ngless-toolkit/ngless

Issues

• Error: resource vanished (Broken pipe)

  #121 opened 5 years ago by ycl6
  4

• custom pattern recognition load_fastq_directory

  #145 opened 4 years ago by uloeber
  1

• Reading .bz2 files fails to decompress or segfaults

  #116 opened 5 years ago by unode
  14

• To use the motus module for newer versions, you need to download it and import it with 'local import'

  #154 opened 2 years ago by zckoo007
  1

• fd:12: hPutBuf: resource vanished (Broken pipe)

  #153 opened 3 years ago by uloeber
  0

• sdist lacks files necessary to run test suite

  #152 opened 3 years ago by sternenseemann
  2

• Implement readset return type types for modules

  #119 opened 5 years ago by mkuhn
  2

• ngless --install-reference-data defaults to script version 0.0

  #107 opened 3 years ago by unode
  0

• Reference data includes bwa indices under incorrect name

  #108 opened 3 years ago by unode
  2

• ngless complains about igc version

  #123 opened 3 years ago by ycl6
  1

• Requesting qcstats when none exist fails

  #113 opened 3 years ago by unode
  0

• Error while generating reports for mOTUs. (fails integration tests)

  #134 opened 3 years ago by nairsajjal
  2

• NGLess contain the adapter removel or not?

  #151 opened 3 years ago by timeresistance1996
  7

• NGless v2.5 URL was not found while running it for the first time

  #150 opened 3 years ago by evilvenom
  2

• Documentation for smoothtrim

  #148 opened 3 years ago by mkuhn
  0

• ngless-1.3.0-bwa not found

  #147 opened 3 years ago by liuxianghui
  3

• error message write ofile

  #144 opened 4 years ago by uloeber
  1

• Loading map file gmgc emapper2 annotations fails

  #143 opened 4 years ago by uloeber
  4

• Error ir mapping step

  #142 opened 4 years ago by chodarq
  7

• Parallel module exits with error, if the data are not in the same directory as the script

  #141 opened 4 years ago by vpuller
  2

• Home directory does not have enough space for ngless

  #140 opened 4 years ago by liuxianghui
  8

• Feature request: Filter mapped reads by minimum match fraction

  #139 opened 4 years ago by luispedro
  0

• Installation issue on Mac

  #125 opened 4 years ago by dkinkj
  10

• No HTML report is generated when using the parallel module

  #133 opened 5 years ago by unode
  2

• Using collect on countables from mapstats gives a funny result

  #138 opened 4 years ago by mettejoe
  0

• Reading in fastq.gz files

  #115 opened 4 years ago by luispedro
  8

• Better debug message for files missing for collect()

  #136 opened 5 years ago by unode
  0

• bioconda recipe no longer works

  #101 opened 5 years ago by notestaff
  2

• Introduce computation stages - validation, download, prepare, ...

  #135 opened 5 years ago by unode
  1

• Update Documentation: Add developer test details on how new developers can test .ngl scripts

  #131 opened 5 years ago by nairsajjal
  2

• Add ability to strip sequences/qualities from SAM/BAM files

  #102 opened 6 years ago by unode
  7

• Update Documentation: regarding the developer docs change in accordance with Ngless Version 1.1.0

  #129 opened 5 years ago by nairsajjal
  2

• Console throws an error while activating ngless environment

  #128 opened 5 years ago by dmahajan980
  1

• load_mocat_sample fails when given file names with multiple pair identifiers

  #127 opened 5 years ago by jakob-wirbel
  2

• Update documentation for motus profiling to reflect motus2

  #114 opened 5 years ago by theavanrossum
  3

• Add read_length() to ShortRead type

  #126 opened 5 years ago by unode
  2

• load_mocat_sample - missing pair.2 fails, missing pair.1 succeeds

  #120 opened 5 years ago by unode
  5

• Broken pipe with samtools view upon conversion from minimap2 SAM -> BAM

  #124 opened 5 years ago by unode
  1

• Inconsistent use of `local import`

  #117 opened 5 years ago by unode
  1

• Docs for load_mocat_sample

  #122 opened 5 years ago by mkuhn
  2

• Allow collect()'ing when all processing is complete

  #112 opened 6 years ago by unode
  2

• Output unmapped PE fastq files

  #118 opened 5 years ago by ycl6
  1

• Reinjected sequences on matches containing inserts are invalid according to samtools

  #109 opened 6 years ago by unode
  0

• Default zstd compression breaks streaming

  #110 opened 6 years ago by unode
  0

• Reference genomes not available Mus musculus

  #106 opened 6 years ago by kunstner
  6

• Filtering a SAM/BAM file in a select() block inverts samline order

  #105 opened 6 years ago by unode
  0

• can_gzip=False is not respected

  #104 opened 6 years ago by unode
  1

• ZStandard compression breaks saving BAM files

  #103 opened 6 years ago by unode
  2

• 0.9 catalogs misnamed gene column

  #100 opened 6 years ago by unode
  1

• Implement API to cleanup unnecessary files

  #99 opened 6 years ago by unode
  0