percyfal/snakemakelib

Issues

• Wrong smltemplate import in qualimap_plot_summary.rule

  #48 opened 9 years ago by percyfal
  0

• star ignores extra references

  #49 opened 9 years ago by percyfal
  1

• Improve treatment of numerical sample names

  #45 opened 9 years ago by percyfal
  0

• Update dependency to bokehutils 0.1.6

  #46 opened 9 years ago by percyfal
  0

• Make documentation build show version number only

  #47 opened 9 years ago by percyfal
  0

• Make summary rules find sample names from inputs

  #42 opened 9 years ago by percyfal
  2

• Update dependency to snakemake 3.4.2

  #44 opened 9 years ago by percyfal
  0

• Make javascript library for common functions

  #43 opened 9 years ago by percyfal
  0

• Create summary rule for rpkmforgenes

  #40 opened 9 years ago by percyfal
  1

• picard merge rule for scrnaseq makes a symlink but should copy

  #41 opened 9 years ago by percyfal
  1

• Custom rnaseq annotations are wrong

  #39 opened 9 years ago by percyfal
  0

• Remove all magic initializations of config

  #35 opened 9 years ago by percyfal
  0

• Make rules independent of snakemakelib package

  #7 opened 9 years ago by percyfal
  1

• Add library for interacting with module system

  #10 opened 9 years ago by percyfal
  0

• Make default configurations tuples

  #2 opened 9 years ago by percyfal
  1

• Write generic slurm file modeled on inodb's variant so as to calculate dependencies and runtimes on the fly

  #32 opened 9 years ago by percyfal
  1

• Add hooks for python2 calls

  #36 opened 9 years ago by percyfal
  1

• Make sml_path functions variables

  #38 opened 9 years ago by percyfal
  0

• Convert all configuration names to config

  #37 opened 9 years ago by percyfal
  0

• snakemake.workflow missing from setup.py

  #34 opened 9 years ago by percyfal
  0

• bowtie configuration mismatch in version 0.1-alpha.8

  #23 opened 9 years ago by percyfal
  0

• Allow for quality control modularity

  #33 opened 9 years ago by percyfal
  0

• Make configuration routines like emacs lisp

  #31 opened 9 years ago by percyfal
  0

• Reimplement halo pipeline

  #30 opened 9 years ago by percyfal
  0

• Modify GATK region rules to include label

  #29 opened 9 years ago by percyfal
  0

• Write "standalone" command to export used tasks to standalone snakemake file

  #28 opened 9 years ago by percyfal
  0

• Set samples first time targets generator run so that we don't have to re-read sampleinfo file?

  #27 opened 9 years ago by percyfal
  0

• Test updated chart plotting facilities to see if custom functions can be made obsolete

  #26 opened 9 years ago by percyfal
  0

• Create settings file for each application level

  #25 opened 9 years ago by percyfal
  0

• Add REQUIRED_RULES to rule loading

  #24 opened 9 years ago by percyfal
  0

• Multiple calls to update_sml_config necessary for recursive dependencies

  #1 opened 9 years ago by percyfal
  1

• pip install from github fails to install external dependency bokehutils

  #16 opened 9 years ago by percyfal
  0

• Add configuration option to exclude samples

  #3 opened 10 years ago by percyfal
  1

• Add sphinx rst templates

  #8 opened 9 years ago by percyfal
  0

• Make standalone scripts for collecting results

  #9 opened 9 years ago by percyfal
  0

• cutadapt paired-end rule duplicates parameters with "file:"

  #17 opened 9 years ago by percyfal
  0

• Documentation build is failing

  #21 opened 9 years ago by percyfal
  2

• Make rule for each command

  #12 opened 9 years ago by percyfal
  1

• Build failing with bokeh 0.9.3

  #22 opened 9 years ago by percyfal
  0

• Rewrite update_config to mirror bitbucket PR

  #18 opened 9 years ago by percyfal
  0

• Remove obsolete BaseConfig class

  #19 opened 9 years ago by percyfal
  0

• Use pytest instead of nose

  #20 opened 9 years ago by percyfal
  1

• setup.py develop currently fails

  #15 opened 9 years ago by percyfal
  0

• Jinja templates have been moved

  #14 opened 9 years ago by percyfal
  0

• Data files and rules not included on pip install

  #13 opened 9 years ago by percyfal
  0

• Erroneous bowtie2 command line

  #11 opened 9 years ago by percyfal
  0

• Workflows hang when generating targets

  #6 opened 9 years ago by percyfal
  1

• Add support for qualimap

  #5 opened 9 years ago by percyfal
  1

• Create new rule from template in library

  #4 opened 9 years ago by percyfal
  0