save checkpoint to a designated directory?

[LiQian-XC]

Hi,

Thank you for developing this useful tool.

When I run cellbender (v.0.3.0), I found that the checkpoint file (ckpt.tar.gz) was saved under the current directory, not in the same directory as output (I saved output in a different directory). I'm wondering whether I can specify a path for the checkpoint.

Thank you in advance.

Best,
Qian

[shahrozeabbas]

Having a similar problem, Cellbender needs to be run/called in the directory with your data as you can't provide a path to the checkpoint. Not a major issue, but it hinders usage in a workflow.

[ergonyc]

+1
This is a crucial feature for running this in most workflows.

[nfancy]

+1
I agree, my array jobs on PBSpro are failing due to a mismatch between the ckpt.tar.gz hashes. I am using the singularity image of cellbender and the default directory is my home dir. So, each new job is replacing the ckpt.tar.gz of a previous job.

[esrice]

I'm also having this issue. Would be great if there were an argument to choose where to save this file.

[nfancy]

If it is helpful to anyone, I've managed to save the ckpt.tar.gz in the sample directory using singularity var $HOME in the following way:

singularity exec \
--nv -B ${in_dir}:$HOME \
us.gcr.io-broad-dsde-methods-cellbender-0.3.0.img \
cellbender remove-background \
--input $input_file \
--output $output_dir/output.h5

This way, the cpkt.tar.gz are saved in the individual sample directory thus are not overwritten by another.