no complaining about missing seqtk

hivlab / quantify-virome

quantify-virome: identify and quantify viruses from metagenomic shotgun sequences

MIT License

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no complaining about missing seqtk #17

Closed tpall closed 5 years ago

tpall commented 5 years ago

fastp rule was not complaining about missing seqtk program, instead 'Wildcards' object has no attribute 'output '. Updated envs/fastp.yaml with seqtk cd1d6a45

tpall commented 5 years ago

Ha-ha, accidentally entered newline after {cluster.output } in sbatch command caused the error... like so

snakemake --cluster "sbatch -J {cluster.name} -p {cluster.partition} -t {cluster.time} --mem {cluster.mem} --output {cluster.output }" -u ~/fastq/prjna361402/cluster.json -j 40 -d ~/fastq/prjna361402 --use-conda --rerun-incomplete --keep-going --max-jobs-per-second 1 --until fastq_join