Add indices and meta

modules/gatk4/filtervarianttranches/main.nf

@@ -8,15 +8,16 @@ process GATK4_FILTERVARIANTTRANCHES {
         'quay.io/biocontainers/gatk4:4.2.6.1--hdfd78af_0' }"
 
     input:
-    tuple val(meta), path(vcf), path(intervals)
+    tuple val(meta), path(vcf), path(tbi),path(intervals)
-    path ressources
+    path resources
+    path resources_index
     path fasta
     path fai
     path dict
 
 
     output:
-    tuple val(meta), path("*.bam"), emit: bam
+    tuple val(meta), path("*.vcf.gz"), emit: vcf
     path "versions.yml"              , emit: versions
 
     when:
@@ -26,7 +27,7 @@ process GATK4_FILTERVARIANTTRANCHES {
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
-    def ressources = ressources.collect{"--ressources $it"}.join(' ')
+    def resources = resources.collect{"--resource $it"}.join(' ')
     def avail_mem = 3
     if (!task.memory) {
         log.info '[GATK FilterVariantTranches] Available memory not known - defaulting to 3GB. Specify process memory requirements to change this.'
@@ -36,7 +37,7 @@ process GATK4_FILTERVARIANTTRANCHES {
     """
     gatk --java-options "-Xmx${avail_mem}g" FilterVariantTranches \\
         --variant $vcf \\
-        $ressources \\
+        $resources \\
         --output ${prefix}.filtered.vcf.gz \\
         --tmp-dir . \\
         $args

modules/gatk4/filtervarianttranches/meta.yml

@@ -1,51 +1,64 @@
 name: "gatk4_filtervarianttranches"
-## TODO nf-core: Add a description of the module and list keywords
+description: Apply tranche filtering
-description: write your description here
 keywords:
-  - sort
+  - gatk4
+  - filtervarianttranches
+
 tools:
   - "gatk4":
-      ## TODO nf-core: Add a description and other details for the software below
+      description: Genome Analysis Toolkit (GATK4)
-      description: "Genome Analysis Toolkit (GATK4)"
+      homepage: https://gatk.broadinstitute.org/hc/en-us
-      homepage: "None"
+      documentation: https://gatk.broadinstitute.org/hc/en-us
-      documentation: "None"
+      tool_dev_url: https://github.com/broadinstitute/gatk
-      tool_dev_url: "https://github.com/broadinstitute/gatk"
+      doi: "10.1158/1538-7445.AM2017-3590"
-      doi: ""
+      licence: ["BSD-3-clause"]
-      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 ]
-  # 
+  - vcf:
-  ## TODO nf-core: Delete / customise this example input
-  - bam:
       type: file
-      description: BAM/CRAM/SAM file
+      description: a VCF file containing variants, must have info key:CNN_2D
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.vcf.gz"
+  - tbi:
+      type: file
+      description: tbi file matching with -vcf
+      pattern: "*.vcf.gz.tbi"
+  - resources:
+      type: list
+      description: resource A VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
+      pattern: "*.vcf.gz"
+  - resources_index:
+      type: list
+      description: Index of resource VCF containing known SNP and or INDEL sites. Can be supplied as many times as necessary
+      pattern: "*.vcf.gz"
+  - fasta:
+      type: file
+      description: The reference fasta file
+      pattern: "*.fasta"
+  - fai:
+      type: file
+      description: Index of reference fasta file
+      pattern: "fasta.fai"
+  - dict:
 
-## 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
+  - vcf:
-  - bam:
       type: file
-      description: Sorted BAM/CRAM/SAM file
+      description: VCF file
-      pattern: "*.{bam,cram,sam}"
+      pattern: "*.vcf.gz"
 
 authors:
   - "@FriederikeHanssen"

tests/modules/gatk4/filtervarianttranches/main.nf

@@ -6,10 +6,33 @@ include { GATK4_FILTERVARIANTTRANCHES } from '../../../../modules/gatk4/filterva
 
 workflow test_gatk4_filtervarianttranches {
 
-    input = [
+    input = [ [ id:'test' ], // meta map
-        [ id:'test', single_end:false ], // meta map
+                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz'], checkIfExists: true),
-        file(params.test_data['sarscov2']['illumina']['test_paired_end_bam'], checkIfExists: true)
+                file(params.test_data['homo_sapiens']['illumina']['test2_haplotc_ann_vcf_gz_tbi'], checkIfExists: true),
+                []
             ]
 
-    GATK4_FILTERVARIANTTRANCHES ( input )
+    resources = [
+                    file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz'], checkIfExists: true),
+                    //file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz'], checkIfExists: true),
+                    //file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz'], checkIfExists: true),
+                    //file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz'], checkIfExists: true)
+                ]
+    resources_index  =[              file(params.test_data['homo_sapiens']['genome']['hapmap_3_3_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    //file(params.test_data['homo_sapiens']['genome']['res_1000g_omni2_5_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    //file(params.test_data['homo_sapiens']['genome']['res_1000g_phase1_snps_hg38_21_vcf_gz_tbi'], checkIfExists: true),
+                    //file(params.test_data['homo_sapiens']['genome']['dbsnp_138_hg38_21_vcf_gz_tbi'], checkIfExists: true)
+                ]
+                // , [
+                //     'hapmap,known=false,training=true,truth=true,prior=15.0 hapmap_3.3.hg38.vcf.gz',
+                //     'omni,known=false,training=true,truth=false,prior=12.0 1000G_omni2.5.hg38.vcf.gz',
+                //     '1000G,known=false,training=true,truth=false,prior=10.0 1000G_phase1.snps.hg38.vcf.gz',
+                //     'dbsnp,known=true,training=false,truth=false,prior=2.0 dbsnp_138.hg38.vcf.gz'
+                // ]]
+
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_21_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_21_dict'], checkIfExists: true)
+
+    GATK4_FILTERVARIANTTRANCHES ( input, resources, resources_index, fasta, fai, dict)
 }