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I uploaded the workflow here https://github.com/dib-lab/portable-snakemake-workflows/blob/main/workflows/sgc-prep-cluster
To use this as a downloading workflow, change this line in the config to your metadata file containing a 'Run' column and this command to only run the fasterq-dump command:
snakemake -s sgc-prep-cluster --resources allowed_jobs=100 --profile slurm -R --until dump
This should get you the files that you need.
Think I should break it down though as it got bigger than I had wanted. I am thinking of changing into three workflows:
That way I can build off of each in interesting ways instead of needing to use the -R --until type system.
-R --until
The text was updated successfully, but these errors were encountered:
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I uploaded the workflow here https://github.com/dib-lab/portable-snakemake-workflows/blob/main/workflows/sgc-prep-cluster
To use this as a downloading workflow, change this line in the config to your metadata file containing a 'Run' column and this command to only run the fasterq-dump command:
snakemake -s sgc-prep-cluster --resources allowed_jobs=100 --profile slurm -R --until dumpThis should get you the files that you need.
Think I should break it down though as it got bigger than I had wanted. I am thinking of changing into three workflows:
That way I can build off of each in interesting ways instead of needing to use the
-R --until type system.The text was updated successfully, but these errors were encountered: