process}:" > versions.yml
+    echo ' arriba: 2.2.1' >> versions.yml
+    """
 }
diff --git a/modules/arriba/meta.yml b/modules/arriba/meta.yml
index 4bde2f08..119dd912 100644
--- a/modules/arriba/meta.yml
+++ b/modules/arriba/meta.yml
@@ -30,6 +30,26 @@ input:
       type: file
       description: Annotation GTF file
       pattern: "*.{gtf}"
+  - blacklist:
+      type: file
+      description: Blacklist file
+      pattern: "*.{tsv}"
+  - known_fusions:
+      type: file
+      description: Known fusions file
+      pattern: "*.{tsv}"
+  - structural_variants:
+      type: file
+      description: Structural variants file
+      pattern: "*.{tsv}"
+  - tags:
+      type: file
+      description: Tags file
+      pattern: "*.{tsv}"
+  - protein_domains:
+      type: file
+      description: Protein domains file
+      pattern: "*.{gff3}"
 
 output:
   - meta:
@@ -51,4 +71,4 @@ output:
       pattern: "*.{fusions.discarded.tsv}"
 
 authors:
-  - "@praveenraj2018"
+  - "@praveenraj2018,@rannick"

From eed874ace79a40a3ce1a50b7d1df560cefecfed4 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Mon, 9 May 2022 14:55:18 +0200
Subject: [PATCH 08/29] update arriba tests

---
 tests/modules/arriba/main.nf  | 4 ++--
 tests/modules/arriba/test.yml | 5 +++--
 2 files changed, 5 insertions(+), 4 deletions(-)

diff --git a/tests/modules/arriba/main.nf b/tests/modules/arriba/main.nf
index 60741275..205adf0f 100644
--- a/tests/modules/arriba/main.nf
+++ b/tests/modules/arriba/main.nf
@@ -20,7 +20,7 @@ workflow test_arriba_single_end {
 
     STAR_GENOMEGENERATE ( fasta, gtf )
     STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
+    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf , [], [], [], [], [])
 }
 
 workflow test_arriba_paired_end {
@@ -38,5 +38,5 @@ workflow test_arriba_paired_end {
 
     STAR_GENOMEGENERATE ( fasta, gtf )
     STAR_ALIGN ( input, STAR_GENOMEGENERATE.out.index, gtf, star_ignore_sjdbgtf, seq_platform, seq_center )
-    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf )
+    ARRIBA ( STAR_ALIGN.out.bam, fasta, gtf, [], [], [], [], [])
 }
diff --git a/tests/modules/arriba/test.yml b/tests/modules/arriba/test.yml
index 52743167..c2032df3 100644
--- a/tests/modules/arriba/test.yml
+++ b/tests/modules/arriba/test.yml
@@ -13,7 +13,7 @@
     - path: output/star/star/SA
       md5sum: 8c3edc46697b72c9e92440d4cf43506c
     - path: output/star/star/SAindex
-      md5sum: 9f085c626553b1c52f2827421972ac10
+      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
     - path: output/star/star/chrLength.txt
       md5sum: c81f40f27e72606d7d07097c1d56a5b5
     - path: output/star/star/chrName.txt
@@ -29,7 +29,7 @@
     - path: output/star/star/geneInfo.tab
       md5sum: 8b608537307443ffaee4927d2b428805
     - path: output/star/star/genomeParameters.txt
-      md5sum: 9e42067b1ec70b773257529230dd7b3a
+      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
     - path: output/star/star/sjdbInfo.txt
       md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
     - path: output/star/star/sjdbList.fromGTF.out.tab
@@ -39,6 +39,7 @@
     - path: output/star/star/transcriptInfo.tab
       md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
     - path: output/star/test.Aligned.out.bam
+      md5sum: b9f5e2f6a624b64c300fe25dc3ac801f
     - path: output/star/test.Log.final.out
     - path: output/star/test.Log.out
     - path: output/star/test.Log.progress.out

From ac3034696bba9adb98841bda8e9f085ded059c68 Mon Sep 17 00:00:00 2001
From: Annick Renevey <47788523+rannick@users.noreply.github.com>
Date: Mon, 9 May 2022 15:19:16 +0200
Subject: [PATCH 09/29] update md5sum

---
 tests/modules/arriba/test.yml | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/tests/modules/arriba/test.yml b/tests/modules/arriba/test.yml
index c2032df3..b1e34db0 100644
--- a/tests/modules/arriba/test.yml
+++ b/tests/modules/arriba/test.yml
@@ -4,7 +4,7 @@
     - arriba
   files:
     - path: output/arriba/test.fusions.discarded.tsv
-      md5sum: cad8c215b938d1e45b747a5b7898a4c2
+      md5sum: 7602ab4ccbbb0c54fbca12a942877e6d
     - path: output/arriba/test.fusions.tsv
       md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
     - path: output/star/star/Genome
@@ -13,7 +13,7 @@
     - path: output/star/star/SA
       md5sum: 8c3edc46697b72c9e92440d4cf43506c
     - path: output/star/star/SAindex
-      md5sum: 2a0c675d8b91d8e5e8c1826d3500482e
+      md5sum: 9f085c626553b1c52f2827421972ac10
     - path: output/star/star/chrLength.txt
       md5sum: c81f40f27e72606d7d07097c1d56a5b5
     - path: output/star/star/chrName.txt
@@ -29,7 +29,7 @@
     - path: output/star/star/geneInfo.tab
       md5sum: 8b608537307443ffaee4927d2b428805
     - path: output/star/star/genomeParameters.txt
-      md5sum: 3097677f4d8b2cb66770b9e55d343a7f
+      md5sum: 9e42067b1ec70b773257529230dd7b3a
     - path: output/star/star/sjdbInfo.txt
       md5sum: 5690ea9d9f09f7ff85b7fd47bd234903
     - path: output/star/star/sjdbList.fromGTF.out.tab
@@ -39,7 +39,7 @@
     - path: output/star/star/transcriptInfo.tab
       md5sum: 0c3a5adb49d15e5feff81db8e29f2e36
     - path: output/star/test.Aligned.out.bam
-      md5sum: b9f5e2f6a624b64c300fe25dc3ac801f
+      md5sum: 4fa079d11f8938e51015e3e477fa7149
     - path: output/star/test.Log.final.out
     - path: output/star/test.Log.out
     - path: output/star/test.Log.progress.out
@@ -51,7 +51,7 @@
     - arriba
   files:
     - path: output/arriba/test.fusions.discarded.tsv
-      md5sum: 85e36c887464e4deaa65f45174d3b8fd
+      md5sum: cdc6cfbc75e68ce29a766f50f390274d
     - path: output/arriba/test.fusions.tsv
       md5sum: 7c3383f7eb6d79b84b0bd30a7ef02d70
     - path: output/star/star/Genome

From d6dd4c2e2d094b18c2027bc636eaa88358381fb4 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Mon, 9 May 2022 15:35:16 +0200
Subject: [PATCH 10/29] Update tests/modules/rtgtools/vcfeval/test.yml

Co-authored-by: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
---
 tests/modules/rtgtools/vcfeval/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index 73ed8cc6..025581a6 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -18,4 +18,3 @@
     - path: output/rtgtools/test_results.txt
       md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
     - path: output/rtgtools/versions.yml
-      md5sum: 8d0407000988c78fa43fe5cfe3d4449d

From f6262b4a103124c6ebf1bd650a297e6942f437ec Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 9 May 2022 15:47:07 +0200
Subject: [PATCH 11/29] fixed some issues

---
 modules/rtgtools/vcfeval/main.nf        |  3 ++-
 modules/rtgtools/vcfeval/meta.yml       |  6 +++---
 tests/modules/rtgtools/vcfeval/main.nf  | 12 +++++++-----
 tests/modules/rtgtools/vcfeval/test.yml |  1 -
 4 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 83895b64..c7e8a12e 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -8,8 +8,9 @@ process RTGTOOLS_VCFEVAL {
         'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(query_vcf), path(query_vcf_tbi), path(bed)
+    tuple val(meta), path(query_vcf), path(query_vcf_tbi) 
     tuple path(truth_vcf), path(truth_vcf_tbi)
+    path(bed)
     path(sdf)
 
     output:
diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
index 061ea876..36e1b290 100644
--- a/modules/rtgtools/vcfeval/meta.yml
+++ b/modules/rtgtools/vcfeval/meta.yml
@@ -40,9 +40,9 @@ input:
       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}"
+      type: file
+      description: The SDF (RTG Sequence Data File) folder of the reference genome
+      pattern: "*"
 
 output:
   - meta:
diff --git a/tests/modules/rtgtools/vcfeval/main.nf b/tests/modules/rtgtools/vcfeval/main.nf
index 35a2206b..9a28e2d7 100644
--- a/tests/modules/rtgtools/vcfeval/main.nf
+++ b/tests/modules/rtgtools/vcfeval/main.nf
@@ -10,8 +10,7 @@ workflow test_rtgtools_vcfeval {
     input = [
         [ id:'test' ], // meta map
         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)        
+        file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_vcf_gz_tbi'], checkIfExists: true),        
     ]
 
     truth = [
@@ -19,6 +18,8 @@ workflow test_rtgtools_vcfeval {
         file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
     ]
 
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
     compressed_sdf = [
         [],
         file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
@@ -31,7 +32,7 @@ workflow test_rtgtools_vcfeval {
         })
     
 
-    RTGTOOLS_VCFEVAL ( input, truth, sdf )
+    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
 }
 
 workflow test_rtgtools_vcfeval_no_index {
@@ -40,7 +41,6 @@ workflow test_rtgtools_vcfeval_no_index {
         [ id:'test' ], // meta map
         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)        
     ]
 
     truth = [
@@ -48,6 +48,8 @@ workflow test_rtgtools_vcfeval_no_index {
         []
     ]
 
+    bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
     compressed_sdf = [
         [],
         file(params.test_data['homo_sapiens']['genome']['genome_21_sdf'])
@@ -59,5 +61,5 @@ workflow test_rtgtools_vcfeval_no_index {
                 [folder]
         })
 
-    RTGTOOLS_VCFEVAL ( input, truth, sdf )
+    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
 }
diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index 025581a6..86252c68 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -7,7 +7,6 @@
     - path: output/rtgtools/test_results.txt
       md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
     - path: output/rtgtools/versions.yml
-      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

From 1b63d03f8e6d5b964c3f5215cb3c99f5604098ed Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 9 May 2022 15:51:19 +0200
Subject: [PATCH 12/29] adjusted the bed variable name

---
 modules/rtgtools/vcfeval/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index c7e8a12e..a2f5244f 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -10,7 +10,7 @@ process RTGTOOLS_VCFEVAL {
     input:
     tuple val(meta), path(query_vcf), path(query_vcf_tbi) 
     tuple path(truth_vcf), path(truth_vcf_tbi)
-    path(bed)
+    path(truth_regions)
     path(sdf)
 
     output:
@@ -23,7 +23,7 @@ process RTGTOOLS_VCFEVAL {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def regions = bed ? "--bed-regions=$bed" : ""
+    def regions = truth_regions ? "--bed-regions=$truth_regions" : ""
     def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
     def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
 

From bd7e1414a453af7605a67dcc166e3a98aeec3689 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Mon, 9 May 2022 15:55:48 +0200
Subject: [PATCH 13/29] Fixed meta.yml

---
 modules/rtgtools/vcfeval/main.nf  | 2 +-
 modules/rtgtools/vcfeval/meta.yml | 4 ++--
 2 files changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index a2f5244f..1d981204 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -8,7 +8,7 @@ process RTGTOOLS_VCFEVAL {
         'quay.io/biocontainers/rtg-tools:3.12.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(query_vcf), path(query_vcf_tbi) 
+    tuple val(meta), path(query_vcf), path(query_vcf_tbi)
     tuple path(truth_vcf), path(truth_vcf_tbi)
     path(truth_regions)
     path(sdf)
diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
index 36e1b290..baf9e87a 100644
--- a/modules/rtgtools/vcfeval/meta.yml
+++ b/modules/rtgtools/vcfeval/meta.yml
@@ -35,9 +35,9 @@ input:
       type: file
       description: The index of the called VCF (optional)
       pattern: "*.tbi"
-  - bed:
+  - truth_regions:
       type: file
-      description: The BED file of the called VCF
+      description: The BED file containing the truth regions
       pattern: "*.bed"
   - sdf:
       type: file

From c69d5cc23e76d5560b763111a167a15d8cd08424 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 09:35:42 +0200
Subject: [PATCH 14/29] Added evaluation-regions and adjusted the output to now
 contain all output (and not only the summary)

---
 modules/rtgtools/vcfeval/main.nf        | 14 ++---
 modules/rtgtools/vcfeval/meta.yml       | 10 ++--
 tests/modules/rtgtools/vcfeval/main.nf  | 14 +++--
 tests/modules/rtgtools/vcfeval/test.yml | 69 ++++++++++++++++++++++---
 4 files changed, 87 insertions(+), 20 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 1d981204..4e27ed6b 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -11,19 +11,21 @@ process RTGTOOLS_VCFEVAL {
     tuple val(meta), path(query_vcf), path(query_vcf_tbi)
     tuple path(truth_vcf), path(truth_vcf_tbi)
     path(truth_regions)
+    path(evaluation_regions)
     path(sdf)
 
     output:
-    tuple val(meta), path("*.txt"), emit: results
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("${task.ext.prefix ?: meta.id}/*")    , emit: results
+    path "versions.yml"                                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
+    def args = task.ext.args ?: ""
     def prefix = task.ext.prefix ?: "${meta.id}"
-    def regions = truth_regions ? "--bed-regions=$truth_regions" : ""
+    def bed_regions = truth_regions ? "--bed-regions=$truth_regions" : ""
+    def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : ""
     def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
     def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
 
@@ -34,12 +36,12 @@ process RTGTOOLS_VCFEVAL {
     rtg vcfeval \\
         $args \\
         --baseline=$truth_vcf \\
-        $regions \\
+        $bed_regions \\
+        $eval_regions \\
         --calls=$query_vcf \\
         --output=$prefix \\
         --template=$sdf \\
         --threads=$task.cpus \\
-        > ${prefix}_results.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
index baf9e87a..1f448fdc 100644
--- a/modules/rtgtools/vcfeval/meta.yml
+++ b/modules/rtgtools/vcfeval/meta.yml
@@ -37,7 +37,11 @@ input:
       pattern: "*.tbi"
   - truth_regions:
       type: file
-      description: The BED file containing the truth regions
+      description: A BED file containining the strict regions where VCFeval should only evaluate the fully overlapping variants (optional)
+      pattern: "*.bed"
+  - evaluation_regions:
+      type: file
+      description: A BED file containing the regions where VCFeval will evaluate every fully and partially overlapping variant (optional)
       pattern: "*.bed"
   - sdf:
       type: file
@@ -56,8 +60,8 @@ output:
       pattern: "versions.yml"
   - results:
       type: file
-      description: A text file containing the results of the benchmark
-      pattern: "*.txt"
+      description: A folder containing all results of the evaluation
+      pattern: "*"
 
 authors:
   - "@nvnieuwk"
diff --git a/tests/modules/rtgtools/vcfeval/main.nf b/tests/modules/rtgtools/vcfeval/main.nf
index 9a28e2d7..9a1c3c71 100644
--- a/tests/modules/rtgtools/vcfeval/main.nf
+++ b/tests/modules/rtgtools/vcfeval/main.nf
@@ -18,7 +18,9 @@ workflow test_rtgtools_vcfeval {
         file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true)
     ]
 
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    truth_regions = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+
+    evaluation_regions = file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true)
 
     compressed_sdf = [
         [],
@@ -32,10 +34,10 @@ workflow test_rtgtools_vcfeval {
         })
     
 
-    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
+    RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
 }
 
-workflow test_rtgtools_vcfeval_no_index {
+workflow test_rtgtools_vcfeval_no_optional_inputs {
     
     input = [
         [ id:'test' ], // meta map
@@ -48,7 +50,9 @@ workflow test_rtgtools_vcfeval_no_index {
         []
     ]
 
-    bed = file(params.test_data['homo_sapiens']['genome']['genome_21_multi_interval_bed'], checkIfExists: true)
+    truth_regions = []
+
+    evaluation_regions = []
 
     compressed_sdf = [
         [],
@@ -61,5 +65,5 @@ workflow test_rtgtools_vcfeval_no_index {
                 [folder]
         })
 
-    RTGTOOLS_VCFEVAL ( input, truth, bed, sdf )
+    RTGTOOLS_VCFEVAL ( input, truth, truth_regions, evaluation_regions, sdf )
 }
diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index 86252c68..06d39701 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -4,16 +4,73 @@
     - rtgtools
     - rtgtools/vcfeval
   files:
-    - path: output/rtgtools/test_results.txt
-      md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
+    - path: output/rtgtools/test/done
+      md5sum: 8b5623b26ee9b8722816afbec270bff0
+    - path: output/rtgtools/test/fn.vcf.gz
+      md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
+    - path: output/rtgtools/test/fn.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/fp.vcf.gz
+      md5sum: 1417bb8ac7a0e202df660291a74de0db
+    - path: output/rtgtools/test/fp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/non_snp_roc.tsv.gz
+      md5sum: 8fd51a1e5084d15d43880cb1e31a0180
+    - path: output/rtgtools/test/phasing.txt
+      md5sum: 133677dbd8be657439ea2b03fdfb8795
+    - path: output/rtgtools/test/progress
+    - path: output/rtgtools/test/snp_roc.tsv.gz
+      md5sum: ff2ece544adfcefaa06da054876a9ae3
+    - path: output/rtgtools/test/summary.txt
+      md5sum: f4c8df93c8bdab603036bbc27b4a28c3
+    - path: output/rtgtools/test/tp-baseline.vcf.gz
+      md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
+    - path: output/rtgtools/test/tp-baseline.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/tp.vcf.gz
+      md5sum: 1417bb8ac7a0e202df660291a74de0db
+    - path: output/rtgtools/test/tp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/vcfeval.log
+    - path: output/rtgtools/test/weighted_roc.tsv.gz
+      md5sum: 5209f1bdeb03704714ae92b183d08e0f
     - path: output/rtgtools/versions.yml
 
-- 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
+- name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
+  command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config
   tags:
     - rtgtools
     - rtgtools/vcfeval
   files:
-    - path: output/rtgtools/test_results.txt
-      md5sum: 2e011aa6e54d258fcc3b45b2dda02ae4
+    - path: output/rtgtools/test/done
+      md5sum: 8b5623b26ee9b8722816afbec270bff0
+    - path: output/rtgtools/test/fn.vcf.gz
+      md5sum: e51420e4be520ae309a2384830bf4c15
+    - path: output/rtgtools/test/fn.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/fp.vcf.gz
+      md5sum: 7d818cf526983de6cbb5cf517c44a8f7
+    - path: output/rtgtools/test/fp.vcf.gz.tbi
+      md5sum: 092a7a3162e7cff25d273525751eb284
+    - path: output/rtgtools/test/non_snp_roc.tsv.gz
+      md5sum: a535fb80081b43b19788347152b6b8b4
+    - path: output/rtgtools/test/phasing.txt
+      md5sum: 133677dbd8be657439ea2b03fdfb8795
+    - path: output/rtgtools/test/progress
+    - path: output/rtgtools/test/snp_roc.tsv.gz
+      md5sum: 6006656c4a534935c7873398287bc110
+    - path: output/rtgtools/test/summary.txt
+      md5sum: f33feb32f84958fb931063044fba369b
+    - path: output/rtgtools/test/tp-baseline.vcf.gz
+      md5sum: ed68ea567a26d3b864ada79e9253bc97
+    - path: output/rtgtools/test/tp-baseline.vcf.gz.tbi
+      md5sum: 3518deff814eed340b0f5386294b5879
+    - path: output/rtgtools/test/tp.vcf.gz
+      md5sum: 92fd51021d101c99da066324655d24c9
+    - path: output/rtgtools/test/tp.vcf.gz.tbi
+      md5sum: 169063c1f570f0055059f3cb3518a8b4
+    - path: output/rtgtools/test/vcfeval.log
+    - path: output/rtgtools/test/weighted_roc.tsv.gz
+      md5sum: 0ba825084bd6b94accdf54fff23ea18c
     - path: output/rtgtools/versions.yml
+

From f0e8f6ce4d748c3eacceedc1f2821d885df47f70 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 09:36:54 +0200
Subject: [PATCH 15/29] Linting

---
 tests/modules/rtgtools/vcfeval/test.yml | 1 -
 1 file changed, 1 deletion(-)

diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index 06d39701..c1cbf236 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -73,4 +73,3 @@
     - path: output/rtgtools/test/weighted_roc.tsv.gz
       md5sum: 0ba825084bd6b94accdf54fff23ea18c
     - path: output/rtgtools/versions.yml
-

From 42fbf80c7273050a1c6de3e1d179bf1c8704ad15 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 09:57:49 +0200
Subject: [PATCH 16/29] Fixed a test issue with wrong md5sum

---
 tests/modules/rtgtools/vcfeval/test.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index c1cbf236..ea76cb15 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -5,7 +5,7 @@
     - rtgtools/vcfeval
   files:
     - path: output/rtgtools/test/done
-      md5sum: 8b5623b26ee9b8722816afbec270bff0
+      contains: - Finished Succesfully in
     - path: output/rtgtools/test/fn.vcf.gz
       md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
     - path: output/rtgtools/test/fn.vcf.gz.tbi
@@ -43,7 +43,7 @@
     - rtgtools/vcfeval
   files:
     - path: output/rtgtools/test/done
-      md5sum: 8b5623b26ee9b8722816afbec270bff0
+      contains: - Finished Succesfully in
     - path: output/rtgtools/test/fn.vcf.gz
       md5sum: e51420e4be520ae309a2384830bf4c15
     - path: output/rtgtools/test/fn.vcf.gz.tbi

From 96c3f895b9c8bba0ea629bb31869a14aaf2e9c83 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 10:19:13 +0200
Subject: [PATCH 17/29] test issue fix?

---
 tests/modules/rtgtools/vcfeval/test.yml | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index ea76cb15..299fe91c 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -5,7 +5,8 @@
     - rtgtools/vcfeval
   files:
     - path: output/rtgtools/test/done
-      contains: - Finished Succesfully in
+      contains: 
+        - Finished Succesfully in
     - path: output/rtgtools/test/fn.vcf.gz
       md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
     - path: output/rtgtools/test/fn.vcf.gz.tbi
@@ -43,7 +44,8 @@
     - rtgtools/vcfeval
   files:
     - path: output/rtgtools/test/done
-      contains: - Finished Succesfully in
+      contains: 
+        - Finished Succesfully in
     - path: output/rtgtools/test/fn.vcf.gz
       md5sum: e51420e4be520ae309a2384830bf4c15
     - path: output/rtgtools/test/fn.vcf.gz.tbi

From 60086196038fd5e0cf9006a9aa6d797cb9c4380a Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 10:20:54 +0200
Subject: [PATCH 18/29] test issue fix?

---
 tests/modules/rtgtools/vcfeval/test.yml | 4 ----
 1 file changed, 4 deletions(-)

diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index 299fe91c..194e0cac 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -5,8 +5,6 @@
     - rtgtools/vcfeval
   files:
     - path: output/rtgtools/test/done
-      contains: 
-        - Finished Succesfully in
     - path: output/rtgtools/test/fn.vcf.gz
       md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
     - path: output/rtgtools/test/fn.vcf.gz.tbi
@@ -44,8 +42,6 @@
     - rtgtools/vcfeval
   files:
     - path: output/rtgtools/test/done
-      contains: 
-        - Finished Succesfully in
     - path: output/rtgtools/test/fn.vcf.gz
       md5sum: e51420e4be520ae309a2384830bf4c15
     - path: output/rtgtools/test/fn.vcf.gz.tbi

From 3a064b0a9952e6e0f00cc8570d2fd72b11aff449 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 12:05:42 +0200
Subject: [PATCH 19/29] Split the output to different channels

---
 modules/rtgtools/vcfeval/main.nf        | 10 +++-
 modules/rtgtools/vcfeval/meta.yml       | 66 ++++++++++++++++++++++--
 tests/modules/rtgtools/vcfeval/test.yml | 68 ++++++++++++-------------
 3 files changed, 105 insertions(+), 39 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 4e27ed6b..1963bfe0 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -15,8 +15,12 @@ process RTGTOOLS_VCFEVAL {
     path(sdf)
 
     output:
-    tuple val(meta), path("${task.ext.prefix ?: meta.id}/*")    , emit: results
-    path "versions.yml"                                         , emit: versions
+    tuple val(meta), path("done"), path("progress"), path("*.log") , emit: logs
+    tuple val(meta), path("*{tp,fn,fp,baseline}.vcf.gz.tbi"), path("*{tp,fn,fp,baseline}.vcf.gz") , emit: vcf
+    tuple val(meta), path("*.tsv.gz")           , emit: roc    
+    tuple val(meta), path("summary.txt")        , emit: summary
+    tuple val(meta), path("phasing.txt")        , emit: phasing
+    path "versions.yml"                         , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -43,6 +47,8 @@ process RTGTOOLS_VCFEVAL {
         --template=$sdf \\
         --threads=$task.cpus \\
 
+    mv ${prefix}/* .
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         rtg-tools: \$(echo \$(rtg version | head -n 1 | awk '{print \$4}'))
diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
index 1f448fdc..e568852c 100644
--- a/modules/rtgtools/vcfeval/meta.yml
+++ b/modules/rtgtools/vcfeval/meta.yml
@@ -58,10 +58,70 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - results:
+  - done:
       type: file
-      description: A folder containing all results of the evaluation
-      pattern: "*"
+      description: A file containing the message on succesful completion
+      pattern: "done"
+  - progress:
+      type: file
+      description: A file containing the simplified logging of the process
+      pattern: "progress"
+  - vcfeval_log:
+      type: file
+      description: A file containing the extended logging of the process
+      pattern: "*.log"
+  - false_negatives_vcf:
+      type: file
+      description: A VCF file containing the false negative variants
+      pattern: "fn.vcf.gz"
+  - false_negatives_index:
+      type: file
+      description: The index file for the false negatives' VCF file
+      pattern: "fn.vcf.gz.tbi"
+  - false_positive_vcf:
+      type: file
+      description: A VCF file containing the false positive variants
+      pattern: "fp.vcf.gz"
+  - false_positives_index:
+      type: file
+      description: The index file for the false positives' VCF file
+      pattern: "fp.vcf.gz.tbi"
+  - true_positive_vcf:
+      type: file
+      description: A VCF file containing the true positive variants
+      pattern: "tp.vcf.gz"
+  - true_positives_index:
+      type: file
+      description: The index file for the true positives' VCF file
+      pattern: "tp.vcf.gz.tbi"
+  - true_positive_baseline_vcf:
+      type: file
+      description: A VCF file containing the true positive baseline variants
+      pattern: "tp-baseline.vcf.gz"
+  - true_positives_baseline_index:
+      type: file
+      description: The index file for the baseline true positives' VCF file
+      pattern: "tp-baseline.vcf.gz.tbi"
+  - non_snp_roc:
+      type: file
+      description: A TSV file containing the ROC data for the non-SNP variants
+      pattern: "non_snp_roc.tsv.gz"
+  - snp_roc:
+      type: file
+      description: A TSV file containing the ROC data for the SNP variants
+      pattern: "snp_roc.tsv.gz"
+  - weighted_roc:
+      type: file
+      description: A TSV file containing the weighted ROC data
+      pattern: "weighted_roc.tsv.gz"
+  - summary:
+      type: file
+      description: A TXT file containing the summary of the evaluation
+      pattern: "summary.txt"
+  - phasing:
+      type: file
+      description: A TXT file containing the data on the phasing
+      pattern: "phasing.txt"
 
 authors:
   - "@nvnieuwk"
diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index 194e0cac..70d014bf 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -4,36 +4,36 @@
     - rtgtools
     - rtgtools/vcfeval
   files:
-    - path: output/rtgtools/test/done
-    - path: output/rtgtools/test/fn.vcf.gz
+    - path: output/rtgtools/done
+    - path: output/rtgtools/fn.vcf.gz
       md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
-    - path: output/rtgtools/test/fn.vcf.gz.tbi
+    - path: output/rtgtools/fn.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test/fp.vcf.gz
+    - path: output/rtgtools/fp.vcf.gz
       md5sum: 1417bb8ac7a0e202df660291a74de0db
-    - path: output/rtgtools/test/fp.vcf.gz.tbi
+    - path: output/rtgtools/fp.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test/non_snp_roc.tsv.gz
+    - path: output/rtgtools/non_snp_roc.tsv.gz
       md5sum: 8fd51a1e5084d15d43880cb1e31a0180
-    - path: output/rtgtools/test/phasing.txt
+    - path: output/rtgtools/phasing.txt
       md5sum: 133677dbd8be657439ea2b03fdfb8795
-    - path: output/rtgtools/test/progress
-    - path: output/rtgtools/test/snp_roc.tsv.gz
+    - path: output/rtgtools/progress
+    - path: output/rtgtools/snp_roc.tsv.gz
       md5sum: ff2ece544adfcefaa06da054876a9ae3
-    - path: output/rtgtools/test/summary.txt
+    - path: output/rtgtools/summary.txt
       md5sum: f4c8df93c8bdab603036bbc27b4a28c3
-    - path: output/rtgtools/test/tp-baseline.vcf.gz
+    - path: output/rtgtools/tp-baseline.vcf.gz
       md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
-    - path: output/rtgtools/test/tp-baseline.vcf.gz.tbi
+    - path: output/rtgtools/tp-baseline.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test/tp.vcf.gz
+    - path: output/rtgtools/tp.vcf.gz
       md5sum: 1417bb8ac7a0e202df660291a74de0db
-    - path: output/rtgtools/test/tp.vcf.gz.tbi
+    - path: output/rtgtools/tp.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test/vcfeval.log
-    - path: output/rtgtools/test/weighted_roc.tsv.gz
-      md5sum: 5209f1bdeb03704714ae92b183d08e0f
+    - path: output/rtgtools/vcfeval.log
     - path: output/rtgtools/versions.yml
+    - path: output/rtgtools/weighted_roc.tsv.gz
+      md5sum: 5209f1bdeb03704714ae92b183d08e0f
 
 - name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
   command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config
@@ -41,33 +41,33 @@
     - rtgtools
     - rtgtools/vcfeval
   files:
-    - path: output/rtgtools/test/done
-    - path: output/rtgtools/test/fn.vcf.gz
+    - path: output/rtgtools/done
+    - path: output/rtgtools/fn.vcf.gz
       md5sum: e51420e4be520ae309a2384830bf4c15
-    - path: output/rtgtools/test/fn.vcf.gz.tbi
+    - path: output/rtgtools/fn.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test/fp.vcf.gz
+    - path: output/rtgtools/fp.vcf.gz
       md5sum: 7d818cf526983de6cbb5cf517c44a8f7
-    - path: output/rtgtools/test/fp.vcf.gz.tbi
+    - path: output/rtgtools/fp.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/test/non_snp_roc.tsv.gz
+    - path: output/rtgtools/non_snp_roc.tsv.gz
       md5sum: a535fb80081b43b19788347152b6b8b4
-    - path: output/rtgtools/test/phasing.txt
+    - path: output/rtgtools/phasing.txt
       md5sum: 133677dbd8be657439ea2b03fdfb8795
-    - path: output/rtgtools/test/progress
-    - path: output/rtgtools/test/snp_roc.tsv.gz
+    - path: output/rtgtools/progress
+    - path: output/rtgtools/snp_roc.tsv.gz
       md5sum: 6006656c4a534935c7873398287bc110
-    - path: output/rtgtools/test/summary.txt
+    - path: output/rtgtools/summary.txt
       md5sum: f33feb32f84958fb931063044fba369b
-    - path: output/rtgtools/test/tp-baseline.vcf.gz
+    - path: output/rtgtools/tp-baseline.vcf.gz
       md5sum: ed68ea567a26d3b864ada79e9253bc97
-    - path: output/rtgtools/test/tp-baseline.vcf.gz.tbi
+    - path: output/rtgtools/tp-baseline.vcf.gz.tbi
       md5sum: 3518deff814eed340b0f5386294b5879
-    - path: output/rtgtools/test/tp.vcf.gz
+    - path: output/rtgtools/tp.vcf.gz
       md5sum: 92fd51021d101c99da066324655d24c9
-    - path: output/rtgtools/test/tp.vcf.gz.tbi
+    - path: output/rtgtools/tp.vcf.gz.tbi
       md5sum: 169063c1f570f0055059f3cb3518a8b4
-    - path: output/rtgtools/test/vcfeval.log
-    - path: output/rtgtools/test/weighted_roc.tsv.gz
-      md5sum: 0ba825084bd6b94accdf54fff23ea18c
+    - path: output/rtgtools/vcfeval.log
     - path: output/rtgtools/versions.yml
+    - path: output/rtgtools/weighted_roc.tsv.gz
+      md5sum: 0ba825084bd6b94accdf54fff23ea18c

From 5db26f9f3588a1934d64690c0627a22adee57d76 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 12:07:11 +0200
Subject: [PATCH 20/29] Linting

---
 modules/rtgtools/vcfeval/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 1963bfe0..b32d544b 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -17,7 +17,7 @@ process RTGTOOLS_VCFEVAL {
     output:
     tuple val(meta), path("done"), path("progress"), path("*.log") , emit: logs
     tuple val(meta), path("*{tp,fn,fp,baseline}.vcf.gz.tbi"), path("*{tp,fn,fp,baseline}.vcf.gz") , emit: vcf
-    tuple val(meta), path("*.tsv.gz")           , emit: roc    
+    tuple val(meta), path("*.tsv.gz")           , emit: roc  
     tuple val(meta), path("summary.txt")        , emit: summary
     tuple val(meta), path("phasing.txt")        , emit: phasing
     path "versions.yml"                         , emit: versions

From f3d5584ab0e277310a147ff5ed165c3a9203c6f4 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 12:08:23 +0200
Subject: [PATCH 21/29] Linting

---
 modules/rtgtools/vcfeval/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index b32d544b..826fec43 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -17,7 +17,7 @@ process RTGTOOLS_VCFEVAL {
     output:
     tuple val(meta), path("done"), path("progress"), path("*.log") , emit: logs
     tuple val(meta), path("*{tp,fn,fp,baseline}.vcf.gz.tbi"), path("*{tp,fn,fp,baseline}.vcf.gz") , emit: vcf
-    tuple val(meta), path("*.tsv.gz")           , emit: roc  
+    tuple val(meta), path("*.tsv.gz")           , emit: roc
     tuple val(meta), path("summary.txt")        , emit: summary
     tuple val(meta), path("phasing.txt")        , emit: phasing
     path "versions.yml"                         , emit: versions

From ef4857ec541864f41d9068a2a31b20e9b24953fb Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 12:20:01 +0200
Subject: [PATCH 22/29] Updated meta.yml

---
 modules/rtgtools/vcfeval/meta.yml | 62 +++++--------------------------
 1 file changed, 9 insertions(+), 53 deletions(-)

diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
index e568852c..587c2d3e 100644
--- a/modules/rtgtools/vcfeval/meta.yml
+++ b/modules/rtgtools/vcfeval/meta.yml
@@ -58,62 +58,18 @@ output:
       type: file
       description: File containing software versions
       pattern: "versions.yml"
-  - done:
+  - logging:
       type: file
-      description: A file containing the message on succesful completion
-      pattern: "done"
-  - progress:
+      description: Files containing logging from vcfeval
+      pattern: "*{done,progress,.log}"
+  - vcf:
       type: file
-      description: A file containing the simplified logging of the process
-      pattern: "progress"
-  - vcfeval_log:
+      description: VCF files containing the false negatives, false positives and true positives with their index files
+      pattern: "*.vcf{.gz,.gz.tbi}"
+  - roc:
       type: file
-      description: A file containing the extended logging of the process
-      pattern: "*.log"
-  - false_negatives_vcf:
-      type: file
-      description: A VCF file containing the false negative variants
-      pattern: "fn.vcf.gz"
-  - false_negatives_index:
-      type: file
-      description: The index file for the false negatives' VCF file
-      pattern: "fn.vcf.gz.tbi"
-  - false_positive_vcf:
-      type: file
-      description: A VCF file containing the false positive variants
-      pattern: "fp.vcf.gz"
-  - false_positives_index:
-      type: file
-      description: The index file for the false positives' VCF file
-      pattern: "fp.vcf.gz.tbi"
-  - true_positive_vcf:
-      type: file
-      description: A VCF file containing the true positive variants
-      pattern: "tp.vcf.gz"
-  - true_positives_index:
-      type: file
-      description: The index file for the true positives' VCF file
-      pattern: "tp.vcf.gz.tbi"
-  - true_positive_baseline_vcf:
-      type: file
-      description: A VCF file containing the true positive baseline variants
-      pattern: "tp-baseline.vcf.gz"
-  - true_positives_baseline_index:
-      type: file
-      description: The index file for the baseline true positives' VCF file
-      pattern: "tp-baseline.vcf.gz.tbi"
-  - non_snp_roc:
-      type: file
-      description: A TSV file containing the ROC data for the non-SNP variants
-      pattern: "non_snp_roc.tsv.gz"
-  - snp_roc:
-      type: file
-      description: A TSV file containing the ROC data for the SNP variants
-      pattern: "snp_roc.tsv.gz"
-  - weighted_roc:
-      type: file
-      description: A TSV file containing the weighted ROC data
-      pattern: "weighted_roc.tsv.gz"
+      description: TSV files containing ROC data for the evaluated variants
+      pattern: "*.tsv.gz"
   - summary:
       type: file
       description: A TXT file containing the summary of the evaluation

From 29f2d3c28417f935a2688bf5ea9ad8f0e25da679 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 10 May 2022 12:22:49 +0200
Subject: [PATCH 23/29] Update modules/rtgtools/vcfeval/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
---
 modules/rtgtools/vcfeval/main.nf | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 826fec43..a34f3514 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -15,11 +15,14 @@ process RTGTOOLS_VCFEVAL {
     path(sdf)
 
     output:
-    tuple val(meta), path("done"), path("progress"), path("*.log") , emit: logs
-    tuple val(meta), path("*{tp,fn,fp,baseline}.vcf.gz.tbi"), path("*{tp,fn,fp,baseline}.vcf.gz") , emit: vcf
-    tuple val(meta), path("*.tsv.gz")           , emit: roc
-    tuple val(meta), path("summary.txt")        , emit: summary
-    tuple val(meta), path("phasing.txt")        , emit: phasing
+    tuple val(meta), path("**{done,progress,.log}") , emit: logs
+    tuple val(meta), path("**tp.vcf.gz"), path("**tp.vcf.gz.tbi") , emit: tp
+    tuple val(meta), path("**fn.vcf.gz"), path("**fn.vcf.gz.tbi") , emit: fn
+    tuple val(meta), path("**fp.vcf.gz"), path("**fp.vcf.gz.tbi") , emit: fp
+    tuple val(meta), path("**baseline.vcf.gz"), path("**baseline.vcf.gz.tbi") , emit: baseline
+    tuple val(meta), path("**.tsv.gz")           , emit: roc
+    tuple val(meta), path("**summary.txt")        , emit: summary
+    tuple val(meta), path("**phasing.txt")        , emit: phasing
     path "versions.yml"                         , emit: versions
 
     when:

From 2eb77bd64e62f6c050fb95cc7bbc402240c3e7d8 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 10 May 2022 12:22:56 +0200
Subject: [PATCH 24/29] Update modules/rtgtools/vcfeval/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
---
 modules/rtgtools/vcfeval/main.nf | 1 -
 1 file changed, 1 deletion(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index a34f3514..8ab73dec 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -50,7 +50,6 @@ process RTGTOOLS_VCFEVAL {
         --template=$sdf \\
         --threads=$task.cpus \\
 
-    mv ${prefix}/* .
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From c18391aa4983cd801211c34b4493f330ffab1a07 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 12:26:13 +0200
Subject: [PATCH 25/29] Updated meta.yml

---
 modules/rtgtools/vcfeval/meta.yml | 18 +++++++++++++++---
 1 file changed, 15 insertions(+), 3 deletions(-)

diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
index 587c2d3e..c2d286c8 100644
--- a/modules/rtgtools/vcfeval/meta.yml
+++ b/modules/rtgtools/vcfeval/meta.yml
@@ -62,10 +62,22 @@ output:
       type: file
       description: Files containing logging from vcfeval
       pattern: "*{done,progress,.log}"
-  - vcf:
+  - true_positives:
       type: file
-      description: VCF files containing the false negatives, false positives and true positives with their index files
-      pattern: "*.vcf{.gz,.gz.tbi}"
+      description: VCF files containing true positives with their index files
+      pattern: "tp.vcf{.gz,.gz.tbi}"
+  - true_positives_baseline:
+      type: file
+      description: VCF files containing baseline true positives with their index files
+      pattern: "tp-baseline.vcf{.gz,.gz.tbi}"
+  - false_positives:
+      type: file
+      description: VCF files containing false positives with their index files
+      pattern: "fp.vcf{.gz,.gz.tbi}"
+  - false_negatives:
+      type: file
+      description: VCF files containing false negatives with their index files
+      pattern: "fn.vcf{.gz,.gz.tbi}"
   - roc:
       type: file
       description: TSV files containing ROC data for the evaluated variants

From b7134855e41d77b0fee9349c9b5eb43687e74925 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 12:34:52 +0200
Subject: [PATCH 26/29] Small update on the output channels

---
 modules/rtgtools/vcfeval/main.nf        |  8 +-
 tests/modules/rtgtools/vcfeval/test.yml | 98 +++++++++++++------------
 2 files changed, 54 insertions(+), 52 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 8ab73dec..dd50c54c 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -15,14 +15,14 @@ process RTGTOOLS_VCFEVAL {
     path(sdf)
 
     output:
-    tuple val(meta), path("**{done,progress,.log}") , emit: logs
+    tuple val(meta), path("**results/{done,progress,*.log}") , emit: logs
     tuple val(meta), path("**tp.vcf.gz"), path("**tp.vcf.gz.tbi") , emit: tp
     tuple val(meta), path("**fn.vcf.gz"), path("**fn.vcf.gz.tbi") , emit: fn
     tuple val(meta), path("**fp.vcf.gz"), path("**fp.vcf.gz.tbi") , emit: fp
     tuple val(meta), path("**baseline.vcf.gz"), path("**baseline.vcf.gz.tbi") , emit: baseline
     tuple val(meta), path("**.tsv.gz")           , emit: roc
-    tuple val(meta), path("**summary.txt")        , emit: summary
-    tuple val(meta), path("**phasing.txt")        , emit: phasing
+    tuple val(meta), path("**results/summary.txt")        , emit: summary
+    tuple val(meta), path("**results/phasing.txt")        , emit: phasing
     path "versions.yml"                         , emit: versions
 
     when:
@@ -46,7 +46,7 @@ process RTGTOOLS_VCFEVAL {
         $bed_regions \\
         $eval_regions \\
         --calls=$query_vcf \\
-        --output=$prefix \\
+        --output=${prefix}_results \\
         --template=$sdf \\
         --threads=$task.cpus \\
 
diff --git a/tests/modules/rtgtools/vcfeval/test.yml b/tests/modules/rtgtools/vcfeval/test.yml
index 70d014bf..33720f66 100644
--- a/tests/modules/rtgtools/vcfeval/test.yml
+++ b/tests/modules/rtgtools/vcfeval/test.yml
@@ -4,36 +4,37 @@
     - rtgtools
     - rtgtools/vcfeval
   files:
-    - path: output/rtgtools/done
-    - path: output/rtgtools/fn.vcf.gz
-      md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
-    - path: output/rtgtools/fn.vcf.gz.tbi
+    - path: output/rtgtools/test_results/done
+    - path: output/rtgtools/test_results/fn.vcf.gz
+      md5sum: be9c9106055bfad4c5985bc0d33efd56
+    - path: output/rtgtools/test_results/fn.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/fp.vcf.gz
-      md5sum: 1417bb8ac7a0e202df660291a74de0db
-    - path: output/rtgtools/fp.vcf.gz.tbi
+    - path: output/rtgtools/test_results/fp.vcf.gz
+      md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
+    - path: output/rtgtools/test_results/fp.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/non_snp_roc.tsv.gz
-      md5sum: 8fd51a1e5084d15d43880cb1e31a0180
-    - path: output/rtgtools/phasing.txt
+    - path: output/rtgtools/test_results/non_snp_roc.tsv.gz
+      md5sum: ad5bad32c48f05aef232e2c0e708877a
+    - path: output/rtgtools/test_results/phasing.txt
       md5sum: 133677dbd8be657439ea2b03fdfb8795
-    - path: output/rtgtools/progress
-    - path: output/rtgtools/snp_roc.tsv.gz
-      md5sum: ff2ece544adfcefaa06da054876a9ae3
-    - path: output/rtgtools/summary.txt
+    - path: output/rtgtools/test_results/progress
+    - path: output/rtgtools/test_results/snp_roc.tsv.gz
+      md5sum: 6785b83d66486e7e6c75c5a5b1574c09
+    - path: output/rtgtools/test_results/summary.txt
       md5sum: f4c8df93c8bdab603036bbc27b4a28c3
-    - path: output/rtgtools/tp-baseline.vcf.gz
-      md5sum: 4577a8c3226b9f8ed9e260c3bd4b1259
-    - path: output/rtgtools/tp-baseline.vcf.gz.tbi
+    - path: output/rtgtools/test_results/tp-baseline.vcf.gz
+      md5sum: be9c9106055bfad4c5985bc0d33efd56
+    - path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/tp.vcf.gz
-      md5sum: 1417bb8ac7a0e202df660291a74de0db
-    - path: output/rtgtools/tp.vcf.gz.tbi
+    - path: output/rtgtools/test_results/tp.vcf.gz
+      md5sum: e0f0ff841dc63e9fb61fd3a5db137ced
+    - path: output/rtgtools/test_results/tp.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/vcfeval.log
+    - path: output/rtgtools/test_results/vcfeval.log
+    - path: output/rtgtools/test_results/weighted_roc.tsv.gz
+      md5sum: fa7c046ea0084172f1ef91f19de07b2b
     - path: output/rtgtools/versions.yml
-    - path: output/rtgtools/weighted_roc.tsv.gz
-      md5sum: 5209f1bdeb03704714ae92b183d08e0f
+      md5sum: 270ed7a5a8e347b251eb4aa2198f98e8
 
 - name: rtgtools vcfeval test_rtgtools_vcfeval_no_optional_inputs
   command: nextflow run tests/modules/rtgtools/vcfeval -entry test_rtgtools_vcfeval_no_optional_inputs -c tests/config/nextflow.config
@@ -41,33 +42,34 @@
     - rtgtools
     - rtgtools/vcfeval
   files:
-    - path: output/rtgtools/done
-    - path: output/rtgtools/fn.vcf.gz
-      md5sum: e51420e4be520ae309a2384830bf4c15
-    - path: output/rtgtools/fn.vcf.gz.tbi
+    - path: output/rtgtools/test_results/done
+    - path: output/rtgtools/test_results/fn.vcf.gz
+      md5sum: c11c889a4f42c8ea325748bd768ea34d
+    - path: output/rtgtools/test_results/fn.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/fp.vcf.gz
-      md5sum: 7d818cf526983de6cbb5cf517c44a8f7
-    - path: output/rtgtools/fp.vcf.gz.tbi
+    - path: output/rtgtools/test_results/fp.vcf.gz
+      md5sum: 138e85c1cd79f8fea9a33e81ce0c734c
+    - path: output/rtgtools/test_results/fp.vcf.gz.tbi
       md5sum: 092a7a3162e7cff25d273525751eb284
-    - path: output/rtgtools/non_snp_roc.tsv.gz
-      md5sum: a535fb80081b43b19788347152b6b8b4
-    - path: output/rtgtools/phasing.txt
+    - path: output/rtgtools/test_results/non_snp_roc.tsv.gz
+      md5sum: 34fb78a008dfc0bef02807b8a7012b07
+    - path: output/rtgtools/test_results/phasing.txt
       md5sum: 133677dbd8be657439ea2b03fdfb8795
-    - path: output/rtgtools/progress
-    - path: output/rtgtools/snp_roc.tsv.gz
-      md5sum: 6006656c4a534935c7873398287bc110
-    - path: output/rtgtools/summary.txt
+    - path: output/rtgtools/test_results/progress
+    - path: output/rtgtools/test_results/snp_roc.tsv.gz
+      md5sum: a4c5761c2653e2d04fc84c1cea13b1f0
+    - path: output/rtgtools/test_results/summary.txt
       md5sum: f33feb32f84958fb931063044fba369b
-    - path: output/rtgtools/tp-baseline.vcf.gz
-      md5sum: ed68ea567a26d3b864ada79e9253bc97
-    - path: output/rtgtools/tp-baseline.vcf.gz.tbi
-      md5sum: 3518deff814eed340b0f5386294b5879
-    - path: output/rtgtools/tp.vcf.gz
-      md5sum: 92fd51021d101c99da066324655d24c9
-    - path: output/rtgtools/tp.vcf.gz.tbi
-      md5sum: 169063c1f570f0055059f3cb3518a8b4
-    - path: output/rtgtools/vcfeval.log
+    - path: output/rtgtools/test_results/tp-baseline.vcf.gz
+      md5sum: d1c2d990899edf127ea5fcca8866fcb0
+    - path: output/rtgtools/test_results/tp-baseline.vcf.gz.tbi
+      md5sum: 3307008fea47adb75c46d395c5567bc0
+    - path: output/rtgtools/test_results/tp.vcf.gz
+      md5sum: e35b4dab82894eee9b77c81f9bc89cca
+    - path: output/rtgtools/test_results/tp.vcf.gz.tbi
+      md5sum: 45d8f8793140944f129e728299918c88
+    - path: output/rtgtools/test_results/vcfeval.log
+    - path: output/rtgtools/test_results/weighted_roc.tsv.gz
+      md5sum: 5b8efc9e9381f604880412800f58e4e9
     - path: output/rtgtools/versions.yml
-    - path: output/rtgtools/weighted_roc.tsv.gz
-      md5sum: 0ba825084bd6b94accdf54fff23ea18c
+      md5sum: 55568e4bbe5ab7e634a1f392abb89cc4

From 7fc4cc5a382214c86ec3577da0cb59823d9becb7 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 10 May 2022 13:23:22 +0200
Subject: [PATCH 27/29] Update modules/rtgtools/vcfeval/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
---
 modules/rtgtools/vcfeval/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index dd50c54c..67640e87 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -33,8 +33,8 @@ process RTGTOOLS_VCFEVAL {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def bed_regions = truth_regions ? "--bed-regions=$truth_regions" : ""
     def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : ""
-    def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
-    def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
+    def truth_index = truth_vcf_tbi ?: "rtg index $truth_vcf"
+    def query_index = query_vcf_tbi ?: "rtg index $query_vcf"
 
     """
     $truth_index

From d3927aae995dbccc4c55d93d96cb4d3fd9e5c6f2 Mon Sep 17 00:00:00 2001
From: nvnieuwk <101190534+nvnieuwk@users.noreply.github.com>
Date: Tue, 10 May 2022 13:26:14 +0200
Subject: [PATCH 28/29] Update modules/rtgtools/vcfeval/main.nf

Co-authored-by: Matthias De Smet <11850640+matthdsm@users.noreply.github.com>
---
 modules/rtgtools/vcfeval/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index 67640e87..dd50c54c 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -33,8 +33,8 @@ process RTGTOOLS_VCFEVAL {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def bed_regions = truth_regions ? "--bed-regions=$truth_regions" : ""
     def eval_regions = evaluation_regions ? "--evaluation-regions=$evaluation_regions" : ""
-    def truth_index = truth_vcf_tbi ?: "rtg index $truth_vcf"
-    def query_index = query_vcf_tbi ?: "rtg index $query_vcf"
+    def truth_index = truth_vcf_tbi ? "" : "rtg index $truth_vcf"
+    def query_index = query_vcf_tbi ? "" : "rtg index $query_vcf"
 
     """
     $truth_index

From fa7c947c35b153ce58ca4806b208b382ecb9a712 Mon Sep 17 00:00:00 2001
From: Nicolas Vannieuwkerke <nicolas.vannieuwkerke@ugent.be>
Date: Tue, 10 May 2022 13:33:37 +0200
Subject: [PATCH 29/29] Adjusted meta

---
 modules/rtgtools/vcfeval/main.nf  |  4 ++--
 modules/rtgtools/vcfeval/meta.yml | 16 ++++++++--------
 2 files changed, 10 insertions(+), 10 deletions(-)

diff --git a/modules/rtgtools/vcfeval/main.nf b/modules/rtgtools/vcfeval/main.nf
index dd50c54c..1bad4231 100644
--- a/modules/rtgtools/vcfeval/main.nf
+++ b/modules/rtgtools/vcfeval/main.nf
@@ -20,10 +20,10 @@ process RTGTOOLS_VCFEVAL {
     tuple val(meta), path("**fn.vcf.gz"), path("**fn.vcf.gz.tbi") , emit: fn
     tuple val(meta), path("**fp.vcf.gz"), path("**fp.vcf.gz.tbi") , emit: fp
     tuple val(meta), path("**baseline.vcf.gz"), path("**baseline.vcf.gz.tbi") , emit: baseline
-    tuple val(meta), path("**.tsv.gz")           , emit: roc
+    tuple val(meta), path("**.tsv.gz")                    , emit: roc
     tuple val(meta), path("**results/summary.txt")        , emit: summary
     tuple val(meta), path("**results/phasing.txt")        , emit: phasing
-    path "versions.yml"                         , emit: versions
+    path "versions.yml"                                   , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/rtgtools/vcfeval/meta.yml b/modules/rtgtools/vcfeval/meta.yml
index c2d286c8..5a5f452e 100644
--- a/modules/rtgtools/vcfeval/meta.yml
+++ b/modules/rtgtools/vcfeval/meta.yml
@@ -62,21 +62,21 @@ output:
       type: file
       description: Files containing logging from vcfeval
       pattern: "*{done,progress,.log}"
-  - true_positives:
+  - tp:
       type: file
-      description: VCF files containing true positives with their index files
+      description: A tuple containing the VCF and TBI file for the true positive variants
       pattern: "tp.vcf{.gz,.gz.tbi}"
-  - true_positives_baseline:
+  - baseline:
       type: file
-      description: VCF files containing baseline true positives with their index files
+      description: A tuple containing the VCF and TBI file for the baseline true positive variants
       pattern: "tp-baseline.vcf{.gz,.gz.tbi}"
-  - false_positives:
+  - fp:
       type: file
-      description: VCF files containing false positives with their index files
+      description: A tuple containing the VCF and TBI file for the false positive variants
       pattern: "fp.vcf{.gz,.gz.tbi}"
-  - false_negatives:
+  - fn:
       type: file
-      description: VCF files containing false negatives with their index files
+      description: A tuple containing the VCF and TBI file for the false negative variants
       pattern: "fn.vcf{.gz,.gz.tbi}"
   - roc:
       type: file