From f2b2f32567de2038e9bba9db7d578c17ca552341 Mon Sep 17 00:00:00 2001
From: James Fellows Yates <jfy133@gmail.com>
Date: Wed, 3 Nov 2021 13:05:46 +0100
Subject: [PATCH] Gets GATK3 UG working, not sure why can't test by manually
 installing

---
 modules/gatk3/unifiedgenotyper/main.nf        |  23 +++++++++++-------
 ...t_versions_yml.cpython-39-pytest-6.2.5.pyc | Bin 3558 -> 3556 bytes
 tests/modules/gatk3/unifiedgenotyper/main.nf  |  13 +++++++---
 tests/modules/gatk3/unifiedgenotyper/test.yml |   3 +--
 4 files changed, 24 insertions(+), 15 deletions(-)

diff --git a/modules/gatk3/unifiedgenotyper/main.nf b/modules/gatk3/unifiedgenotyper/main.nf
index e4b79524..3ad580a7 100644
--- a/modules/gatk3/unifiedgenotyper/main.nf
+++ b/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
     """
 }
diff --git a/tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc b/tests/__pycache__/test_versions_yml.cpython-39-pytest-6.2.5.pyc
index 33acb8369a1bc62b5e66e1ed80e2247dd0e2759f..3d88e5f06747712ca8c564787aa3ed9a731e303f 100644
GIT binary patch
delta 55
zcmaDR{Y08Ok(ZZ?0SMAEsy1?GG0D2?XXNLm>Sv{;=H%p;7wfy^Czs}?=9Ludr)QRI
Jp28Hw4FJl;5zGJp

delta 57
zcmaDN{Y;uWk(ZZ?0SIRG=5FN9Vv_gN&&bbB)h|vj&8$i+O3@F`FUr<;NiEY)&n(F(
LP1-z(DTo^Y`Rfv!

diff --git a/tests/modules/gatk3/unifiedgenotyper/main.nf b/tests/modules/gatk3/unifiedgenotyper/main.nf
index 7ea71cc3..9de53c5f 100644
--- a/tests/modules/gatk3/unifiedgenotyper/main.nf
+++ b/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 )
 }
diff --git a/tests/modules/gatk3/unifiedgenotyper/test.yml b/tests/modules/gatk3/unifiedgenotyper/test.yml
index 0ca98e0f..f1f534a3 100644
--- a/tests/modules/gatk3/unifiedgenotyper/test.yml
+++ b/tests/modules/gatk3/unifiedgenotyper/test.yml
@@ -6,5 +6,4 @@
     - gatk3
     - gatk3/unifiedgenotyper
   files:
-    - path: output/gatk3/test.bam
-      md5sum: e667c7caad0bc4b7ac383fd023c654fc
+    - path: output/gatk3/test.vcf.gz