Issues

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

  ngless-toolkit/ngless#154 · Filter by author zckoo007 opened on Jul 15, 2022
  1

• custom pattern recognition load_fastq_directory

  ngless-toolkit/ngless#145 · Filter by author uloeber opened on Mar 3, 2021
  1

• Feature request: Filter mapped reads by minimum match fraction

  enhancement
  ngless-toolkit/ngless#139 · Filter by author luispedro opened on Oct 12, 2020

• Better debug message for files missing for collect()

  better error messageenhancement
  ngless-toolkit/ngless#136 · Filter by author unode opened on Apr 23, 2020

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

  enhancementperformance
  ngless-toolkit/ngless#135 · Filter by author unode opened on Mar 4, 2020
  1

• No HTML report is generated when using the parallel module

  bughelp wanted
  ngless-toolkit/ngless#133 · Filter by author unode opened on Feb 27, 2020
  2

• Add read_length() to ShortRead type

  enhancement
  ngless-toolkit/ngless#126 · Filter by author unode opened on Dec 5, 2019
  2

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

  ngless-toolkit/ngless#124 · Filter by author unode opened on Oct 15, 2019
  1

• Implement readset return type types for modules

  enhancement
  ngless-toolkit/ngless#119 · Filter by author mkuhn opened on Aug 20, 2019
  2

• Inconsistent use of local import

  bug
  ngless-toolkit/ngless#117 · Filter by author unode opened on Aug 12, 2019
  1

• Update documentation for motus profiling to reflect motus2

  documentation
  ngless-toolkit/ngless#114 · Filter by author theavanrossum opened on Jul 17, 2019
  3

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

  enhancement
  ngless-toolkit/ngless#112 · Filter by author unode opened on Jun 19, 2019
  2

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

  good first issuehelp wanted
  ngless-toolkit/ngless#102 · Filter by author unode opened on Feb 28, 2019
  7

• Implement API to cleanup unnecessary files

  enhancementgood first issue
  ngless-toolkit/ngless#99 · Filter by author unode opened on Feb 7, 2019

• API for querying available versions of modules

  enhancement
  ngless-toolkit/ngless#87 · Filter by author unode opened on Oct 15, 2018

• mapstats() should error with position sorted sam/bam files

  ngless-toolkit/ngless#80 · Filter by author unode opened on Sep 19, 2018

• Improvements to qcstats (fastq, mapping) formats - explicit behavior?

  enhancementhelp wantedquestion
  ngless-toolkit/ngless#75 · Filter by author unode opened on Jun 26, 2018
  2

• Decouple stats machinery from HTML reporting

  enhancement
  ngless-toolkit/ngless#74 · Filter by author unode opened on Jun 26, 2018

• Include file grouping information in fqstats

  enhancement
  ngless-toolkit/ngless#73 · Filter by author unode opened on Jun 19, 2018

• as_reads should not require that BAM file be sorted

  enhancementhelp wanted
  ngless-toolkit/ngless#72 · Filter by author luispedro opened on Jun 19, 2018

• Implement a setup phase for external modules

  enhancement
  ngless-toolkit/ngless#71 · Filter by author unode opened on Jun 13, 2018
  

• select/filter reads matching/not-matching regions of interest

  enhancement
  ngless-toolkit/ngless#69 · Filter by author unode opened on May 17, 2018
  2

• Compute mapstats after select()

  enhancement
  ngless-toolkit/ngless#65 · Filter by author luispedro opened on May 2, 2018

• NGLess should restart when using parallel and tasks are not finished

  enhancement
  ngless-toolkit/ngless#60 · Filter by author luispedro opened on Mar 28, 2018

• Filetype in external modules does not enforce number of inputs passed

  ngless-toolkit/ngless#54 · Filter by author unode opened on Jan 16, 2018