Eco-Flow/synteny

Issues

• SCORE module is taking way too long

  #61 opened 2 months ago by chriswyatt1
  1

• Downloaded size of pipeline large

  #77 opened 4 months ago by chriswyatt1
  0

• Add a script to combine results of multiple runs

  #76 opened 4 months ago by chriswyatt1
  1

• Add all other flags you can choose in MCScanX

  #74 opened 4 months ago by chriswyatt1
  1

• Add average distance to translocation type break

  #73 opened 4 months ago by chriswyatt1
  0

• Check -bg are being set correctly in GO

  #72 opened 4 months ago by chriswyatt1
  0

• Fix unit testing

  #70 opened 4 months ago by chriswyatt1
  0

• Apptainer container location not looking in cache on HPC

  #69 opened 4 months ago by chriswyatt1
  0

• * --cutoff (10): Value is [integer] but should be [string]

  #68 opened 4 months ago by chriswyatt1
  1

• Barplots (GO) should have headers

  #62 opened 4 months ago by chriswyatt1
  1

• Create options for GO cutoff percentage

  #66 opened 5 months ago by chriswyatt1
  2

• Merge the score for reciprocal # of syntenic breaks

  #49 opened 5 months ago by chriswyatt1
  1

• Ribbon plot cannot deal well with 100+ contig genomes

  #65 opened 5 months ago by chriswyatt1
  0

• Integrate the GO pipeline

  #16 opened 5 months ago by chriswyatt1
  0

• Summary of chromosome equivalence and flipping

  #64 opened 5 months ago by chriswyatt1
  1

• Gffread takes all features

  #37 opened 5 months ago by chriswyatt1
  2

• last version should be printed to versions yml

  #60 opened 5 months ago by chriswyatt1
  1

• Longest module should summarise

  #46 opened 5 months ago by chriswyatt1
  2

• High_memory is too much for gitpod

  #47 opened 5 months ago by chriswyatt1
  1

• Add Ribbon plots

  #57 opened 6 months ago by chriswyatt1
  1

• Add optional (without filtering step)

  #58 opened 6 months ago by chriswyatt1
  1

• Fails with nextflow version 24

  #59 opened 6 months ago by chriswyatt1
  1

• nf validation change causes nf-test schema build to fail

  #53 opened 7 months ago by chriswyatt1
  1

• Using nf-test

  #41 opened 7 months ago by chriswyatt1
  3

• Additional information on job submission

  #54 opened 7 months ago by chriswyatt1
  0

• Can last (synteny module) be multithreaded to increase speed, if not pick smaller genomes for demo and testing as they will be faster

  #26 opened 8 months ago by SimonDMurray
  1

• New longest module using AGAT taking ages

  #42 opened 8 months ago by chriswyatt1
  6

• Clean up output tables and provide better explanation

  #50 opened 8 months ago by chriswyatt1
  0

• Add busco

  #48 opened 8 months ago by chriswyatt1
  0

• Duplicate output names

  #43 opened 8 months ago by chriswyatt1
  1

• Working on Myriad

  #20 opened 8 months ago by lewisrevely
  16

• Synteny nf-test does not have the correct input

  #45 opened 9 months ago by chriswyatt1
  2

• Longest/synteny fails due to time limits

  #39 opened 9 months ago by chriswyatt1
  2

• gffread is producing transcript IDs, and not gene IDs

  #30 opened 9 months ago by chriswyatt1
  4

• Create provisional hymenopteran result from pipeline to present at launch

  #35 opened 9 months ago by SimonDMurray
  2

• style / risks

  #33 opened 9 months ago by yannickwurm
  1

• Crazy load

  #34 opened 9 months ago by yannickwurm
  1

• Alter logic of inversion and translocation counting in Synteny Pipeline

  #18 opened 9 months ago by chriswyatt1
  3

• Create a genome summary statistic for each genome (in ncbi_download), that WARNs the user that the species may not run correctly, as it is in too many contigs (>50) should have a warning.

  #29 opened 10 months ago by chriswyatt1
  2

• seqera platforms stuff

  #31 opened 9 months ago by SimonDMurray
  1

• Collect versions of every tool used in each module

  #25 opened 10 months ago by SimonDMurray
  3

• Write automatic method

  #27 opened 10 months ago by SimonDMurray
  6

• Add an nf-core module to pipeline (exisiting or create a new one with ncbi_download)

  #28 opened 10 months ago by SimonDMurray
  2

• Chromo.nf tag should be name of species

  #24 opened 10 months ago by chriswyatt1
  0

• Rewrite main nextflow config

  #10 opened 10 months ago by SimonDMurray
  2

• Implement nf-test in synteny pipeline

  #15 opened 10 months ago by SimonDMurray
  4

• Find and test a minimal dataset

  #23 opened 10 months ago by chriswyatt1
  2

• this is a test issue

  #21 opened 10 months ago by SimonDMurray
  1

• Move DockerHub images to EcoFlow user

  #14 opened a year ago by SimonDMurray
  2

• Unknown recognition error on startup

  #11 opened a year ago by SimonDMurray
  2