snakemake: default remote prefix duplicated for checkpoint output on cloud

Snakemake version 5.22.1

Describe the bug Using the --default-remote-prefix parameter will cause MissingInputException errors to arise for the outputs of checkpoint rules.

Steps to Reproduce Follow the Google Life Sciences Executor Tutorial but convert the bwa_map rule into a checkpoint like this

diff --git Snakefile Snakefile
index 68974d1..d519d4f 100644
--- Snakefile
+++ Snakefile
@@ -4,7 +4,7 @@ rule all:
     input:
         "plots/quals.svg"

-rule bwa_map:
+checkpoint bwa_map:
     input:
         fastq="samples/{sample}.fastq",
         idx=multiext("genome.fa", ".amb", ".ann", ".bwt", ".pac", ".sa")
@@ -19,7 +19,7 @@ rule bwa_map:

 rule samtools_sort:
     input:
-        "mapped_reads/{sample}.bam"
+        lambda wildcards: checkpoints.bwa_map.get(sample=wildcards.sample).output[0]
     output:
         "sorted_reads/{sample}.bam"
     conda:

and then you should see the following when running the pipeline:

Building DAG of jobs...
MissingInputException in line 20 of Snakefile:
Missing input files for rule samtools_sort:
snakemake-testing-data/snakemake-testing-data/mapped_reads/A.bam

Notice how snakemake-testing-data appears prepended twice?

Bug Hypothesis I think rules.apply_default_remote() is being applied to the output more than once. It might help to check whether incomplete is true on this line before executing rules.apply_default_remote()?

It might be possible that this is a bug that extends beyond the life sciences executor (to other cloud environments), but I haven’t tested that yet.