Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / ngless-toolkit/ngless issues and pull requests

#155 - Inconsistency in folder naming in documentation

Pull Request - State: closed - Opened by Vedanth-Ramji about 2 years ago

#153 - fd:12: hPutBuf: resource vanished (Broken pipe)

Issue - State: open - Opened by uloeber over 2 years ago

#152 - sdist lacks files necessary to run test suite

Issue - State: closed - Opened by sternenseemann over 2 years ago - 2 comments

#151 - NGLess contain the adapter removel or not?

Issue - State: closed - Opened by timeresistance1996 almost 3 years ago - 7 comments

#150 - NGless v2.5 URL was not found while running it for the first time

Issue - State: closed - Opened by evilvenom about 3 years ago - 2 comments

#149 - update smoothtrim: even window size

Pull Request - State: closed - Opened by mkuhn about 3 years ago - 1 comment

#148 - Documentation for smoothtrim

Issue - State: closed - Opened by mkuhn about 3 years ago
Labels: documentation

#147 - ngless-1.3.0-bwa not found

Issue - State: closed - Opened by liuxianghui over 3 years ago - 3 comments
Labels: better error message

#146 - Build static Linux image with GitHub Actions

Pull Request - State: closed - Opened by unode over 3 years ago

#145 - custom pattern recognition load_fastq_directory

Issue - State: open - Opened by uloeber almost 4 years ago - 1 comment

#144 - error message write ofile

Issue - State: closed - Opened by uloeber almost 4 years ago - 1 comment

#143 - Loading map file gmgc emapper2 annotations fails

Issue - State: closed - Opened by uloeber about 4 years ago - 4 comments
Labels: better error message

#142 - Error ir mapping step

Issue - State: open - Opened by chodarq about 4 years ago - 7 comments
Labels: better error message

#140 - Home directory does not have enough space for ngless

Issue - State: closed - Opened by liuxianghui about 4 years ago - 8 comments

#139 - Feature request: Filter mapped reads by minimum match fraction

Issue - State: open - Opened by luispedro over 4 years ago
Labels: enhancement

#137 - Github Actions Test mac

Pull Request - State: closed - Opened by psj1997 over 4 years ago - 3 comments

#136 - Better debug message for files missing for collect()

Issue - State: open - Opened by unode almost 5 years ago
Labels: enhancement, better error message

#135 - Introduce computation stages - validation, download, prepare, ...

Issue - State: open - Opened by unode almost 5 years ago - 1 comment
Labels: enhancement, performance

#134 - Error while generating reports for mOTUs. (fails integration tests)

Issue - State: closed - Opened by nairsajjal almost 5 years ago - 2 comments

#133 - No HTML report is generated when using the parallel module

Issue - State: open - Opened by unode almost 5 years ago - 2 comments
Labels: bug, help wanted

#132 - Added references to developer test scripts

Pull Request - State: closed - Opened by nairsajjal almost 5 years ago

#130 - Added reference to the whats-new section for NGless V1.1.0

Pull Request - State: closed - Opened by nairsajjal almost 5 years ago - 1 comment

#128 - Console throws an error while activating ngless environment

Issue - State: closed - Opened by dmahajan980 almost 5 years ago - 1 comment

#127 - load_mocat_sample fails when given file names with multiple pair identifiers

Issue - State: closed - Opened by jakob-wirbel about 5 years ago - 2 comments

#126 - Add read_length() to ShortRead type

Issue - State: open - Opened by unode about 5 years ago - 2 comments
Labels: enhancement

#125 - Installation issue on Mac

Issue - State: closed - Opened by dkinkj about 5 years ago - 10 comments

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

Issue - State: open - Opened by unode over 5 years ago - 1 comment

#123 - ngless complains about igc version

Issue - State: closed - Opened by ycl6 over 5 years ago - 1 comment

#122 - Docs for load_mocat_sample

Issue - State: closed - Opened by mkuhn over 5 years ago - 2 comments
Labels: documentation

#121 - Error: resource vanished (Broken pipe)

Issue - State: closed - Opened by ycl6 over 5 years ago - 4 comments

#120 - load_mocat_sample - missing pair.2 fails, missing pair.1 succeeds

Issue - State: closed - Opened by unode over 5 years ago - 5 comments
Labels: bug

#119 - Implement readset return type types for modules

Issue - State: open - Opened by mkuhn over 5 years ago - 2 comments
Labels: enhancement

#118 - Output unmapped PE fastq files

Issue - State: closed - Opened by ycl6 over 5 years ago - 1 comment

#117 - Inconsistent use of `local import`

Issue - State: open - Opened by unode over 5 years ago - 1 comment
Labels: bug

#116 - Reading .bz2 files fails to decompress or segfaults

Issue - State: open - Opened by unode over 5 years ago - 14 comments

#115 - Reading in fastq.gz files

Issue - State: closed - Opened by luispedro over 5 years ago - 8 comments

#114 - Update documentation for motus profiling to reflect motus2

Issue - State: open - Opened by theavanrossum over 5 years ago - 3 comments
Labels: documentation

#113 - Requesting qcstats when none exist fails

Issue - State: closed - Opened by unode over 5 years ago
Labels: bug, better error message

#112 - Allow collect()'ing when all processing is complete

Issue - State: open - Opened by unode over 5 years ago - 2 comments
Labels: enhancement

#111 - Fix CIGAR size calculation for insertions

Pull Request - State: closed - Opened by unode over 5 years ago - 6 comments

#110 - Default zstd compression breaks streaming

Issue - State: closed - Opened by unode over 5 years ago

#108 - Reference data includes bwa indices under incorrect name

Issue - State: closed - Opened by unode over 5 years ago - 2 comments

#107 - ngless --install-reference-data defaults to script version 0.0

Issue - State: closed - Opened by unode over 5 years ago

#106 - Reference genomes not available Mus musculus

Issue - State: closed - Opened by kunstner over 5 years ago - 6 comments

#105 - Filtering a SAM/BAM file in a select() block inverts samline order

Issue - State: closed - Opened by unode almost 6 years ago

#104 - can_gzip=False is not respected

Issue - State: closed - Opened by unode almost 6 years ago - 1 comment
Labels: bug

#103 - ZStandard compression breaks saving BAM files

Issue - State: closed - Opened by unode almost 6 years ago - 2 comments
Labels: bug

#102 - Add ability to strip sequences/qualities from SAM/BAM files

Issue - State: open - Opened by unode almost 6 years ago - 7 comments
Labels: good first issue, help wanted

#101 - bioconda recipe no longer works

Issue - State: closed - Opened by notestaff almost 6 years ago - 2 comments

#100 - 0.9 catalogs misnamed gene column

Issue - State: closed - Opened by unode almost 6 years ago - 1 comment

#99 - Implement API to cleanup unnecessary files

Issue - State: open - Opened by unode almost 6 years ago
Labels: enhancement, good first issue

#98 - Version resources independently of releases

Issue - State: closed - Opened by unode about 6 years ago

#97 - orf_find(prots_out) usage?

Issue - State: closed - Opened by kubu4 about 6 years ago - 1 comment

#96 - Ngless vs bionix comparison in faq?

Issue - State: closed - Opened by ghost about 6 years ago - 4 comments

#95 - Citations are printed multiple times

Issue - State: closed - Opened by unode about 6 years ago - 1 comment
Labels: enhancement, good first issue

#94 - Dependencies.Versions not found

Issue - State: closed - Opened by rekado about 6 years ago - 5 comments

#93 - MIN Fix errors/warnings with RefSeqInfoVector C code

Pull Request - State: closed - Opened by unode about 6 years ago

#92 - Broken pipe with samtools sort and multiple selects

Issue - State: closed - Opened by unode over 6 years ago - 3 comments

#91 - Strange error when QC some samples

Issue - State: closed - Opened by AlessioMilanese over 6 years ago - 6 comments
Labels: better error message

#90 - Rename --search-dir to --search-path

Pull Request - State: closed - Opened by unode over 6 years ago - 3 comments

#89 - Search-dir expansion with external modules

Pull Request - State: closed - Opened by unode over 6 years ago

#88 - Version files/indices created by bundled tools

Issue - State: closed - Opened by unode over 6 years ago

#87 - API for querying available versions of modules

Issue - State: open - Opened by unode over 6 years ago
Labels: enhancement

#86 - Pass arguments through to megahit

Issue - State: closed - Opened by luispedro over 6 years ago

#85 - --subsample option not working with writing out a FASTQ file.

Issue - State: closed - Opened by aniag over 6 years ago
Labels: bug

#84 - Better error message when user uses MAJOR.MINOR.PATCH in the ngless version string

Issue - State: closed - Opened by luispedro over 6 years ago
Labels: bug, good first issue, better error message

#83 - Support `NO_COLOR` environmental variable

Issue - State: closed - Opened by luispedro over 6 years ago
Labels: enhancement, good first issue, help wanted

#82 - samtools_sort API change

Issue - State: closed - Opened by unode over 6 years ago

#80 - mapstats() should error with position sorted sam/bam files

Issue - State: open - Opened by unode over 6 years ago

#79 - Garbage collect temporary files

Issue - State: closed - Opened by unode over 6 years ago
Labels: enhancement, help wanted, performance

#78 - Ability to cast int/double <-> string

Issue - State: closed - Opened by unode over 6 years ago - 1 comment

#77 - tar expansion should not use so much memory

Issue - State: closed - Opened by luispedro over 6 years ago - 1 comment
Labels: enhancement, help wanted, performance

#76 - Catalogs and Pig reference genome

Pull Request - State: closed - Opened by unode over 6 years ago - 1 comment

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

Issue - State: open - Opened by unode over 6 years ago - 2 comments
Labels: enhancement, question, help wanted

#74 - Decouple stats machinery from HTML reporting

Issue - State: open - Opened by unode over 6 years ago
Labels: enhancement

#73 - Include file grouping information in fqstats

Issue - State: open - Opened by unode over 6 years ago
Labels: enhancement

#72 - `as_reads` should not require that BAM file be sorted

Issue - State: open - Opened by luispedro over 6 years ago
Labels: enhancement, help wanted

#71 - Implement a setup phase for external modules

Issue - State: open - Opened by unode over 6 years ago
Labels: enhancement

#70 - Search path API inconsistency

Issue - State: closed - Opened by unode over 6 years ago

#69 - select/filter reads matching/not-matching regions of interest

Issue - State: open - Opened by unode over 6 years ago - 2 comments
Labels: enhancement

#68 - lock1 fails if provided string contains folders

Issue - State: closed - Opened by unode over 6 years ago - 8 comments

#67 - TravisCI "make fast" error is non-fatal

Issue - State: closed - Opened by unode over 6 years ago - 2 comments

#66 - ENH+TST Expand subfeatures when counting with a GFF file

Pull Request - State: closed - Opened by unode over 6 years ago - 3 comments

#65 - Compute mapstats after select()

Issue - State: open - Opened by luispedro almost 7 years ago
Labels: enhancement

#64 - GFF subfeature counting should be expanded

Issue - State: closed - Opened by unode almost 7 years ago - 1 comment

#63 - Multiple `-1` with count() when multiple features/subfeatures are requested

Issue - State: closed - Opened by unode almost 7 years ago
Labels: bug

#62 - Early check for column headers in `count(.., functional_map="file.map")`

Issue - State: closed - Opened by luispedro almost 7 years ago - 1 comment
Labels: enhancement

#61 - Check whether file is sorted in countsfile()

Issue - State: closed - Opened by luispedro almost 7 years ago - 1 comment
Labels: enhancement

#56 - --search-dir is not expanded prior to passing to external module

Issue - State: closed - Opened by unode about 7 years ago - 4 comments
Labels: bug

#55 - Add interleaved FastQ support

Issue - State: closed - Opened by unode about 7 years ago - 4 comments
Labels: enhancement, performance

#42 - Support compressing output files with collect()

Issue - State: closed - Opened by unode about 7 years ago
Labels: enhancement

#33 - Argument not checked prior to execution

Issue - State: closed - Opened by unode over 7 years ago - 1 comment
Labels: better error message

#22 - Compress temporary files

Issue - State: closed - Opened by luispedro almost 8 years ago - 3 comments
Labels: enhancement