Recommended way to do multiple shell commands with shell()

Question

In snakemake, what is the recommended way to use the shell() function to execute multiple commands?

Answer 1

You can call shell() multiple times within the run block of a rule (rules can specify run: rather than shell:):

rule processing_step:
    input:
        # [...]
    output:
        # [...]
    run:
        shell("somecommand {input} > tempfile")
        shell("othercommand tempfile {output}")

Otherwise, since the run block accepts Python code, you could build a list of commands as strings and iterate over them:

rule processing_step:
    input:
        # [...]
    output:
        # [...]
    run:
        commands = [
            "somecommand {input} > tempfile",
            "othercommand tempfile {output}"
        ]
        for c in commands:
            shell(c)

If you don't need Python code during the execution of the rule, you can use triple-quoted strings within a shell block, and write the commands as you would within a shell script. This is arguably the most readable for pure-shell rules:

rule processing_step:
    input:
        # [...]
    output:
        # [...]
    shell:
        """
        somecommand {input} > tempfile
        othercommand tempfile {output}
        """

If the shell commands depend on the success/failure of the preceding command, they can be joined with the usual shell script operators like || and &&:

rule processing_step:
    input:
        # [...]
    output:
        # [...]
    shell:
        "command_one && echo 'command_one worked' || echo 'command_one failed'"