add pipeline tests

qbic-pipelines · Dec 10, 2024 · 577b7d2 · 577b7d2
1 parent 7bf1719
commit 577b7d2
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Showing 5 changed files with 14 additions and 13 deletions.
diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv
@@ -1,5 +1,4 @@
 sample,gvcf,vcf_path,vcf_index_path
-FFPE,false,/Users/famke/01-japan-project/test-files/variant_calling/haplotypecaller/S1/S1.haplotypecaller.filtered.vcf.gz,/Users/famke/01-japan-project/test-files/variant_calling/haplotypecaller/S1/S1.haplotypecaller.filtered.vcf.gz.tbi
-FFPE,false,/Users/famke/01-japan-project/test-files/variant_calling/freebayes/S1/S1.freebayes.vcf.gz,/Users/famke/01-japan-project/test-files/variant_calling/freebayes/S1/S1.freebayes.vcf.gz.tbi
-WES,false,/Users/famke/01-japan-project/test-files/S1.haplotypecaller.vcf.gz,/Users/famke/01-japan-project/test-files/S1.haplotypecaller.vcf.gz.tbi
-strelka,false,/Users/famke/01-japan-project/test-files/variant_calling/strelka/S1/S1.strelka.genome.vcf.gz,
+SAMPLE-1,false,path/to/vcf.gz,path/to/.vcf.gz.tbi
+SAMPLE-1,false,path/to/vcf.gz,path/to/.vcf.gz.tbi
+SAMPLE-2,true,path/to/g.vcf.gz,path/to/g.vcf.gz.tbi
diff --git a/conf/test.config b/conf/test.config
@@ -23,10 +23,8 @@ params {
     config_profile_description = 'Minimal test dataset to check pipeline function'
 
     // Input data
-    // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input  = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv'
+    input  = "${projectDir}/tests/csv/input.csv"
 
     // Genome references
-    genome = 'R64-1-1'
+    genome = 'GATK.GrCh38'
 }
diff --git a/conf/test_full.config b/conf/test_full.config
@@ -14,11 +14,9 @@ params {
     config_profile_name        = 'Full test profile'
     config_profile_description = 'Full test dataset to check pipeline function'
 
-    // Input data for full size test
-    // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA)
-    // TODO nf-core: Give any required params for the test so that command line flags are not needed
-    input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv'
+    // Input data
+    input  = "${projectDir}/tests/csv/input-full.csv"
 
     // Genome references
-    genome = 'R64-1-1'
+    genome = 'GATK.GrCh38'
 }
diff --git a/tests/input-full.csv b/tests/input-full.csv
@@ -0,0 +1,4 @@
+sample,gvcf,vcf_path,vcf_index_path
+ch22,false,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz,
+gvcf,true,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/gvcf/test.genome.g.vcf.gz,
+indexed,false,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/vcf/NA12878_chrM.vcf.gz.tbi
diff --git a/tests/input.csv b/tests/input.csv
@@ -0,0 +1,2 @@
+sample,gvcf,vcf_path,vcf_index_path
+ch22,false,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz,
Original file line number	Diff line number	Diff line change
		@@ -0,0 +1,2 @@
		sample,gvcf,vcf_path,vcf_index_path
		ch22,false,https://github.com/nf-core/test-datasets/raw/refs/heads/modules/data/genomics/homo_sapiens/illumina/vcf/NA12878.chr22.1X.vcf.gz,