--use-ingularity breaks shadow usage in non-singularity rules

[giesselmann]

Snakemake version
5.7.4

Describe the bug
In a workflow with some rules using singularity and some not, the ones without singularity container will not switch into a shadow directory if the workflow is executed with --use-singularity.

Logs
running the minimal example with snakemake all produces the correct
test.out, test_a.out, test-b.out and test_c.out

running the minimal example with snakemake --use-singularity -k all fails in rule_b and rule_c and produces:
test_a.out, junk_b.out, junk_c.out

Minimal example
Consider the following example

rule all:
    input: "test.out"

rule singularity_ok:
    input:
        "test_a.out",
        "test_b.out",
        "test_c.out"
    output:
        touch("test.out")
    shell:
        """
        test ! -f junk_a.out
        test ! -f junk_b.out
        test ! -f junk_c.out
        """

rule a:
    output:
        "test_a.out"
    singularity:
        "docker://bash"
    shadow:
        "minimal"
    shell:
        'echo 1 > junk_a.out; echo "test" > {output}'

rule b:
    output:
        "test_b.out"
    shadow:
        "minimal"
    shell:
        'echo 1 > junk_b.out; echo "test" > {output}'

rule c:
    output:
        "test_c.out"
    shadow:
        "minimal"
    run:
        with open(output[0], 'w') as fp:
            print("test", file=fp)
        with open('junk_c.out', 'w') as fp:
            print("junk", file=fp)

Additional context
I played a bit around, seems to be related to code in executor.py:

# Change workdir if shadow defined and not using singularity.
# Otherwise, we do the change from inside the container.
passed_shadow_dir = None
if use_singularity and job_rule.singularity_img:
    passed_shadow_dir = shadow_dir
    shadow_dir = None

This is a duplicate of issue 1280 in the bitbucket repo.

Pay

[johanneskoester]

Thanks for reporting! Should be fixed by PR #89.

[giesselmann]

Thank you for the prompt reaction. And for the great software!

[johanneskoester]

Thanks!