Add full size test NA12878

CHANGELOG.md

@@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#594](https://github.com/nf-core/sarek/pull/594) - Add parameter `--save_output_as_bam` to allow output of result files in BAM format
 - [#597](https://github.com/nf-core/sarek/pull/597) - Added tiddit for tumor variant calling
 - [#600](https://github.com/nf-core/sarek/pull/600) - Added description for UMI related params in schema
+- [#604](https://github.com/nf-core/sarek/pull/604) - Added full size tests WGS 30x NA12878
 
 ### Changed
 

conf/test_full.config

@@ -15,10 +15,11 @@ params {
     config_profile_description = 'Full test dataset to check pipeline function'
 
     // Input data for full size test
-    input = "${projectDir}/tests/csv/3.0/test_full_data.csv"
+    input = '${projectDir}/tests/csv/3.0/test_full_data.csv'
 
-    wes   = true
-
-    // Ignore `--input` as otherwise the parameter validation will throw an error
+    // Other params
+    tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep'
+    genome = 'GATK.GRCh38'
+    vep_cache_version = 105
     schema_ignore_params = 'genomes'
 }

tests/csv/3.0/test_full_data.csv

@@ -1,2 +1,2 @@
 patient,status,sample,lane,fastq_1,fastq_2
-HG002,0,HG002,1,s3://giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/reads/D1_S1_L001_R1_001.fastq.gz,s3://giab/data/AshkenazimTrio/HG002_NA24385_son/NIST_Illumina_2x250bps/reads/D1_S1_L001_R2_001.fastq.gz
+NA12878,0,NA12878,1,s3://nf-core-awsmegatests/sarek/input/NA12878_1.merged.fastq.gz,s3://nf-core-awsmegatests/sarek/input/NA12878_2.merged.fastq.gz