Typo in the snakemake file

[aleighbrown]

Didn't do a pull request, but

rule selectSolution:
    input:
        #ploidyDirs=expand("results/titan/hmm/titanCNA_ploidy{ploidy}/", ploidy=PLOIDY[config["TitanCNA_maxPloidy"]]),
        resultFiles=expand("results/titan/hmm/titanCNA_ploidy{ploidy}/{tumor}_cluster{clustNum}.titan.txt", tumor=config["pairings"], clustNum=CLUST[config["TitanCNA_maxNumClonalClusters"]], ploidy=PLOIDY[config["TitanCNA_maxPloidy"]])
    output:
        "results/titan/hmm/optimalClusterSolution.txt"
    params:
        solutionRscript=config["TitanCNA_selectSolutionRscript"],
        threshold=config["TitanCNA_solutionThreshold"]
    log:
        "logs/titan/selectSolution.log"
    shell:
        """
                 **ploidyRun2=results/titan/titanCNA_ploidy2/** #currently

        **ploidyRun2=results/titan/hmm/titanCNA_ploidy2/** #but should actually read
        if [ -d results/titan/hmm/titanCNA_ploidy3/ ]; then
            ploidyRun3=results/titan/hmm/titanCNA_ploidy3/
        else
            ploidyRun3=NULL
        fi
        if [ -d results/titan/hmm/titanCNA_ploidy4/ ]; then
            ploidyRun4=results/titan/hmm/titanCNA_ploidy4/
        else
            ploidyRun4=NULL
        fi
        Rscript {params.solutionRscript} --ploidyRun2 $ploidyRun2 --ploidyRun3 $ploidyRun3 --ploidyRun4 $ploidyRun4 --threshold {params.threshold} --outFile {output} > {log} 2> {log}
        """

The first line of the shell command has the wrong foldering. New update working awesome otherwise!!

[gavinha]

Hi @aleighgreen

Thanks for catching this.

Best, Gavin