Gets GATK3 UG working, not sure why can't test by manually installing

modules/gatk3/unifiedgenotyper/main.nf

@@ -5,7 +5,7 @@ params.options = [:]
 options        = initOptions(params.options)
 
 process GATK3_UNIFIEDGENOTYPER {
-    tag '$bam'
+    tag "$meta.id"
     label 'process_low'
     publishDir "${params.outdir}",
         mode: params.publish_dir_mode,
@@ -15,32 +15,37 @@ process GATK3_UNIFIEDGENOTYPER {
     //               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 ? "YOUR-TOOL-HERE" : null)
+    conda (params.enable_conda ? "bioconda::gatk=3.5" : null)
     if (workflow.containerEngine == 'singularity' && !params.singularity_pull_docker_container) {
-        container "https://depot.galaxyproject.org/singularity/YOUR-TOOL-HERE"
+        container "https://depot.galaxyproject.org/singularity/gatk:3.5--hdfd78af_11"
     } else {
-        container "quay.io/biocontainers/YOUR-TOOL-HERE"
+        container "quay.io/biocontainers/gatk:3.5--hdfd78af_11"
     }
 
     input:
-    path bam
+    tuple val(meta), path(bam), path(bai)
     path ref
+    path fai
+    path dict
 
     output:
-    path "*.vcf",        emit: vcf
+    path "*.vcf.gz",        emit: vcf
     path "versions.yml", emit: versions
 
     script:
+    def prefix = options.suffix ? "${meta.id}${options.suffix}" : "${meta.id}"
     """
-    gatk -T UnifiedGenotyper \\
+    gatk3 -T UnifiedGenotyper \\
         -R $ref \\
         -I $bam \\
-        -o $vcf \\
+        -o ${prefix}.vcf \\
         $options.args
 
+    gzip --no-name ${prefix}.vcf
+
     cat <<-END_VERSIONS > versions.yml
     ${getProcessName(task.process)}:
-        ${getSoftwareName(task.process)}: \$( samtools --version 2>&1 | sed 's/^.*samtools //; s/Using.*\$//' )
+        ${getSoftwareName(task.process)}: \$( gatk3 --version )
     END_VERSIONS
     """
 }

tests/modules/gatk3/unifiedgenotyper/main.nf

@@ -5,9 +5,14 @@ nextflow.enable.dsl = 2
 include { GATK3_UNIFIEDGENOTYPER } from '../../../../modules/gatk3/unifiedgenotyper/main.nf' addParams( options: [:] )
 
 workflow test_gatk3_unifiedgenotyper {
-    
-    input = file(params.test_data['sarscov2']['illumina']['test_single_end_bam'], checkIfExists: true)
-    ref = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
 
-    GATK3_UNIFIEDGENOTYPER ( input, ref )
+    input = [ [ id:'test' ], // meta map
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true),
+              file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam_bai'], checkIfExists: true)
+            ]
+    ref = file(params.test_data['sarscov2']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['sarscov2']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['sarscov2']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK3_UNIFIEDGENOTYPER ( input, ref, fai, dict )
 }

tests/modules/gatk3/unifiedgenotyper/test.yml

@@ -6,5 +6,4 @@
     - gatk3
     - gatk3/unifiedgenotyper
   files:
-    - path: output/gatk3/test.bam
+    - path: output/gatk3/test.vcf.gz
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc