wiz-inc-8da00b022c[bot]
commented
1 month ago 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 |
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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.
/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/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 updated filepaths and whether or not they resolve to a file is included below. Where the original paths still exist due to symlinks I verified that they resolve to the same file as the updated path.
/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz/hot/ref/tool-specific-input/GATK/GRCh37/af-only-gnomad.raw.sites.vcf/hot/resource/tool-specific-input/GATK/GRCh37/af-only-gnomad.raw.sites.vcf/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz/hot/ref/tool-specific-input/GATK/GRCh38/1000g_pon.hg38.vcf.gz/hot/resource/tool-specific-input/GATK/GRCh38/1000g_pon.hg38.vcf.gz/hot/ref/tool-specific-input/Strelka2/GRCh38/strelka2_call_region.bed.gz/hot/resource/tool-specific-input/Strelka2/GRCh38/strelka2_call_region.bed.gz/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta/hot/ref/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz/hot/resource/database/dbSNP-155/original/GRCh38/GCF_000001405.39.gz/hot/resource/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam/hot/data/unregistered/SMC-HET/normal/bams/A-mini/n2/output/HG002.N-n2.bam/hot/resource/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam/hot/data/unregistered/SMC-HET/tumours/A-mini/bams/n2/output/S2.T-n2.bam/hot/ref/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz.tbi/hot/resource/tool-specific-input/GATK/GRCh38/af-only-gnomad.hg38.vcf.gz.tbi/hot/ref/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.gz.tbi/hot/resource/tool-specific-input/pipeline-call-sSNV-6.0.0/GRCh38-BI-20160721/Homo_sapiens_assembly38_no-decoy.bed.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