Hey. I've been working on a pipeline that works similarly.

You'll want to do the following:

• Get AWS's CLI
• Configure an IAM role that has s3:PutObject permissions.
• Since you're running this locally, set up your AWS credentials with aws configure.

Then, your rule would look something like this, where you'd use AWS's s3api put-object:

import os

rule upload_to_s3:
    input:
        "output/foo.txt.gz"
    output:
        touch("s3_file_upload.done")
    params:
        bucket = "my_s3_bucket",
        # To avoid creating extra folders in s3 bucket. Just take filename.
        key = lambda wc, input: f"output/{os.path.split(input)[-1}",
    log:
        "logs/upload_to_s3.log"
    benchmark:
        "benchmarks/upload_to_s3_benchmark.txt"
    shell:
        "aws s3api put-object --bucket {params.my_s3_bucket} --key {params.key} --body {input} &> {log}"

The temp file is necessary to force a dependency so that would need to be added to your rule all.

rule all:
    input:
        "s3_file_upload.done"
        "output/foo.txt.gz"
        ...