ewels/clusterflow

Issues

• Clusterflow doesn't work with Lmod modulefile system

  #124 opened 6 years ago by s-andrews
  4

• Custom SLURM command is broken

  #125 opened 6 years ago by s-andrews
  0

• Wall time

  #120 opened 6 years ago by fjames003
  4

• Samtools module is outdated

  #122 opened 6 years ago by ewels
  0

• Software installation

  #121 opened 6 years ago by YuntaoTan
  1

• Posible to specify output dir ?

  #118 opened 8 years ago by arontommi
  5

• Print standardised software versions

  #113 opened 8 years ago by ewels
  1

• Negative complete jobs in qstat output

  #111 opened 8 years ago by s-andrews
  13

• BWA module memory

  #112 opened 8 years ago by arontommi
  5

• Picard dedup module does not use the TMPDIR

  #109 opened 8 years ago by jherrero
  0

• Add to bioconda

  #104 opened 8 years ago by ewels
  1

• Use less controversial colours for --qstatcols

  #102 opened 8 years ago by ewels
  6

• Move the website out of the main repo

  #90 opened 8 years ago by ewels
  1

• Remove preseq_plot.cfmod.py

  #94 opened 8 years ago by ewels
  0

• cf --qstat is ridiculously slow when a significant number of jobs is running

  #100 opened 9 years ago by s-andrews
  13

• Create genomes.d folder?

  #96 opened 9 years ago by s-andrews
  3

• Change config syntax?

  #97 opened 9 years ago by ewels
  3

• Restructure dependencies

  #93 opened 9 years ago by s-andrews
  6

• Get Bismark summary module to use new bismark command

  #87 opened 9 years ago by ewels
  3

• Write methylation coverage analysis module

  #49 opened 10 years ago by ewels
  3

• Torque compatibility

  #69 opened 9 years ago by jrkirk61
  4

• Have genome details available in modules

  #75 opened 9 years ago by ewels
  3

• Add ability to read CWL module descriptions

  #78 opened 9 years ago by ewels
  1

• Clusterflow with MultiQC

  #70 opened 9 years ago by darogan
  9

• snpEff module

  #86 opened 9 years ago by darogan
  1

• Clusterflow and Nextflow

  #84 opened 9 years ago by machbio
  1

• Passing an Environment Variable to a Cluster in Clusterflow

  #83 opened 9 years ago by machbio
  4

• Cluster Flow for Perl 5.22 +

  #81 opened 9 years ago by machbio
  7

• how to pass-through extra parameters to modules from top-level cf command?

  #79 opened 9 years ago by avilella
  1

• Add annotation requirement to module api

  #74 opened 9 years ago by ewels
  0

• Pipeline / Module repository

  #71 opened 9 years ago by ewels
  4

• Feature requests

  #72 opened 9 years ago by s-andrews
  1

• RSeQC

  #51 opened 10 years ago by ewels
  2

• Create a test to run once installed

  #59 opened 10 years ago by ewels
  2

• Special value for @environment_module_alias to allow 'no module'

  #67 opened 10 years ago by ewels
  1

• Sum queued download tasks

  #64 opened 10 years ago by ewels
  5

• Split website into its own repository

  #65 opened 10 years ago by ewels
  1

• Support multiple outputs

  #63 opened 10 years ago by ewels
  0

• Add support for running summary modules on command line

  #60 opened 10 years ago by ewels
  0

• Errors generated by summary modules are not highlighted

  #61 opened 10 years ago by ewels
  0

• featureCounts

  #50 opened 10 years ago by ewels
  1

• methylkit module

  #48 opened 10 years ago by ewels
  2

• Make UPPMAX genomes file

  #54 opened 10 years ago by ewels
  3

• Build UPPMAX jobstats module

  #57 opened 10 years ago by ewels
  0

• Genomes wizard BWA bug

  #58 opened 10 years ago by ewels
  1

• Rewrite job negotiation / module command line handling

  #47 opened 10 years ago by ewels
  4

• Change downloads module behaviour

  #55 opened 10 years ago by ewels
  2

• cf --setup broken

  #52 opened 10 years ago by robinandeer
  0

• Perl error

  #53 opened 10 years ago by robinandeer
  0

• Add command line flag for running locally

  #46 opened 10 years ago by ewels
  0