From 230224700edcdf3a8c2d241cafc974e4724e48f4 Mon Sep 17 00:00:00 2001
From: SusiJo <susanne.jodoin@gmx.de>
Date: Fri, 3 Jun 2022 12:45:52 +0200
Subject: [PATCH] change prefix

---
 modules/gatk4/markduplicatesspark/main.nf          |  2 +-
 tests/modules/gatk4/markduplicatesspark/main.nf    | 14 ++++++++++++++
 .../gatk4/markduplicatesspark/nextflow.config      |  8 ++++++++
 3 files changed, 23 insertions(+), 1 deletion(-)

diff --git a/modules/gatk4/markduplicatesspark/main.nf b/modules/gatk4/markduplicatesspark/main.nf
index 703623d5..55049fba 100644
--- a/modules/gatk4/markduplicatesspark/main.nf
+++ b/modules/gatk4/markduplicatesspark/main.nf
@@ -23,7 +23,7 @@ process GATK4_MARKDUPLICATES_SPARK {
 
     script:
     def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}.bam"
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def input_list = bam.collect{"--input $it"}.join(' ')
 
 
diff --git a/tests/modules/gatk4/markduplicatesspark/main.nf b/tests/modules/gatk4/markduplicatesspark/main.nf
index ac89b1b3..004fbb1e 100644
--- a/tests/modules/gatk4/markduplicatesspark/main.nf
+++ b/tests/modules/gatk4/markduplicatesspark/main.nf
@@ -3,6 +3,7 @@
 nextflow.enable.dsl = 2
 
 include { GATK4_MARKDUPLICATES_SPARK } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
+include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_CRAM } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
 include { GATK4_MARKDUPLICATES_SPARK as GATK4_MARKDUPLICATES_SPARK_METRICS } from '../../../../modules/gatk4/markduplicatesspark/main.nf'
 
 workflow test_gatk4_markduplicates_spark {
@@ -29,6 +30,19 @@ workflow test_gatk4_markduplicates_spark_multiple_bams {
     GATK4_MARKDUPLICATES_SPARK ( input, fasta, fai, dict )
 }
 
+// chr 22
+workflow test_gatk4_markduplicates_spark_multiple_bams_cram_out {
+    input = [ [ id:'test', single_end:false ], // meta map
+            [   file(params.test_data['homo_sapiens']['illumina']['test_paired_end_name_sorted_bam'], checkIfExists: true),
+                file(params.test_data['homo_sapiens']['illumina']['test2_paired_end_name_sorted_bam'], checkIfExists: true)
+            ] ]
+    fasta = file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)
+    fai = file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)
+    dict = file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)
+
+    GATK4_MARKDUPLICATES_SPARK_CRAM ( input, fasta, fai, dict )
+}
+
 // chr 22
 workflow test_gatk4_markduplicates_spark_multiple_bams_metrics {
     input = [ [ id:'test', single_end:false ], // meta map
diff --git a/tests/modules/gatk4/markduplicatesspark/nextflow.config b/tests/modules/gatk4/markduplicatesspark/nextflow.config
index 495a42f3..565016b7 100644
--- a/tests/modules/gatk4/markduplicatesspark/nextflow.config
+++ b/tests/modules/gatk4/markduplicatesspark/nextflow.config
@@ -2,9 +2,17 @@ process {
 
     publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
 
+    withName: GATK4_MARKDUPLICATES_SPARK {
+        ext.prefix = { "${meta.id}.bam" }
+    }
+    withName: GATK4_MARKDUPLICATES_SPARK_CRAM {
+        ext.prefix = { "${meta.id}.cram" }
+    }
     withName: GATK4_MARKDUPLICATES_SPARK_METRICS {
+        ext.prefix = { "${meta.id}.bam" }
         ext.args = '--metrics-file test.metrics'
     }
+
 }
 // override tests/config/nextflow.config
 docker.userEmulation = false