Update cluster reference paths

[nwiltsie]

This PR updates reference paths that were renamed during the most recent cluster downtime.

I was specifically looking for single lines containing one (or more) of the following keys, so I missed any paths split across multiple lines.

Search String
/hot/ref/
/hot/ref/cohort/TCGA/CCG-AIM/
/hot/ref/cohort/TCGA/PanCanAtlas/
/hot/ref/database/1000Genomes/
/hot/ref/database/GDC-34.0/
/hot/ref/database/PCAWG/
/hot/ref/database/ProstateTumor/Boutros-Yamaguchi-PRAD-CPCG/
/hot/ref/reference/
/hot/resource/SMC-HET/

A table of update filepaths is included below. The original paths still work due to symlinks, so I was able to verify that the updated paths resolve to the same files as the original paths.

Original	Updated
/hot/ref/reference/GRCh38-BI-20160721	/hot/resource/reference-genome/GRCh38-BI-20160721
/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict	/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.dict
/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta	/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta
/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai	/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta.fai
/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz	/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz
/hot/ref/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi	/hot/resource/tool-specific-input/GATK/GRCh38/Biallelic/hapmap_3.3.hg38.BIALLELIC.PASS.2021-09-01.vcf.gz.tbi
/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz	/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz
/hot/ref/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi	/hot/resource/tool-specific-input/GATK/GRCh38/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi
/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz	/hot/resource/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
/hot/ref/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi	/hot/resource/tool-specific-input/GATK/GRCh38/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz	/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz
/hot/ref/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi	/hot/resource/tool-specific-input/GATK/GRCh38/resources_broad_hg38_v0_Homo_sapiens_assembly38.dbsnp138.vcf.gz.tbi
/hot/resource/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam	/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n1/output/S2.T-n1.bam

[wiz-inc-8da00b022c]

Wiz Scan Summary

Scan Module						Total
IaC Misconfigurations	0	0	0	0	0	0
Vulnerabilities	0	0	0	0	0	0
Sensitive Data	0	0	0	0	1	1
Secrets	0	0	0	0	0	0
Total	0	0	0	0	1	1

View scan details in Wiz

To detect these findings earlier in the dev lifecycle, try using Wiz Code VS Code Extension.

[yashpatel6]

Looks good! I verified the file paths as well

[rhughwhite]

Looks good!