Cluster submission changes input files

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Issue #1298 resolved
paul created an issue

I stumbled across a weird behaviour:

When submitting my workflow to the cluster snakemake uses a wrong input file. When executed locally the workflow uses the correct input files.

This might be related to: https://bitbucket.org/snakemake/snakemake/issues/1284/requesting-checkpoint-output-in-rule-all

I can’t provide a minimal example at the moment, but wanted to document the occurrence of this bug.

This occurred on version 5.5.3.

I launched the cluster workflow with

snakemake --use-conda    --cluster-config config/cluster.yaml --cluster "bsub  -q [..] -n {cluster.nCPU} -M {cluster.mem}  -e {cluster.error} -R {cluster.resources}  -o {cluster.output} -J {cluster.name}" -p -j 1

and the local execution with:

snakemake -p --use-conda

The workflow uses checkpoints (several of them) and input functions. Thus narrowing the problem down, will take time and effort.

I know submission without a example is not perfect, thus I don’t expect any help or acknowledgement, but in case in the future someone has a similar bug, I wanted to document it.