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Clinical-Genomics-Lund / nextflow_wgs

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Don't write /access/ symlink paths to case.yaml when running with `--dev` #154

Open alkc opened 7 months ago

alkc commented 7 months ago

Several paths are pointed to /access/ in the final case yaml file when running the pipeline in --dev, although dev samples are not symlinked in /access/ by default.

sample.bam_path is pointed to /access/ for wgs, oncov1 and oncov2. All VCF and plot paths are pointed to access for oncov2.

To make scout testing easier and quicker anything run with --dev should by default not point to access, or a flag could be added that omits this behavior and keeps the original results_dev data paths when writing to the yaml.

alkc commented 7 months ago

As in #139 I just don't wanna waste time editing stuff by hand or remembering to run auxiliary scripts