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Future implementation to automate viralrecon execution #244

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Shettland opened this issue Jan 11, 2024 · 0 comments
Closed

Future implementation to automate viralrecon execution #244

Shettland opened this issue Jan 11, 2024 · 0 comments

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@Shettland
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Right now in order to launch viralrecon all the work has to be done manually. A new module could be implemented to do the following tasks:

  1. Create folder structure to launch viralrecon in the desired folder (HPC), taking support from buisciii-tools
  2. Copy/move the fastq files to RAW
  3. Extract metadata from json with .get("r1/r2_fastq_filepath") to create the samplesheet
  4. Load the necessary modules
  5. Launch viralrecon if possible
@Shettland Shettland mentioned this issue Jan 23, 2024
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@Shettland Shettland closed this as not planned Won't fix, can't repro, duplicate, stale Jan 23, 2024
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@Shettland