DennisSchmitz/Jovian_archive

Issues

• Difficulties in installing Jovian helper environment

  #177 opened 2 years ago by tengfei-emory
  1

• The IGVjs index seems to be too taxing for the browser, even on the "Explanation" tabs

  #138 opened 4 years ago by DennisSchmitz
  1

• Use readthedocs instead of GitHub README

  #82 opened 4 years ago by DennisSchmitz
  1

• FAQ: in v0.9.7 I get error "line 38: unpigz: command not found"/"division by zero attempted"

  #142 opened 4 years ago by DennisSchmitz
  1

• Improvement: change to mimimap2 aligner in ILM-RA workflow

  #159 opened 4 years ago by DennisSchmitz
  0

• In IGV, "Unsatisfiable Range" error is thrown

  #158 opened 4 years ago by DennisSchmitz
  0

• IGV can't access the data resources when using WSL

  #151 opened 4 years ago by florianzwagemaker
  1

• Add HuGo to the standard database installation process

  #149 opened 4 years ago by florianzwagemaker
  1

• SPAdes error correction takes very long for some samples

  #144 opened 4 years ago by samnooij
  4

• The script `database_updater.sh` is incorrect on Ubuntu

  #147 opened 4 years ago by DennisSchmitz
  3

• Remove Krona-LCA from workflow and required databases

  #148 opened 4 years ago by florianzwagemaker
  0

• Save disk space by compressing fastq files (after trimming and filtering)

  #136 opened 4 years ago by samnooij
  5

• FAQ: SPAdes, and thus Jovian, is only comparable across systems/installations if the same amount of threads are used for assembly.

  #145 opened 4 years ago by DennisSchmitz
  0

• HuGo_removal_pt1 crashes on big datasets

  #124 opened 5 years ago by DennisSchmitz
  0

• FAQ: LoFreq gives error "OSError: [Errno 7] Argument list too long: `lofreq`

  #143 opened 4 years ago by DennisSchmitz
  1

• Stop assuming logical $PATH configurations of end-users

  #137 opened 4 years ago by DennisSchmitz
  0

• Typingtool changes, compatibility issues?

  #97 opened 4 years ago by DennisSchmitz
  1

• Missing checkers for installation functions

  #89 opened 4 years ago by DennisSchmitz
  1

• Improvement: optional automatic virustyping in on_success clause

  #125 opened 4 years ago by DennisSchmitz
  1

• Improvement/clarification: make a cluster-queue flag in the wrapper with priority

  #126 opened 4 years ago by DennisSchmitz
  1

• Jovian crashes when there aren't enough reads matching the specified background organism (default: HuGo)

  #113 opened 4 years ago by DennisSchmitz
  2

• FastQC: Java Thread exception: internal language error

  #135 opened 4 years ago by florianzwagemaker
  1

• Automate the detection and configuration of local and remote system resources

  #127 opened 5 years ago by florianzwagemaker
  0

• Jovian cannot handle certain input filenames

  #112 opened 5 years ago by DennisSchmitz
  1

• Make Jovian citable and create DOIs through Zenodo

  #71 opened 5 years ago by samnooij
  5

• Improvement: reorder project

  #94 opened 5 years ago by DennisSchmitz
  0

• Validation and incorporation of new BLAST databases

  #115 opened 5 years ago by DennisSchmitz
  2

• Generating a new Unique identifier does not work in embedded terminals

  #121 opened 5 years ago by florianzwagemaker
  1

• Fragment_length_analysis step crashes on low-quality/low-abundance samples

  #117 opened 5 years ago by DennisSchmitz
  0

• 'grid' mode does not seem to work with Open Grid Scheduler

  #105 opened 5 years ago by samnooij
  5

• "Unbound variable" error when upgrading from v0.9.5 to v0.9.6.

  #111 opened 5 years ago by DennisSchmitz
  0

• Enhancement: use tabs for different samples in IGVjs

  #107 opened 5 years ago by DennisSchmitz
  1

• /tmp/etc/nginx/default-sites/[unique_hash] gives permission denied error.

  #104 opened 5 years ago by DennisSchmitz
  2

• SVG export

  #80 opened 5 years ago by thierryjanssens
  2

• Count_mapped_reads rule is extremely slow

  #99 opened 5 years ago by DennisSchmitz
  16

• IGVjs has been hardcoded to version 2.2.15, later versions are incompatible.

  #98 opened 5 years ago by DennisSchmitz
  4

• Script `generate_sample_sheet.py` is not compatible with some filenames.

  #88 opened 5 years ago by DennisSchmitz
  3

• SNP_calling rule crashes for samples with more than 131072 contigs per sample due to a limitation in LoFreq

  #102 opened 5 years ago by DennisSchmitz
  1

• HuGo_removal_pt1_alignment samtools sort memory

  #103 opened 5 years ago by thierryjanssens
  1

• Enhancement: scaffolds ends are sometimes of poor quality

  #101 opened 5 years ago by DennisSchmitz
  0

• IGVjs does not install: "failed to download Chromium"

  #95 opened 5 years ago by DennisSchmitz
  2

• QC_raw_data , QC_clean_data fails to generate output: {sample}_{read}_fastqc.html

  #78 opened 5 years ago by alakob
  2

• Superkingdom heatmap: leave fields with 0 contigs/reads blank

  #79 opened 5 years ago by samnooij
  3

• Last step of Jovian fails (/tmp/etc/nginx/)

  #86 opened 5 years ago by thierryjanssens
  4

• profile_percentages.csv from rule quantify_output

  #76 opened 5 years ago by thierryjanssens
  2

• Continuous dev-branch, setup travis-CI and codecov

  #81 opened 5 years ago by DennisSchmitz
  2

• High coverage samples

  #83 opened 5 years ago by jeroencremer
  2

• Clarify `--unlock`: Explain that you need to specify the input folder otherwise it won't unlock.

  #75 opened 5 years ago by DennisSchmitz
  2

• Improvement: Add bitscore and query scaffold coverage to taxonomic classification output

  #77 opened 5 years ago by DennisSchmitz
  0

• Add functional annotations to the gff files.

  #74 opened 5 years ago by thierryjanssens
  0