From fdcc928513c23f8f007f9d053b9998d3bec58ed3 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Thu, 11 Jan 2024 11:49:23 +0000 Subject: [PATCH 1/2] Add test profile for ncbench --- .github/workflows/cloudtest.yml | 6 +++++ .../test_full_germline_ncbench_agilent.config | 24 +++++++++++++++++++ nextflow.config | 22 ++++++++++------- 3 files changed, 43 insertions(+), 9 deletions(-) create mode 100644 conf/test_full_germline_ncbench_agilent.config diff --git a/.github/workflows/cloudtest.yml b/.github/workflows/cloudtest.yml index 1ad196281f..829d870ff5 100644 --- a/.github/workflows/cloudtest.yml +++ b/.github/workflows/cloudtest.yml @@ -17,6 +17,10 @@ on: description: "Germline full test" type: boolean default: false + germline_ncbench_agilent: + description: "Germline Agilent NCBench test" + type: boolean + default: false aws: description: "AWS Batch" type: boolean @@ -46,6 +50,8 @@ jobs: enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.aws ) ) }} - profile: test_full_germline_azure enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline && inputs.azure ) ) }} + - profile: test_full_germline_ncbench_agilent_aws + enabled: ${{ ( github.repository == 'nf-core/sarek' ) && ( github.event_name != 'workflow_dispatch' || ( inputs.germline_ncbench_agilent && inputs.aws ) ) }} steps: # Launch workflow on AWS Batch diff --git a/conf/test_full_germline_ncbench_agilent.config b/conf/test_full_germline_ncbench_agilent.config new file mode 100644 index 0000000000..23439dfd2a --- /dev/null +++ b/conf/test_full_germline_ncbench_agilent.config @@ -0,0 +1,24 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Nextflow config file for running full-size tests +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + Defines input files and everything required to run a full size pipeline test. + + Use as follows: + nextflow run nf-core/sarek -profile test_full_germline_ncbench_agilent, --outdir + +---------------------------------------------------------------------------------------- +*/ + +params { + config_profile_name = 'Test profile for germline VC' + config_profile_description = 'Agilent test datasets to benchmark germline VC pipeline function using the NCBench framework' + + // Input data for full size test + input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_Agilent_full_test.csv' + + // Other params + tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,vep,snpeff' + intervals = 'https://zenodo.org/record/6513789/files/Agilent_v7.bed' + wes = true +} diff --git a/nextflow.config b/nextflow.config index ad2bd87e3d..7dca8ac1f3 100644 --- a/nextflow.config +++ b/nextflow.config @@ -252,35 +252,39 @@ profiles { } // Basic test profile for CI test { includeConfig 'conf/test.config' } - test_aws { + test_aws { includeConfig 'conf/test.config' params.sentieon_dnascope_model = "s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model" } - test_azure { - includeConfig 'conf/test.config' + test_azure { + includeConfig 'conf/test.config' params.sentieon_dnascope_model = "az://igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Sentieon/SentieonDNAscopeModel1.1.model" } test_cache { includeConfig 'conf/test/cache.config' } // Extra test profiles for full tests on AWS test_full { includeConfig 'conf/test_full.config' } - test_full_aws { - includeConfig 'conf/test_full.config' + test_full_aws { + includeConfig 'conf/test_full.config' } - test_full_azure { + test_full_azure { includeConfig 'conf/test_full.config' params.input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test_azure.csv' params.intervals = 'az://test-data/sarek/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed' params.igenomes_base = "az://igenomes" } test_full_germline { includeConfig 'conf/test_full_germline.config' } - test_full_germline_aws { - includeConfig 'conf/test_full_germline.config' + test_full_germline_aws { + includeConfig 'conf/test_full_germline.config' } - test_full_germline_azure { + test_full_germline_azure { includeConfig 'conf/test_full_germline.config' params.input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test_azure.csv' params.igenomes_base = "az://igenomes" } + test_full_germline_ncbench_agilent { + includeConfig 'conf/test_full_germline_ncbench_agilent.config' + } + // Extra test profiles for more complete CI alignment_to_fastq { includeConfig 'conf/test/alignment_to_fastq.config' } annotation { includeConfig 'conf/test/annotation.config' } From b683965241977216426bc125f323531056cf3838 Mon Sep 17 00:00:00 2001 From: FriederikeHanssen Date: Thu, 11 Jan 2024 11:53:57 +0000 Subject: [PATCH 2/2] update changelog --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 08a95781ea..c5969cf835 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -12,6 +12,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1333](https://github.com/nf-core/sarek/pull/1333) - Back to dev - [#1335](https://github.com/nf-core/sarek/pull/1335) - Add index computation of `bcftools_annotations`, if not provided - [#1340](https://github.com/nf-core/sarek/pull/1340) - Adds Azure test profiles and megatests. +- [#1372](https://github.com/nf-core/sarek/pull/1372) - Add NCBench test profile for Agilent datasets ### Changed