Merge pull request nf-core#1372 from FriederikeHanssen/test_ncbench

Add test profile for ncbench
FriederikeHanssen · Jan 11, 2024 · 78b46de · 78b46de
2 parents 8b492b4 + b683965
commit 78b46de
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Showing 4 changed files with 44 additions and 9 deletions.
diff --git 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/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
 

diff --git a/conf/test_full_germline_ncbench_agilent.config 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,<docker/singularity> --outdir <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
@@ -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' }