diff --git a/CHANGELOG.md b/CHANGELOG.md index 54583b0d0c..65cf02b9a3 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/conf/test_full.config b/conf/test_full.config index cda0459c61..6ee78825d4 100644 --- a/conf/test_full.config +++ b/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' } diff --git a/tests/csv/3.0/test_full_data.csv b/tests/csv/3.0/test_full_data.csv index 97fbf1b837..6506a1be98 100644 --- a/tests/csv/3.0/test_full_data.csv +++ b/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