rseq.smk - BAM index file paths are incorrect (causing occasional crashes with junction_saturation.py)

frattalab / rna_seq_snakemake

Snakemake Pipeline For RNA-Seq in UCL Cluster

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rseq.smk - BAM index file paths are incorrect (causing occasional crashes with junction_saturation.py) #59

Open SamBryce-Smith opened 6 months ago

SamBryce-Smith commented 6 months ago

rule read_distribution:
    input:
        bam = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam"),
        idx = os.path.join(STAR_OUTDIR, "{sample}.Aligned.sorted.out.bam")

This is the case for all RSeQC rules. Might be cause of slow run times for other tools that do not error out when index is not present. Very quick fix

SamBryce-Smith commented 6 months ago

Example errors