Update cluster reference paths #185
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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/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta/hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta/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/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/hapmap_3.3.hg38.vcf.gz/hot/resource/tool-specific-input/GATK/GRCh38/hapmap_3.3.hg38.vcf.gz/hot/ref/tool-specific-input/GATK/GRCh38/1000G_omni2.5.hg38.vcf.gz/hot/resource/tool-specific-input/GATK/GRCh38/1000G_omni2.5.hg38.vcf.gz/hot/ref/tool-specific-input/GATK/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz/hot/resource/tool-specific-input/GATK/GRCh38/1000G_phase1.snps.high_confidence.hg38.vcf.gz/hot/ref/reference/GRCh38-BI-20160721/hot/resource/reference-genome/GRCh38-BI-20160721