Autofix Nextflow configuration regression tests

uclahs-cds · Jun 27, 2024 · 25a0b8e · 25a0b8e
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diff --git a/test/configtest-F16.json b/test/configtest-F16.json
@@ -53,9 +53,13 @@
       "aligner": "BWA-MEM2-2.2.1",
       "blcds_registered_dataset": false,
       "bundle_contest_hapmap_3p3_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz",
+      "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi",
       "bundle_known_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz",
+      "bundle_known_indels_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi",
       "bundle_mills_and_1000g_gold_standard_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+      "bundle_mills_and_1000g_gold_standard_indels_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
       "bundle_v0_dbsnp138_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz",
+      "bundle_v0_dbsnp138_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi",
       "cache_intermediate_pipeline_steps": false,
       "dataset_id": "A-mini",
       "docker_container_registry": "ghcr.io/uclahs-cds",
@@ -225,6 +229,8 @@
         }
       },
       "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
+      "reference_fasta_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
+      "reference_fasta_fai": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
       "samples_to_process": [
         {
           "id": "4915723",

diff --git a/test/configtest-F32.json b/test/configtest-F32.json
@@ -53,9 +53,13 @@
       "aligner": "BWA-MEM2-2.2.1",
       "blcds_registered_dataset": false,
       "bundle_contest_hapmap_3p3_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz",
+      "bundle_contest_hapmap_3p3_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi",
       "bundle_known_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz",
+      "bundle_known_indels_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi",
       "bundle_mills_and_1000g_gold_standard_indels_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz",
+      "bundle_mills_and_1000g_gold_standard_indels_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi",
       "bundle_v0_dbsnp138_vcf_gz": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz",
+      "bundle_v0_dbsnp138_vcf_gz_tbi": "/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi",
       "cache_intermediate_pipeline_steps": false,
       "dataset_id": "A-mini",
       "docker_container_registry": "ghcr.io/uclahs-cds",
@@ -225,6 +229,8 @@
         }
       },
       "reference_fasta": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta",
+      "reference_fasta_dict": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict",
+      "reference_fasta_fai": "/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai",
       "samples_to_process": [
         {
           "id": "4915723",