add filter variant tranches

modules/gatk4/filtervarianttranches/main.nf

@@ -0,0 +1,49 @@
+process GATK4_FILTERVARIANTTRANCHES {
+    tag "$meta.id"
+    label 'process_low'
+
+    conda (params.enable_conda ? "bioconda::gatk4=4.2.6.1" : null)
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://depot.galaxyproject.org/singularity/gatk4:4.2.6.1--hdfd78af_0':
+        'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
+
+    input:
+    tuple val(meta), path(vcf), path(intervals)
+    path ressources
+    path fasta
+    path fai
+    path dict
+
+
+    output:
+    tuple val(meta), path("*.bam"), emit: bam
+    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}"
+
+    def ressources = ressources.collect{"--ressources $it"}.join(' ')
+    def avail_mem = 3
+    if (!task.memory) {
+        log.info '[GATK FilterVariantTranches] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
+    } else {
+        avail_mem = task.memory.giga
+    }
+    """
+    gatk --java-options "-Xmx${avail_mem}g" FilterVariantTranches \\
+        --variant $vcf \\
+        $ressources \\
+        --output ${prefix}.filtered.vcf.gz \\
+        --tmp-dir . \\
+        $args
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        gatk4: \$(echo \$(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*\$//' ))
+    END_VERSIONS
+    """
+}

modules/gatk4/filtervarianttranches/meta.yml

@@ -0,0 +1,51 @@
+name: "gatk4_filtervarianttranches"
+## TODO nf-core: Add a description of the module and list keywords
+description: write your description here
+keywords:
+  - sort
+tools:
+  - "gatk4":
+      ## TODO nf-core: Add a description and other details for the software below
+      description: "Genome Analysis Toolkit (GATK4)"
+      homepage: "None"
+      documentation: "None"
+      tool_dev_url: "https://github.com/broadinstitute/gatk"
+      doi: ""
+      licence: "['BSD-3-clause']"
+
+## 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:
+  - "@FriederikeHanssen"

tests/config/pytest_modules.yml

@@ -755,6 +755,10 @@ gatk4/filtermutectcalls:
   - modules/gatk4/filtermutectcalls/**
   - tests/modules/gatk4/filtermutectcalls/**
 
+gatk4/filtervarianttranches:
+  - modules/gatk4/filtervarianttranches/**
+  - tests/modules/gatk4/filtervarianttranches/**
+
 gatk4/gatherbqsrreports:
   - modules/gatk4/gatherbqsrreports/**
   - tests/modules/gatk4/gatherbqsrreports/**

tests/modules/gatk4/filtervarianttranches/main.nf

@@ -0,0 +1,15 @@
+#!/usr/bin/env nextflow
+
+nextflow.enable.dsl = 2
+
+include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/gatk4/filtervarianttranches/main.nf'
+
+workflow test_gatk4_filtervarianttranches {
+    
+    input = [
+        [ id:'test', single_end:false ], // meta map
+        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+    ]
+
+    GATK4_FILTERVARIANTTRANCHES ( input )
+}

tests/modules/gatk4/filtervarianttranches/nextflow.config

@@ -0,0 +1,5 @@
+process {
+
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    
+}

tests/modules/gatk4/filtervarianttranches/test.yml

@@ -0,0 +1,14 @@
+## TODO nf-core: Please run the following command to build this file:
+#                nf-core modules create-test-yml gatk4/filtervarianttranches
+- name: "gatk4 filtervarianttranches"
+  command: nextflow run ./tests/modules/gatk4/filtervarianttranches -entry test_gatk4_filtervarianttranches -c ./tests/config/nextflow.config -c ./tests/modules/gatk4/filtervarianttranches/nextflow.config
+  tags:
+    - "gatk4"
+    #
+    - "gatk4/filtervarianttranches"
+    #
+  files:
+    - path: "output/gatk4/test.bam"
+      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/gatk4/versions.yml
+      md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b