add another local test job

Author: junjun-zhang

sanger-wxs-variant-calling/tests/local-test.local-2.nf.json

@@ -0,0 +1,21 @@
+{
+  "study_id": "TEST-PR",
+  "tumour_aln_metadata": "data/03905962-f1e1-41e8-9059-62f1e1c1e8fc.analysis.json",
+  "tumour_aln_cram": "data/SA610229.103.20200320.wxs.grch38.cram",
+  "tumour_extra_info": "data/T.SA610229.tsv",
+  "normal_aln_metadata": "data/9940db0f-c100-496a-80db-0fc100d96ac1.analysis.json",
+  "normal_aln_cram": "data/SA610228.67.20200319.wxs.grch38.cram",
+  "normal_extra_info": "data/N.SA610228.tsv",
+  "publish_dir": "outdir",
+  "sangerWxsVariantCaller": {
+    "cpus": 10,
+    "mem": 50,
+    "exclude": "chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr22,chrX,chrY,chrUn%,HLA%,%_alt,%_random,chrM,chrEBV",
+    "vagrent_annot": "/home/ubuntu/references/sanger/VAGrENT_ref_GRCh38_hla_decoy_ebv_ensembl_91.tar.gz",
+    "ref_genome_tar": "/home/ubuntu/references/sanger/core_ref_GRCh38_hla_decoy_ebv.tar.gz",
+    "ref_snv_indel_tar": "/home/ubuntu/references/sanger/SNV_INDEL_ref_GRCh38_hla_decoy_ebv-fragment.tar.gz"  
+  },
+  "generateBas": {
+    "ref_genome_fa": "/home/ubuntu/references/grch38/GRCh38_hla_decoy_ebv.fa"
+  }
+}