From 167f7aa824acbbf56ec1b14ad6355b22b5f15b6f Mon Sep 17 00:00:00 2001 From: ggabernet Date: Mon, 4 Jul 2022 19:54:48 +0200 Subject: [PATCH 1/3] add test full config to aws s3 --- conf/test_full.config | 2 +- tests/csv/3.0/test_full_data.csv | 2 -- 2 files changed, 1 insertion(+), 3 deletions(-) delete mode 100644 tests/csv/3.0/test_full_data.csv diff --git a/conf/test_full.config b/conf/test_full.config index 6ee78825d4..094429e353 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,7 +15,7 @@ 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 = 's3://nf-core-awsmegatests/sarek/input/test_NA12878_WES_30x.csv' // Other params tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep' diff --git a/tests/csv/3.0/test_full_data.csv b/tests/csv/3.0/test_full_data.csv deleted file mode 100644 index 6506a1be98..0000000000 --- a/tests/csv/3.0/test_full_data.csv +++ /dev/null @@ -1,2 +0,0 @@ -patient,status,sample,lane,fastq_1,fastq_2 -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 From 742405e0983a3450a729bab4a4ac3bd0d0a1916c Mon Sep 17 00:00:00 2001 From: ggabernet Date: Mon, 4 Jul 2022 19:57:12 +0200 Subject: [PATCH 2/3] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1da0c0754b..0083f23424 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -33,7 +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 +- [#604](https://github.com/nf-core/sarek/pull/604), [#617](https://github.com/nf-core/sarek/pull/617) - Added full size tests WGS 30x NA12878 ### Changed From 74fdfd6526e922114b08dae88a70a327dff89333 Mon Sep 17 00:00:00 2001 From: ggabernet Date: Tue, 5 Jul 2022 10:01:42 +0200 Subject: [PATCH 3/3] add sampleseet in test-datasets --- conf/test_full.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/test_full.config b/conf/test_full.config index 094429e353..e86e2fd226 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -15,7 +15,7 @@ params { config_profile_description = 'Full test dataset to check pipeline function' // Input data for full size test - input = 's3://nf-core-awsmegatests/sarek/input/test_NA12878_WES_30x.csv' + 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'