As part of a pipeline, I am trying to create a rule which takes a file containing file paths to gVCF files and copies them to a compute node. I would like to have all output files defined in the output of the rule, so they will get delete when I mark them with temp(). Currently I am doing the following:

rule CopyToNode:
        input:
                gVCF_list
        output:
                gVCFs_copy_node
        threads:
                2
        shell:
                """
                cat {input} | xargs -n1 -P{threads} -I% rsync  -avh % {SCRATCH_DIR}
                awk -F/ '{{print $NF}}' {input} | awk '{{printf "{SCRATCH_DIR}%s\\n", $0}}' > {output}
                """

This however doesn't actually have the file names in the rule output (the output is just a file containing the file path).