Commit bf6d628c authored by Mouhamadou Ba's avatar Mouhamadou Ba
Browse files


parent 7ec2afad
......@@ -35,3 +35,9 @@ conda activate snakemake-5.13.0-
snakemake --nolock --verbose --printshellcmds --use-singularity --use-conda --reason --latency-wait 60 --jobs 2 --snakefile get_corpus_from_doiss.snakefile all --cluster "qsub -v PYTHONPATH='' -l mem_free=4G -V -cwd -e log/ -o log/ -q short.q -pe thread 2" --config --config DOIS_FILE=data/pmcids.txt --config CORPUS_FOLDER=data/corpus_3
## todo
* apply to list of dois, pmids, pmcids collected by Open16S project members
* integrate the pipelines to the omnicrobe workflow
* handle the exceptions (missing dois, pmids, texts in epmc, add constraints to enhance the extractions of articles)
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