Update cluster reference paths #87
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nwiltsie
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tyamaguchi-ucla,
yashpatel6 and
Faizal-Eeman
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yashpatel6
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Oct 25, 2024
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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/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.
/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