feat: Add results for sarek 3.4.4 (#48)

Co-authored-by: FriederikeHanssen <[email protected]>
Co-authored-by: Famke Bäuerle <[email protected]>

Author: FriederikeHanssen

config/config.yaml

@@ -609,10 +609,10 @@ variant-calls:
       filename: NA12878x2_78_var.vcf.gz
     benchmark: giab-NA12878-twist
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
-  nf-core-sarek-343-strelka2-agilent-75M:
+  nf-core-sarek-344-strelka2-agilent-75M:
     labels:
       site: nf-core
-      pipeline: nf-core/sarek v3.4.3
+      pipeline: nf-core/sarek v3.4.4
       trimming: FastP v0.23.4
       read-mapping: bwa mem v
       base-quality-recalibration: gatk4 v4.5.0.0
@@ -622,14 +622,14 @@ variant-calls:
       reads: 75M
     subcategory: NA12878-agilent
     zenodo:
-      deposition: 13323665
-      filename: NA12878_75M.strelka.variants.vcf.gzNA12878_75M.strelka.variants.vcf.gz
+      deposition: 13742023
+      filename: NA12878_75M.strelka.variants.vcf.gz
     benchmark: giab-NA12878-agilent-75M
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
-  nf-core-sarek-343-deepvariant-agilent-75M:
+  nf-core-sarek-344-deepvariant-agilent-75M:
     labels:
       site: nf-core
-      pipeline: nf-core/sarek v3.4.3
+      pipeline: nf-core/sarek v3.4.4
       trimming: FastP v0.23.4
       read-mapping: bwa mem v
       base-quality-recalibration: gatk4 v4.5.0.0
@@ -639,14 +639,14 @@ variant-calls:
       reads: 75M
     subcategory: NA12878-agilent
     zenodo:
-      deposition: 13323665
-      filename: NA12878_75M.deepvariant.vcf.gzNA12878_75M.deepvariant.vcf.gz
+      deposition: 13742023
+      filename: NA12878_75M.deepvariant.vcf.gz
     benchmark: giab-NA12878-agilent-75M
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
-  nf-core-sarek-343-freebayes-agilent-75M:
+  nf-core-sarek-344-freebayes-agilent-75M:
     labels:
       site: nf-core
-      pipeline: nf-core/sarek v3.4.3
+      pipeline: nf-core/sarek v3.4.4
       trimming: FastP v0.23.4
       read-mapping: bwa mem v
       base-quality-recalibration: gatk4 v4.5.0.0
@@ -656,14 +656,14 @@ variant-calls:
       reads: 75M
     subcategory: NA12878-agilent
     zenodo:
-      deposition: 13323665
-      filename: NA12878_75M.freebayes.vcf.gzNA12878_75M.freebayes.vcf.gz
+      deposition: 13742023
+      filename: NA12878_75M.freebayes.vcf.gz
     benchmark: giab-NA12878-agilent-75M
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
-  nf-core-sarek-343-haplotypecaller-agilent-75M:
+  nf-core-sarek-344-haplotypecaller-agilent-75M:
     labels:
       site: nf-core
-      pipeline: nf-core/sarek v3.4.3
+      pipeline: nf-core/sarek v3.4.4
       trimming: FastP v0.23.4
       read-mapping: bwa mem v
       base-quality-recalibration: gatk4 v4.5.0.0
@@ -673,14 +673,14 @@ variant-calls:
       reads: 75M
     subcategory: NA12878-agilent
     zenodo:
-      deposition: 13323665
-      filename: NA12878_75M.haplotypecaller.filtered.vcf.gzNA12878_75M.haplotypecaller.filtered.vcf.gz
+      deposition: 13742023
+      filename: NA12878_75M.haplotypecaller.filtered.vcf.gz
     benchmark: giab-NA12878-agilent-75M
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
-  nf-core-sarek-343-strelka2-agilent-200M:
+  nf-core-sarek-344-strelka2-agilent-200M:
     labels:
       site: nf-core
-      pipeline: nf-core/sarek v3.4.3
+      pipeline: nf-core/sarek v3.4.4
       trimming: FastP v0.23.4
       read-mapping: bwa mem v
       base-quality-recalibration: gatk4 v4.5.0.0
@@ -690,14 +690,14 @@ variant-calls:
       reads: 200M
     subcategory: NA12878-agilent
     zenodo:
-      deposition: 13323665
-      filename: NA12878_200M.strelka.variants.vcf.gzNA12878_200M.strelka.variants.vcf.gz
+      deposition: 13742023
+      filename: NA12878_200M.strelka.variants.vcf.gz
     benchmark: giab-NA12878-agilent-200M
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
-  nf-core-sarek-343-deepvariant-agilent-200M:
+  nf-core-sarek-344-deepvariant-agilent-200M:
     labels:
       site: nf-core
-      pipeline: nf-core/sarek v3.4.3
+      pipeline: nf-core/sarek v3.4.4
       trimming: FastP v0.23.4
       read-mapping: bwa mem v
       base-quality-recalibration: gatk4 v4.5.0.0
@@ -707,14 +707,14 @@ variant-calls:
       reads: 200M
     subcategory: NA12878-agilent
     zenodo:
-      deposition: 13323665
-      filename: NA12878_200M.deepvariant.vcf.gzNA12878_200M.deepvariant.vcf.gz
+      deposition: 13742023
+      filename: NA12878_200M.deepvariant.vcf.gz
     benchmark: giab-NA12878-agilent-200M
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
-  nf-core-sarek-343-freebayes-agilent-200M:
+  nf-core-sarek-344-freebayes-agilent-200M:
     labels:
       site: nf-core
-      pipeline: nf-core/sarek v3.4.3
+      pipeline: nf-core/sarek v3.4.4
       trimming: FastP v0.23.4
       read-mapping: bwa mem v
       base-quality-recalibration: gatk4 v4.5.0.0
@@ -724,14 +724,14 @@ variant-calls:
       reads: 200M
     subcategory: NA12878-agilent
     zenodo:
-      deposition: 13323665
-      filename: NA12878_200M.freebayes.vcf.gzNA12878_200M.freebayes.vcf.gz
+      deposition: 13742023
+      filename: NA12878_200M.freebayes.vcf.gz
     benchmark: giab-NA12878-agilent-200M
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
-  nf-core-sarek-343-haplotypecaller-agilent-200M:
+  nf-core-sarek-344-haplotypecaller-agilent-200M:
     labels:
       site: nf-core
-      pipeline: nf-core/sarek v3.4.3
+      pipeline: nf-core/sarek v3.4.4
       trimming: FastP v0.23.4
       read-mapping: bwa mem v
       base-quality-recalibration: gatk4 v4.5.0.0
@@ -741,8 +741,8 @@ variant-calls:
       reads: 200M
     subcategory: NA12878-agilent
     zenodo:
-      deposition: 13323665
-      filename: NA12878_200M.haplotypecaller.filtered.vcf.gzNA12878_200M.haplotypecaller.filtered.vcf.gz
+      deposition: 13742023
+      filename: NA12878_200M.haplotypecaller.filtered.vcf.gz
     benchmark: giab-NA12878-agilent-200M
     rename-contigs: resources/rename-contigs/ucsc-to-ensembl.txt
 custom-benchmarks: