ngless-toolkit

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

Difficulty 3/5 1-2 days Newbie friendliness 25/100

ngless-toolkit/ngless#154 · 1 comment · Opened Jul 15, 2022

custom pattern recognition load_fastq_directory Open

Difficulty 4/5 3-5 days Newbie friendliness 25/100

ngless-toolkit/ngless#145 · 1 comment · Opened Mar 3, 2021

Feature request: Filter mapped reads by minimum match fraction Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ngless-toolkit/ngless#139 · Opened Oct 12, 2020

Using collect on countables from mapstats gives a funny result Open

Difficulty 3/5 1-2 days Newbie friendliness 42/100

ngless-toolkit/ngless#138 · Opened Sep 18, 2020

Better debug message for files missing for collect() Open

better error message enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ngless-toolkit/ngless#136 · Opened Apr 23, 2020

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

enhancement performance

Difficulty 5/5 Over a week Newbie friendliness 30/100

ngless-toolkit/ngless#135 · 1 comment · Opened Mar 4, 2020

No HTML report is generated when using the parallel module Open

bug help wanted

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ngless-toolkit/ngless#133 · 2 comments · Opened Feb 27, 2020

Add read_length() to ShortRead type Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 42/100

ngless-toolkit/ngless#126 · 2 comments · Opened Dec 5, 2019

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

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ngless-toolkit/ngless#124 · 1 comment · Opened Oct 15, 2019

Implement readset return type types for modules Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ngless-toolkit/ngless#119 · 2 comments · Opened Aug 20, 2019

Inconsistent use of `local import` Open

bug

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ngless-toolkit/ngless#117 · 1 comment · Opened Aug 12, 2019

Reading .bz2 files fails to decompress or segfaults Open

Difficulty 4/5 3-5 days Newbie friendliness 30/100

ngless-toolkit/ngless#116 · 14 comments · Opened Jul 31, 2019

Update documentation for motus profiling to reflect motus2 Open

documentation

Difficulty 2/5 1-3 hours Newbie friendliness 38/100

ngless-toolkit/ngless#114 · 3 comments · Opened Jul 17, 2019

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

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ngless-toolkit/ngless#112 · 2 comments · Opened Jun 19, 2019

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

good first issue help wanted

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ngless-toolkit/ngless#102 · 7 comments · Opened Feb 28, 2019

Implement API to cleanup unnecessary files Open

enhancement good first issue

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ngless-toolkit/ngless#99 · Opened Feb 7, 2019

API for querying available versions of modules Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

ngless-toolkit/ngless#87 · Opened Oct 15, 2018

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

Difficulty 3/5 1-2 days Newbie friendliness 48/100

ngless-toolkit/ngless#80 · Opened Sep 19, 2018

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

enhancement help wanted question

Difficulty 5/5 Over a week Newbie friendliness 25/100

ngless-toolkit/ngless#75 · 2 comments · Opened Jun 26, 2018

Decouple stats machinery from HTML reporting Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 45/100

ngless-toolkit/ngless#74 · Opened Jun 26, 2018

Include file grouping information in fqstats Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 35/100

ngless-toolkit/ngless#73 · Opened Jun 19, 2018

`as_reads` should not require that BAM file be sorted Open

enhancement help wanted

Difficulty 4/5 3-5 days Newbie friendliness 25/100

ngless-toolkit/ngless#72 · Opened Jun 19, 2018

Implement a setup phase for external modules Open

enhancement

ngless-toolkit/ngless#71 · 1 assignee · Opened Jun 13, 2018

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

enhancement

Difficulty 5/5 Over a week Newbie friendliness 35/100

ngless-toolkit/ngless#69 · 2 comments · Opened May 17, 2018

Compute mapstats after select() Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ngless-toolkit/ngless#65 · Opened May 2, 2018

NGLess should restart when using `parallel` and tasks are not finished Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 25/100

ngless-toolkit/ngless#60 · Opened Mar 28, 2018

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

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ngless-toolkit/ngless#54 · Opened Jan 16, 2018

map-split: use relative instead of absolute path for symlinks Open

unclear whether it is a bug

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ngless-toolkit/ngless#50 · Opened Dec 4, 2017

Re-create indices if reference is modified Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 38/100

ngless-toolkit/ngless#46 · Opened Nov 15, 2017

Add functionality to pre-install modules Open

enhancement

Difficulty 4/5 3-5 days Newbie friendliness 25/100

ngless-toolkit/ngless#38 · Opened Oct 27, 2017

counts with many features/options should result in many files Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

ngless-toolkit/ngless#34 · 1 comment · 2 reactions · Opened Oct 19, 2017

Support outputting count files in binary format Open

enhancement

Difficulty 5/5 Over a week Newbie friendliness 20/100

ngless-toolkit/ngless#29 · 1 comment · Opened Apr 24, 2017

Explicit way of invalidating locks Open

enhancement

Difficulty 3/5 1-2 days Newbie friendliness 35/100

ngless-toolkit/ngless#15 · 1 comment · Opened Feb 16, 2017

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