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Created with Raphaël 2.2.013Oct25Sep3Aug230Jul25241611130Jun29724FebAdd new filemastermasterAdd new fileAdd new fileAdd new fileAdd new fileDelete .gitkeepAdd new directoryUpload New FileUpload New FileUpload New FileUpload New FileUpload New FileAdd new directoryAdd new directoryUpdate parse_kaiju.pyadjusted kaiju parsing scriptscript for parsing the kaiju output/summary fileadded the '-e' flag to expand viral taxonomiesadded Kaiju rules and updates to all filesadded the vcontact2 parsing python scriptadded parameters for krakenupdated snakefile with kraken2 rulesworking vcontact2 snakefile with associated changesMerge branch 'master' of https://git-r3lab.uni.lu/susheel.busi/cosmic2vcontact2 changed from v0.9.17 to v0.9.18Update snakefileupdated the snakefile and run_snakemake files to include updated vibrantUpdate get_HGT_contig_ID.shscript to retrieve ORIGINAL contigIDs and their locations based on HGT events identified by MetaCHIPadding kraken rules and snakefileupdated the snakefile for correctness of fileschanged the vibrant walltime and ncpus for improved SLURM schedulingcluster.json file updated for all rulesupdated snakefile with vcontact2 rulesconda environment for vContact2reverting to old scikit-learn due to conflictsupdated the scikit-learn requirementedited the snakefile to get the directory stucture for vibrant correctupdated the targets based on VIBRANT's outputsamples list for vibrant. Does not include C118 due to missing V6