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DKFZ-ODCF/SophiaWorkflow

Recurrent artifact in SOPHIA (v35) workflow 2.2.3_v1_0

Dear SOPHIA workflow team, I have found that the SOPHIA workflow v2.2.3_v1_0. I have seen this pop up in Heidelberg HIPO projects and now also in some Berlin projects. My student (@niklasmueboe) looked ...

• naveedishaque
·
• Opened 
  on Sep 6, 2021
·
• #10

DKFZ-ODCF/SophiaWorkflow

Refactor NF sophiaAnnotate task

The sophiaAnnotate needs structural improvements. Simplify the task - Remove duplicate code - Give the task a better structure and consider splitting it into multiple smaller tasks or combining scripts ...

• vinjana
·
• Opened 
  on Dec 7, 2020
·
• #9

DKFZ-ODCF/SophiaWorkflow

Remove temporary file handling from Nextflow task sophiaAnnotate

The sophiaAnnotate Roddy-job is lots of spaghetti code, with duplications, obscure Bash code and too much temporary file handling. Refactor the job after #5 and remove temporary file handling.

• vinjana
·
• Opened 
  on Dec 7, 2020
·
• #8

DKFZ-ODCF/SophiaWorkflow

Containerize

Create a Dockerfile using the Conda environment and run the workflow in Singularity in the cluster. Depends on #6.

• vinjana
·
• Opened 
  on Dec 7, 2020
·
• #7

DKFZ-ODCF/SophiaWorkflow

Conda environment

Create a Conda environment and include it in the Nextflow workflow, including a Conda profile.

• vinjana
·
• Opened 
  on Dec 7, 2020
·
• #6

DKFZ-ODCF/SophiaWorkflow

Port to Nextflow while keeping old jobs/tasks

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 - ...

• vinjana
·
• Opened 
  on Dec 7, 2020
·
• #5

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