Snakefile

# Rule to count the number of lines in input.interleaved.fastq
rule count_lines:
    input:
        "input.interleaved.fastq"
    output:
        "line_count.txt"
    shell:
        "wc -l < {input} > {output}"

# Rule to convert paired-end FASTQ files to interleaved format
# TODO: actually *interleave* them
rule convert_to_interleaved:
    input:
        R1="input_R1.fastq",
        R2="input_R2.fastq"
    output:
        "input.interleaved.fastq"
    shell:
        "cat {input.R1} {input.R2} > {output}"

# Rule to symlink input.fastq to input.interleaved.fastq
rule symlink_input:
    input:
        "input.fastq"
    output:
        "input.interleaved.fastq"
    run:
        import os
        os.symlink(input[0], output[0])