From 0d36a50473eba89c2168175650ab1057e87d9c3a Mon Sep 17 00:00:00 2001 From: Rike Date: Wed, 15 Nov 2023 09:30:03 +0100 Subject: [PATCH] Add SnpEff to full sized tests --- CHANGELOG.md | 1 + conf/test_full.config | 2 +- conf/test_full_germline.config | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 43650db0e7..bd6bd0ac47 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -39,6 +39,7 @@ Pårtetjåkko is a mountain in the south of the park. - [#1318](https://github.com/nf-core/sarek/pull/1218) - Fix writing of params.json on S3 - [#1324](https://github.com/nf-core/sarek/pull/1324) - Fix various typos & code formatting - [#1325](https://github.com/nf-core/sarek/pull/1325) - Update bcfannotate tests and related config files +- [#1330](https://github.com/nf-core/sarek/pull/1330) - Add SnpEff to full sized tests ### Removed diff --git a/conf/test_full.config b/conf/test_full.config index 97390858b1..1ba5ad2c78 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -18,7 +18,7 @@ params { input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv' // Other params - tools = 'strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,ngscheckmate' + tools = 'ngscheckmate,strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep,snpeff' split_fastq = 20000000 intervals = 's3://ngi-igenomes/test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed' wes = true diff --git a/conf/test_full_germline.config b/conf/test_full_germline.config index a8403dd71d..d731a25709 100644 --- a/conf/test_full_germline.config +++ b/conf/test_full_germline.config @@ -18,6 +18,6 @@ params { input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test.csv' // Other params - tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep' + tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep,snpeff' split_fastq = 50000000 }