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organize log level directories #187

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sorelfitzgibbon opened this issue Jun 1, 2023 · 0 comments
Open

organize log level directories #187

sorelfitzgibbon opened this issue Jun 1, 2023 · 0 comments

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@sorelfitzgibbon
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          > `/hot/software/pipeline/pipeline-call-sSNV/Nextflow/development/unreleased/sfitz-fix-vcf-sample-names/a_mini_n2-all-tools-std-input/call-sSNV-6.0.0/TWGSAMIN000001-T001-S01-F/log-call-sSNV-6.0.0-20230524T230134Z/process-log/SomaticSniper-1.0.5.0/somaticsniper`

Log files were moved up from these redundant directory levels, except for compress_index_VCF which is from an external process. I assume the extra level is needed in other pipelines. Perhaps within the submodule it could be renamed with something like -external. E.g. somaticsniper-external? Or an optional parameter to get rid of it?

For log level directory organization, I think we want to make a separate PR as this PR is getting bigger.

Originally posted by @tyamaguchi-ucla in #183 (comment)

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