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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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  • v0.1
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Created with Raphaël 2.2.020Aug19181716141310331Jul302423222017161413109872130Jun2926252414131211109843230May2928272615141312119876130Apr29262524232221201918161525Mar191817Zymo/GSI20 configs: replaced main conda env pathreadme updatenotes: mashmap updateGIS20/Zymo configs: fixed a typonotes: mashmap (issue #35)updated configspolishing update: changed polishing strategy, updated racon conda yaml to replace bwa conda yaml (issue #81)notes: diamond test (issue #78)notes: infernal testreport: numbers of cdhit stats (table)better expression to list targets for assembly stepupdated GDB config: added mapping back to the stepsreport: update to include new assemblers; fixed tool order in cdhit/diamond plotsmash: rm contig-screen analysis, fixed a bug (not all assemblies included in assembly sketch)bbmap/bbduk to rm rrna reads: fixed cmd (issue #49)fixed paths for some mash rules (issue #79)GIS20/Zymo config: sortmerna/bbmap updateGDB config: sortmerna/bbmap updaterm rrna reads: replaced sortmerna by bbmap (not tested) (issue #49)GDB config (slurm): rule mapping_bwa_mem_assembly_hyhyGIS20 configs: updatedzymo configs: updatedchanges need to include imp3 assembly (issue #76)cdhit: changed renaming rule (issue #75), use '-s2 0.5' (issue #68)notes: mmseqs2 example callGDB config: sormerna updatepreproc step: sortmerna targets only if metatmapping step: fixed a bug - wrong names for targetsupdated tax rules: kaiju for all proteins, kraken2 for filtered contigs onlyGDB config: sormerna cores and runtime, other minor changesGDB config: more cores and time for sortmernanotes: diamond hits scripts, mmseqs2 script (cdhit alternative)updated GDB config filesadded canu conda yaml (issue #72)added sortmerna: preproc rule, mapping rule for sr split into metag/metat (issue #49); mapping rule for hyhy assembly (issue #76)updated assembler names and colors in workflow_report/scripts/utils.Rupdated GDB config filesupdated config schemaadded lr assembler canu (issue #72)scripts: add annot to diamond hits and find gene clusters (issue #70): will be included later in the pipeline