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Port to Nextflow while keeping old jobs/tasks #5

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vinjana opened this issue Dec 7, 2020 · 0 comments
Open

Port to Nextflow while keeping old jobs/tasks #5

vinjana opened this issue Dec 7, 2020 · 0 comments

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@vinjana
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vinjana commented Dec 7, 2020

Migrate the sophia and sophiaAnnotate jobs to Nextflow. Do not touch the jobs themselves more than is necessary to for the migration.

  • Set up the NF project.
  • Remove/renome RODDY_ variables
  • Use the plugin XML to set up the default configuration for Nextflow.
  • Migrate the resource requirements from the plugin XML into workflow.
  • Only include the environment-modules based software stack in the migration

Use the https://github.com/DKFZ-ODCF/nf-bam2fastq workflow as an example, of how the workflow should look like in the end.

@vinjana vinjana changed the title Port to Nextflow Port to Nextflow while keeping old jobs/tasks Dec 7, 2020
@vinjana vinjana added this to the Migrate to Nextflow milestone Dec 7, 2020
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