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uclahs-cds / pipeline-align-DNA

Nextflow pipeline to align paired DNA FASTQs and sort, mark duplicates, and index resulting alignment
https://uclahs-cds.github.io/pipeline-align-DNA/
GNU General Public License v2.0
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Update cluster reference paths #335

Closed nwiltsie closed 3 weeks ago

nwiltsie commented 3 weeks ago

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/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.

Original Updated
/hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa :white_check_mark: /hot/resource/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa :white_check_mark:
/hot/ref/reference/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta :white_check_mark: /hot/resource/reference-genome/GRCh38-BI-20160721/Homo_sapiens_assembly38.fasta :white_check_mark:
/hot/ref/tool-specific-input/HISAT2-2.2.1/GRCh38-BI-20160721/index/Homo_sapiens_assembly38 (Parent folders match) /hot/resource/tool-specific-input/HISAT2-2.2.1/GRCh38-BI-20160721/index/Homo_sapiens_assembly38 (Parent folders match)
/hot/ref/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa.* (Parent folders match) /hot/resource/tool-specific-input/BWA-MEM2-2.2.1/GRCh38-BI-20160721/index/genome.fa.* (Parent folders match)
/hot/ref/tool-specific-input/HISAT2-2.2.1/GRCh38-BI-20160721/index/Homo_sapiens_assembly38.*.ht2 (Parent folders match) /hot/resource/tool-specific-input/HISAT2-2.2.1/GRCh38-BI-20160721/index/Homo_sapiens_assembly38.*.ht2 (Parent folders match)
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