keeping temp file option for singularity run

[bioinfogit]

Hi How can I keep temp file to then end of the run while running with singularity?

Bw

[bioinfogit]

then*=the

[paudano]

Add "--nt" to the command-line to instruct the pipeline to leave temp files after it is done with them. All files marked as temporary are written to the temp directory, so all temp files can be removed by deleting the temp directory when you are ready to clear them.

For example: singularity run --bind "$(pwd):$(pwd)" --writable-tmpfs library://becklab/pav/pav:latest --cores 12 --nt

Any Snakemake options, like --nt, can be appended to control the workflow or request specific files be generated (e.g. Can run specific samples or run up to a step and stop).

Let me know if this helps.

[bioinfogit]

Dear Peter

thanks for this. yes it was very helpful

Bw