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update README
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sreichl committed Sep 11, 2024
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Expand Up @@ -30,7 +30,7 @@ There are three different flavors depending on personal preference and if the wo
- Conductor job (recommended)
- One job (on longq) to rule them all: use a sbatch job script to call and manage (conduct) the execution of all workflow jobs.
- Set ```immediate-submit: false``` in [config.v8+.yaml](./config.v8+.yaml).
- For details see [snakejob_conductor.sh](./snakejob_conductor.sh).
- For details see next section and [snakejob_conductor.sh](./snakejob_conductor.sh).
- Advantages
- Snakemake orchestrates the job submission.
- One place to check progress, log errors/failed jobs, and document performance (e.g., duration).
Expand All @@ -51,7 +51,7 @@ There are three different flavors depending on personal preference and if the wo
- Open question: behaviour of ```--retries``` flag unknown. If someone finds out, please let me know.
# 🐍 Snakejob Conductor (recommended)
# 🐍 Snakejob Conductor
If you want to use a conductor job for the submission and execution of your worklfow follow these steps:
1. Copy ```snakejob_conductor.sh``` to the workflow/project root directory.
2. Go through every line and adapt it according to your setup (e.g., set paths to the log folder and use absolute paths).
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