AlexanderLabWHOI/eukrhythmic

Issues

• Couple things

  #78 opened 4 months ago by cnatalie
  2

• Rules

  #77 opened 5 months ago by cnatalie
  1

• Eukrhythmic command not working

  #76 opened 5 months ago by dhwanidesai
  0

• Upgrades to v2

  #73 opened a year ago by halexand
  1

• Spark Plugs

  #74 opened a year ago by halexand
  1

• Add BioPython as a required package to environment file

  #71 opened a year ago by halexand
  0

• Build in some sort readmapping parsing

  #51 opened 4 years ago by halexand
  1

• Documentation notes

  #45 opened 2 years ago by akrinos
  0

• Changing clustering to MMSeqs2

  #43 opened 2 years ago by akrinos
  0

• Annotation rule logs

  #41 opened 2 years ago by cnatalie
  0

• Integrating with PBS as well as slurm?

  #36 opened 2 years ago by halexand
  1

• User parameters?

  #17 opened 2 years ago by halexand
  2

• Salmon subsetting

  #70 opened 2 years ago by halexand
  0

• Clean up final clustered fasta headers

  #69 opened 2 years ago by halexand
  0

• Clustering in protein space

  #68 opened 2 years ago by halexand
  0

• Modules folder

  #56 opened 3 years ago by MichielPerneel
  5

• hmmsearch

  #55 opened 3 years ago by cnatalie
  0

• Hmmer logs

  #52 opened 4 years ago by cnatalie
  0

• How are isoforms handled?

  #50 opened 4 years ago by halexand
  1

• Suggestions for annotations

  #49 opened 4 years ago by cnatalie
  0

• Typo in mmseqs linclust

  #48 opened 4 years ago by cnatalie
  0

• Different levels of clustering

  #46 opened 4 years ago by akrinos
  0

• Change output organization

  #44 opened 4 years ago by akrinos
  1

• metaT sample file naming

  #35 opened 4 years ago by cnatalie
  3

• merged files are not renamed

  #34 opened 4 years ago by cnatalie
  1

• Make sure duplicate Trinity headers aren't a problem

  #1 opened 4 years ago by akrinos
  1

• Picking up after failed assembly jobs?

  #22 opened 4 years ago by halexand
  2

• Check the threads parameter in Trinity?

  #28 opened 4 years ago by halexand
  1

• Trinity running way too slow and only running 2 simultaneous instances

  #25 opened 4 years ago by akrinos
  0

• Strange behavior with `megahit` rule

  #30 opened 4 years ago by halexand
  2

• duplicate logs

  #31 opened 4 years ago by cnatalie
  2

• General cleanup

  #5 opened 4 years ago by halexand
  8

• Adding more command line entries for slurm control

  #24 opened 4 years ago by akrinos
  0

• Optimizing the automated pairing of forward and reverse reads

  #10 opened 4 years ago by halexand
  3

• Check for hard coding?

  #6 opened 4 years ago by halexand
  3

• Subset the requirement and testing in Snakefile to separate scripts

  #14 opened 4 years ago by halexand
  1

• Add a hard clean up?

  #16 opened 4 years ago by halexand
  1

• Add MultiQC

  #15 opened 4 years ago by halexand
  2

• Add bbmap toggle to the slamon rule

  #18 opened 4 years ago by halexand
  1

• Update scripts to enable the sample file creation with new naming scheme

  #12 opened 4 years ago by halexand
  1

• Make a small demo dataset to include as `test`

  #13 opened 4 years ago by halexand
  1

• add metavelvet to velvet-snake

  #19 opened 4 years ago by cnatalie
  1

• prefixes flag in transabyss-merge

  #20 opened 4 years ago by cnatalie
  1

• Conda environments for individual modules / rules

  #4 opened 4 years ago by halexand
  3

• velvet & megahit need to take in bbmap reads

  #2 opened 4 years ago by akrinos
  1

• If you run `dropspike` with no spike to drop bbmap does weird things

  #9 opened 4 years ago by halexand
  1

• Program versioning?

  #8 opened 4 years ago by halexand
  0