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Susheel Busi
COSMIC2
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Created with Raphaël 2.2.0
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Update parse_kaiju.py
adjusted kaiju parsing script
script for parsing the kaiju output/summary file
added the '-e' flag to expand viral taxonomies
added Kaiju rules and updates to all files
added the vcontact2 parsing python script
added parameters for kraken
updated snakefile with kraken2 rules
working vcontact2 snakefile with associated changes
Merge branch 'master' of https://git-r3lab.uni.lu/susheel.busi/cosmic2
vcontact2 changed from v0.9.17 to v0.9.18
Update snakefile
updated the snakefile and run_snakemake files to include updated vibrant
Update get_HGT_contig_ID.sh
script to retrieve ORIGINAL contigIDs and their locations based on HGT events identified by MetaCHIP
adding kraken rules and snakefile
updated the snakefile for correctness of files
changed the vibrant walltime and ncpus for improved SLURM scheduling
cluster.json file updated for all rules
updated snakefile with vcontact2 rules
conda environment for vContact2
reverting to old scikit-learn due to conflicts
updated the scikit-learn requirement
edited the snakefile to get the directory stucture for vibrant correct
updated the targets based on VIBRANT's output
samples list for vibrant. Does not include C118 due to missing V6
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