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  • 65-mock-identify-characterize-genes-in-flye-which-explain-low-q-s-ration-in-diamond-hits
  • bright_future
  • cdhit
  • cleanup
  • master default protected
  • zymo
  • v1.0
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Created with Raphaël 2.2.012Jan22Dec8432130Nov2726241918171613121110965328Oct27201916151413128729Sep221615141110928Aug212019181716141310331Jul302423222017161413109872130Jun2926252414131211109843230May2928272615141312119876130Apr29262524232221config: updated aquiferconfig: updated rumenannotation: plasflow: increased number of threads (to have more mem for the job)annotation: hmmsearch: redirecting stdout to /dev/null to avoid too large log fileszymo extra: gene/blastn search (issue #111)Merge branch 'zymo' into 'bright_future'zymo: config: updated rumen (to match bright_future branch); rm unused zymo configszymozymoconfig: updated rumenzymo: added mummer/dnadiff (issue #111)zymo: genes.R: added kraken2 upsetr plots (issue #111)zymo: plots based on assembly gene summary table (issue #111)report/zymo: utils.R: minor update of func set_tool_order (needed for #111)zymo: get kegg info (kegg api) (issue #111)zymo: config: updated zymo slurm and sbatch fileszymo: gene summary tab: added best kegg hit (issue #111)zymo: gene summary tab: added gene length (issue #111)zymo: updated snakemake (gene summary, issue #111)zymo: updated/modified workflow (not finished)zymo: linked prodigal and diamond envszymo: rm ont fast5 api envzymo: rm prodigal and diamond envszymo: rm tmp files on config/zymozymo: merged with latest bright_future commit (978c9167)config: aquifer updateconfig: rumen updateconfig: gdb updateconfig: zymo updatereport: rgi: if no hits: empty summary and no plot (but pdf) (issue #109)report: added contig cov. segmentation (scatter plot) (issue #108)report: collect_data: cdhit stats: rm id check assertion (increases runtime, wrong ids would fail anyway later)report: added back rgi (issue #109)analysis: cov seg: more threads (rule), rm short contigs (script) (issue #107)analysis: cov seg: parallel processing (issue #107)analysis: step: chnaged target declaration for covannotation: annotation_hmm_kegg: do not redirect stdout to /dev/null, redirect to logconfig: updated nwc (excl canu, incl raven)report: minor updates (excl canu, incl raven; minor changes)assembly: added lr assembler raven (issue #72)workflow_fast5: fix to skip multifast5 step if folder exists (config: single_fast5_dir is an empty str)report: updated report code (NOT finished)