Merge pull request #731 from FriederikeHanssen/aws_fullsize

switch germline and somatic full tests
nf-core · Sep 6, 2022 · 9f08fd8 · evanfloden · Sep 16, 2022 · maxulysse
2 parents 251f690 + b6a867e
commit 9f08fd8
Show file tree

Hide file tree

Showing 5 changed files with 33 additions and 32 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,6 +23,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#720](https://github.com/nf-core/sarek/pull/720) - Sync `TEMPLATE` with `tools` `2.5`
 - [#723](https://github.com/nf-core/sarek/pull/723) - Sync `TEMPLATE` with `tools` `2.5.1`
 - [#730](https://github.com/nf-core/sarek/pull/730) - Reduce number of tests
+- [#731](https://github.com/nf-core/sarek/pull/731) - Run the somatic test as default on `-profile test_full`, the germline can be tested with `-profile test_full_somatic`
 
 ### Fixed
 

diff --git 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 = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/NA12878_WGS_30x_full_test.csv'
+    input = 'https://raw.githubusercontent.com/nf-core/test-datasets/sarek/testdata/csv/HCC1395_WXS_somatic_full_test.csv'
 
     // Other params
-    tools = 'strelka,freebayes,haplotypecaller,deepvariant,manta,tiddit,cnvkit,vep'
-
-    split_fastq = 50000000
+    tools = 'strelka,mutect2,freebayes,ascat,manta,cnvkit,tiddit,controlfreec,vep'
+    split_fastq = 20000000
+    intervals   = 's3://nf-core-awsmegatests/sarek/input/S07604624_Padded_Agilent_SureSelectXT_allexons_V6_UTR.bed'
+    wes         = true
 }
diff --git a/conf/test_full_germline.config b/conf/test_full_germline.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,<docker/singularity> --outdir <OUTDIR>
+
+----------------------------------------------------------------------------------------
+*/
+
+params {
+    config_profile_name        = 'Full test profile for germline VC'
+    config_profile_description = 'Full test dataset to check germline VC pipeline function'
+
+    // Input data for full size test
+    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'
+
+    split_fastq = 50000000
+}
diff --git a/conf/test_full_somatic.config b/conf/test_full_somatic.config
diff --git a/nextflow.config b/nextflow.config
@@ -201,9 +201,9 @@ profiles {
         executor.cpus          = 16
         executor.memory        = 60.GB
     }
-    test              { includeConfig 'conf/test.config' }
-    test_full         { includeConfig 'conf/test_full.config' }
-    test_full_somatic { includeConfig 'conf/test_full_somatic.config' }
+    test               { includeConfig 'conf/test.config' }
+    test_full          { includeConfig 'conf/test_full.config' }
+    test_full_germline { includeConfig 'conf/test_full_germline.config' }
 }