Add --pwd flag to singularity command line string

[PabloNA97]

The --pwd flag changes the initial working directory inside the container. Here I outline why I think it would be a good idea to include it:

I have a biobb workflow running biobb of pydock3 (These are not yet shared but I will do it at some point). pydock3 is run from a singularity container. The issue here is that pydock3 makes assumptions regarding where to find each input/output file with respect to the working directory. Thus in the biobb_pydock module I wrote, the --pwd flag is used to fix the working directory inside the container and avoid errors inside the container (I can explain in more detail if needed).

I was using a modified version of biobb_common in which I added the --pwd option in biobb_object.py -> BiobbObject -> create_cmd_line:

        if self.container_working_dir:
            singularity_cmd.append('--pwd')
            singularity_cmd.append(self.container_working_dir)

For now I will keep using the modified environment to run the workflow but it would be nice if the singularity execution could include this option as well (I think container_working_dir is already used with docker)

[PabloNA97]

I think that adding:

        if self.container_working_dir:
            singularity_cmd.append("--pwd")
            singularity_cmd.append(self.container_working_dir)

To line 293 of biobb_common.py would do the trick :)

[gbayarri]

Hi, we will take it into account for the next issue.

Cheers.

[github-actions]

This issue is stale because it has been open for 30 days with no activity. If there is no more activity in the following 14 days it will be automatically closed.

[github-actions]

This issue is stale because it has been open for 30 days with no activity. If there is no more activity in the following 14 days it will be automatically closed.