Testing some stuff with snakemake ...

Snakefile

rule rawdata:
    output: '{base}.raw.fa'
    shell: 'echo "ACGTTGCA" > {output}'

rule atot:
    input: '{base}.fa'
    output: '{base}.atot.fa'
    shell: 'cat {input} | sed "s/A/T/g" > {output}'

rule ctog:
    input: '{base}.fa'
    output: '{base}.ctog.fa'
    shell: 'cat {input} | sed "s/C/G/g" > {output}'

rule ttoa:
    input: '{base}.fa'
    output: '{base}.ttoa.fa'
    shell: 'cat {input} | sed "s/T/A/g" > {output}'

rule gtoc:
    input: '{base}.fa'
    output: '{base}.gtoc.fa'
    shell: 'cat {input} | sed "s/G/C/g" > {output}'

rule final:
    input: 
        expand("{rid}.raw.atot.ttoa.fa", rid=config["rid"])

Run with e.g:

snakemake final --config='rid=r1'