From d0e4ee3ccd5628e412ea0120eb28266e936c6b0e Mon Sep 17 00:00:00 2001
From: FriederikeHanssen <Friederike.hanssen@qbic.uni-tuebingen.de>
Date: Fri, 15 Oct 2021 10:40:16 +0200
Subject: [PATCH] Add cram files to config (#862)

* add cram files to config

* Update tests/config/test_data.config

Co-authored-by: Harshil Patel <drpatelh@users.noreply.github.com>
---
 tests/config/test_data.config | 14 ++++++++++++++
 1 file changed, 14 insertions(+)

diff --git a/tests/config/test_data.config b/tests/config/test_data.config
index b4443e9f..50fdb858 100644
--- a/tests/config/test_data.config
+++ b/tests/config/test_data.config
@@ -143,6 +143,20 @@ params {
                 test2_paired_end_umi_unsorted_bam              = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.umi_unsorted.bam"
                 test2_paired_end_umi_unsorted_tagged_bam       = "${test_data_dir}/genomics/homo_sapiens/illumina/bam/umi/test2.paired_end.unsorted_tagged.bam"
 
+                test_paired_end_sorted_cram                      = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram"
+                test_paired_end_sorted_cram_crai                 = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.sorted.cram.crai"
+                test_paired_end_markduplicates_sorted_cram       = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram"
+                test_paired_end_markduplicates_sorted_cram_crai  = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.markduplicates.sorted.cram.crai"
+                test_paired_end_recalibrated_sorted_cram         = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram"
+                test_paired_end_recalibrated_sorted_cram_crai    = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test.paired_end.recalibrated.sorted.cram.crai"
+
+                test2_paired_end_sorted_cram                     = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram"
+                test2_paired_end_sorted_cram_crai                = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.sorted.cram.crai"
+                test2_paired_end_markduplicates_sorted_cram      = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram"
+                test2_paired_end_markduplicates_sorted_cram_crai = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.markduplicates.sorted.cram.crai"
+                test2_paired_end_recalibrated_sorted_cram        = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram"
+                test2_paired_end_recalibrated_sorted_cram_crai   = "${test_data_dir}/genomics/homo_sapiens/illumina/cram/test2.paired_end.recalibrated.sorted.cram.crai"
+
                 test_1_fastq_gz                                = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_1.fastq.gz"
                 test_2_fastq_gz                                = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test_2.fastq.gz"
                 test_umi_1_fastq_gz                            = "${test_data_dir}/genomics/homo_sapiens/illumina/fastq/test.umi_1.fastq.gz"