WIP Internal Benchmarking

conf/benchmark.config

@@ -0,0 +1,18 @@
+params {
+    config_profile_name        = 'Full benchmark profile for germline VC'
+    config_profile_description = 'Full benchmark dataset to check germline VC pipeline '
+
+    // 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,vep'
+    intervals   = 's3://ngi-igenomes/test-data/sarek/Agilent_v7.bed'
+    wes         = true
+    trim_fastq  = true
+
+    // Benchmark
+    benchmark = true
+    truth_vcf = 'https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.vcf.gz'
+    truth_bed = 'https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/release/NA12878_HG001/NISTv4.2.1/GRCh38/HG001_GRCh38_1_22_v4.2.1_benchmark.bed'
+}

main.nf

@@ -147,6 +147,10 @@ workflow NFCORE_SAREK {
         known_snps,
         pon)
 
+    // Gather Benchmark data from params
+    truth_vcf = params.truth_vcf ? Channel.fromPath(params.truth_vcf).map{ it -> [ [id:'truth_vcf'], it ] }.collect() : Channel.empty()
+    truth_bed = params.truth_bed ? Channel.fromPath(params.truth_bed).map{ it -> [ [id:'truth_bed'], it ] }.collect() : Channel.empty()
+
     // Gather built indices or get them from the params
     // Built from the fasta file:
     dict        = params.dict       ? Channel.fromPath(params.dict).map{ it -> [ [id:'dict'], it ] }.collect()
@@ -305,7 +309,9 @@ workflow NFCORE_SAREK {
         vep_extra_files,
         vep_fasta,
         vep_genome,
-        vep_species
+        vep_species,
+        truth_vcf,
+        truth_bed
     )
     emit:
     multiqc_report = SAREK.out.multiqc_report // channel: /path/to/multiqc_report.html

modules.json

@@ -21,6 +21,11 @@
                         "git_sha": "d1e0ec7670fa77905a378627232566ce54c3c26d",
                         "installed_by": ["modules"]
                     },
+                    "bcftools/index": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
                     "bcftools/mpileup": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
@@ -354,6 +359,16 @@
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
                         "installed_by": ["bam_ngscheckmate"]
                     },
+                    "rtgtools/format": {
+                        "branch": "master",
+                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "installed_by": ["modules"]
+                    },
+                    "rtgtools/vcfeval": {
+                        "branch": "master",
+                        "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd",
+                        "installed_by": ["modules"]
+                    },
                     "samblaster": {
                         "branch": "master",
                         "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",