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WatsonLab / MAGpy

Snakemake pipeline for downstream analysis of metagenome-assembled genomes (MAGs) (pronounced mag-pie)
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error in magpy3 test #16

Closed duvayu closed 4 years ago

duvayu commented 4 years ago

snakemake --use-conda -s MAGpy test SyntaxError in line 66 of /MAGpy/MAGpy: Command must be given as string after the shell keyword. (MAGpy, line 66)

duvayu commented 4 years ago

making this change will solve the problem.

rule diamond_bin_summary:
    input: expand("diamond_report/bin.{sample}.tsv", sample=IDS)
    output: "diamond_bin_report.tsv"
    shell:'''echo -e 'name\tnprots\tnhits\tnfull\tgenus\tngenus\tspecies\tnspecies\tavgpid' >> {output}
    find diamond_report/ -name "bin*.tsv" | xargs -I {{}} cat {{}} >> {output}'''
mw55309 commented 4 years ago

Yeah sorry about this, it all looked fine to me, but replacing tabs with spaces, in a way that doesn't make sense, fixed it for me in Python 3.6