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ammaraziz / ctgap

Chlamydia trachomatis Genome Assembly Pipeline
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error: #6

Closed ammaraziz closed 8 months ago

ammaraziz commented 8 months ago

error:

RuleException in rule scrub in file /home/oolago2/assembly_pipeline/fullTest_Dec23/CtGAP_test/ctgap/workflow/rules/2-scrub.smk, line 1:
AttributeError: 'OutputFiles' object has no attribute 'r1tmp', when formatting the following:

    scrubby scrub-reads     -i {input.r1} {input.r2}        -o {output.r1tmp} {output.r2tmp}        --kraken-db {params.db}         --kraken-taxa "Archaea Eukaryota Holozoa Nucletmycea"   --min-len {params.minlen}       --minimap2-index {params.human}         --kraken-threads {threads}      --workdir {params.workdir:q} 2> {log}

    echo -e "
Scrubby Kraken Extract
" >> {log}

    scrubby scrub-kraken    -i {output.r1tmp} {output.r2tmp}        -o {output.r1} {output.r2}      --extract       --kraken-taxa {params.kraken_taxa_extract}      --kraken-reads {params.workdir}/0-standardDB.kraken     --kraken-report {params.workdir}/0-standardDB.report    --kraken-threads {threads} 2>> {log}

    touch {output.status}

Originally posted by @gokeson in https://github.com/ammaraziz/ctgap/issues/2#issuecomment-1877600797

ammaraziz commented 8 months ago

should be fixed!