CODEWITHSUNDEEP
snakemakepicard
Genetics
Genetics

Reputation: 301

Why is Picard MarkDuplicates deleting .bam files in place of .bai files in my Snakemake workflow?

I have done some looking but I cant figure out why picard markduplicates is deleting my bam files and replacing with bai files? I am wanting the metrics and bam files. I am also wanting the bai files and then rename this file to .bam.bai for downstream work. When I leave out CREATE_INDEX=true, I get my metrics and bam. With it in, I get bai files and that isn't renamed either.

rule picard_dupes:
    input: rules.star_aligner.output.bam
    output:
        bam = 'picard/{sampleID}_marked_duplicates.bam',
        metric = 'picard/{sampleID}_marked_dup_metrics.txt'
    threads: 12
    run:
        shell('picard MarkDuplicates \
            -Xmx4G \
            I={input} \
            O={output.bam} \
            M={output.metric} \
            ASSUME_SORT_ORDER=coordinate CREATE_INDEX=true \
            -XX:ParallelGCThreads={threads}')
        shell('mv /PATH/{sampleID}_marked_duplicates.bai /Path/{sampleID}_marked_duplicates.bam.bai')

Upvotes: 0

Views: 115

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