Snakemake combine ambiguous rules

Question

I am trying to combine some rules. The rule1 creates in automatics {sample}_unmapped.bam file taking information from library_params.txt file, which I cannot specify as output as program outputs it itself, but which I need to use in the rule2. Is there a way for program to attend the rule1 to finish and then run rule2 using the output from rule1? Because the error it is giving me now is: {sample}_unmapped.bam file is missing.

rule rule1:
    input:
        basecalls_dir="/RUN1/Data/Intensities/BaseCalls/",
        barcodes_dir=directory("barcodes"),
        library_params="library_params.txt",
        metrics_file="metrics_output.txt"
    output:
        log="barcodes.log"
    shell:
        """
        java -Djava.io.tmpdir=/path/to/tmp -Xmx2g -jar picard.jar IlluminaBasecallsToSam BASECALLS_DIR={input.basecalls_dir} BARCODES_DIR={input.barcodes_dir} LANE=1 READ_STRUCTURE=151T8B9M8B151T RUN_BARCODE=run1 LIBRARY_PARAMS={input.library_params} MOLECULAR_INDEX_TAG=RX ADAPTERs_TO_CHECK=INDEXED READ_GROUP_ID=BO NUM_PROCESSORS=2 IGNORE_UNEXPECTED_BARCODES=true > {output.log}
        """
        
rule rule2:
    input:
        log="barcodes.log",
        infile="{sample}_unmapped.bam"
    params:
        ref="ref.fasta"
    output:
        outfile="{sample}.mapped.bam"
    shell:
        """
        java -Djava.io.tmpdir=/path/to/tmp -Xmx2g -jar picard.jar SamToFastq I={input.infile} F=/dev/stdout INTERLEAVE=true | bwa mem -p -t 7 {params.ref} /dev/stdin | java -Djava.io.tmpdir=/path/to/tmp -Xmx4g -jar picard.jar MergeBamAlignment UNMAPPED={input.infile} ALIGNED=/dev/stdin O={output.outfile} R={params.ref} SORT_ORDER=coordinate MAX_GAPS=-1 ORIENTATIONS=FR

Answer 1

In rule2 I would move infile="{sample}_unmapped.bam" from the input directive to the params directive. And of course you would change the shell script from I={input.infile} to I={params.infile}.

rule2 will still wait for rule1 to complete because you give barcodes.log as input to rule2.