TBradley27/FilTar

Issues

• FilTar error message

  #36 opened 4 years ago by ntinamu001
  1

• Where appropriate denote rule input/output dependency relationships explicitly

  #35 opened 4 years ago by TBradley27
  0

• Eliminate use of shell scripts

  #34 opened 4 years ago by TBradley27
  0

• Standardise and minimise name space throughout the repository

  #33 opened 4 years ago by TBradley27
  0

• Add gene symbol metadata when executing APAtrap

  #32 opened 4 years ago by TBradley27
  0

• Speed up the process of generating average bedgraph coverage values from many bedgraph files

  #31 opened 4 years ago by TBradley27
  0

• Add rule to validate generated bedgraph files

  #30 opened 4 years ago by TBradley27
  0

• Generate a report regarding the extent of 3'UTR reannotation

  #29 opened 4 years ago by TBradley27
  0

• Implement a more sophisticated method of mapping chromosome/scaffold identifiers

  #28 opened 4 years ago by TBradley27
  0

• Add a line at the top of each script stating its function

  #27 opened 4 years ago by TBradley27
  0

• Switch to using toplevel genomes only

  #26 opened 4 years ago by TBradley27
  0

• Process genomic data not split into sequencing block (i.e. contig level assemblies)

  #25 opened 4 years ago by TBradley27
  0

• Switch away from using three letter species initials

  #24 opened 4 years ago by TBradley27
  0

• Allow the user to set library type if this information is known in advance

  #23 opened 4 years ago by TBradley27
  0

• Linting and formatting

  #22 opened 4 years ago by TBradley27
  0

• Make use of snakemake resource usage profiles

  #21 opened 4 years ago by TBradley27
  0

• Version tracking of dependencies

  #20 opened 4 years ago by TBradley27
  0

• All tabular data read-in by FilTar scripts should explicitly declare column names

  #12 opened 4 years ago by TBradley27
  0

• Manage targetscan dependencies within a single conda environment

  #16 opened 4 years ago by TBradley27
  0

• Few general queries

  #7 opened 4 years ago by ashokpatowary
  1

• Move rule configuration values backwards into YAML config files

  #5 opened 4 years ago by TBradley27
  0

• Resolve the issue of different conda installation methods

  #9 opened 4 years ago by TBradley27
  0

• Improve cluster support/integration

  #15 opened 4 years ago by TBradley27
  0

• Reduce inefficiency in use of whole-genome alignments

  #14 opened 4 years ago by TBradley27
  0

• Collect the 'with_reannotation' and 'without_reannotation' modules into the same directory

  #13 opened 4 years ago by TBradley27
  0

• Add script-level comments at the top of scripts

  #11 opened 4 years ago by TBradley27
  0

• Add a basic workflow to the README

  #10 opened 4 years ago by TBradley27
  0

• Throw an error if the user does not specify a valid target prediction algorithm

  #6 opened 4 years ago by TBradley27
  1

• Simplify conda environment management

  #3 opened 5 years ago by TBradley27
  0

• Encode metadata in TSV format rather than YAML

  #4 opened 4 years ago by TBradley27
  1

• Enable processing of non-Ensembl GTF files

  #8 opened 4 years ago by TBradley27
  0

• Make read trimming optional

  #1 opened 5 years ago by TBradley27
  0

• Make some data download functionality non-default

  #2 opened 5 years ago by TBradley27
  0