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Created with Raphaël 2.2.018Nov171613121110965328Oct27201916151413128729Sep221615141110928Aug212019181716141310331Jul302423222017161413109872130Jun2926252414131211109843230May2928272615141312119876130Apr29262524232221201918161525Mar1918report: updated report code (NOT finished)report: next update (NOT finished)report: rm unsued conda yamlreport: updated report code (NOT finished)config: updated nwcupdated gitignoreanalysis: contig cov segmentation w/ segclust2d (issue #107)conda: YAML for segclust2d (issue #107)config: updates for gdb/zymo/nwc (others - NOT done yet)analysis: minor changes (renamed some rules and log files)updated environmentsworking snakefile with VG's suggested modiifcationsannotation: fixed a bug in rgi cmd (issue #106)updated zymo rules and filesupdated rules for zymo download and prodigal runspreproc: fixed a bug when linking to SR filesconfig: mv sub-folders: lowcase sample namestax: added prefix to log file namespreproc: fixed a bug in linking LR file, local rulesinit: added localrule for linking filesupdated folder nameassembly: operams cmd update (keep clustering) (issue #104)assembly: operams cmd update (issue #104), metaspadeshybrid - scaffolds as output (issue #105)reprocessing: rm realpath when linkingconda: updated snakemake YAML (requirements)config: major updateconfig: rm gis20config: added rumen (fast5)conda: bbmap: added missing '=' between name and versionanalysis/taxonomy: fixed a bug: proc LR/SR for mash and kraken2mapping: fixed a bug: proc LR instead of raw ones for mappingupdated rules for running SibeliaZ against zymoupdated slurm and Snakefile(s)fixed errorsfinal SibeliaZ rule updatedadded rules and config parameters for SibeliaZfast5/preproc: mv basecalling to fast5 workflow (issue #103)fast5/preproc: mv basecalling to fast5 workflow (issue #103)analysis: mv gene cov from mapping to analysisassembly: replaced realpath when linking