Ecosyste.ms: Issues

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

GitHub / artic-network/rampart issues and pull requests

#117 - rampart with dorado's .fastq

Issue - State: open - Opened by doloacu 16 days ago - 1 comment

#116 - Update environment.yml to pin "nodejs"

Pull Request - State: closed - Opened by Desperate-Dan about 2 months ago

#115 - Be able to provide a barcode to sample name mapping from a CSV/TSV file

Issue - State: open - Opened by rambaut about 1 year ago
Labels: enhancement

#114 - File watching doesn't work in Windows Subsystem for Linux

Issue - State: open - Opened by rambaut about 1 year ago
Labels: bug

#113 - Multiples genomes

Issue - State: open - Opened by SergioBuenestadoSerrano over 1 year ago - 1 comment

#112 - Bump minimist, mkdirp, loader-fs-cache and handlebars

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#111 - Bump json5 from 1.0.1 to 1.0.2

Pull Request - State: open - Opened by dependabot[bot] over 1 year ago
Labels: dependencies

#110 - Bump express from 4.17.1 to 4.17.3

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#109 - Bump qs from 6.5.2 to 6.5.3

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#108 - Bump decode-uri-component from 0.2.0 to 0.2.2

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#107 - Bump engine.io and socket.io

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#106 - Bump loader-utils and react-scripts

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#105 - Bump socket.io-parser from 3.3.0 to 3.3.3

Pull Request - State: open - Opened by dependabot[bot] almost 2 years ago
Labels: dependencies

#104 - Bump socket.io-parser from 3.3.0 to 3.3.2

Pull Request - State: closed - Opened by dependabot[bot] almost 2 years ago - 1 comment
Labels: dependencies

#103 - Bump @hapi/hoek from 8.5.0 to 8.5.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#102 - Bump d3-color from 1.4.0 to 3.1.0

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#101 - Bump terser from 4.4.2 to 4.8.1

Pull Request - State: open - Opened by dependabot[bot] about 2 years ago
Labels: dependencies

#100 - Bump eventsource from 1.0.7 to 1.1.1

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#99 - Bump async from 2.6.3 to 2.6.4

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#98 - Bump url-parse from 1.4.7 to 1.5.10

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#97 - Bump url-parse from 1.4.7 to 1.5.7

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#96 - Bump follow-redirects from 1.9.0 to 1.14.8

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#95 - Bump ajv from 6.10.2 to 6.12.6

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#94 - Bump handlebars from 4.5.3 to 4.7.7

Pull Request - State: open - Opened by dependabot[bot] over 2 years ago
Labels: dependencies

#93 - Bump follow-redirects from 1.9.0 to 1.14.7

Pull Request - State: closed - Opened by dependabot[bot] over 2 years ago - 1 comment
Labels: dependencies

#92 - Latest release: v1.0.6 or v1.2.0?

Issue - State: closed - Opened by sassy-crick about 3 years ago - 1 comment

#91 - using the fastq.gz files demultiplexed

Issue - State: closed - Opened by josephhughes over 3 years ago - 1 comment

#90 - System limit for number of file watchers reached when using millions of reads

Issue - State: open - Opened by jagos01 over 3 years ago - 1 comment

#88 - Add custom_barcodes to the annotationOptions config choices

Issue - State: open - Opened by JudoWill over 3 years ago - 1 comment

#86 - showing different samples

Issue - State: closed - Opened by dinavb over 3 years ago - 2 comments

#85 - Bump socket.io from 2.2.0 to 2.4.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#83 - Inclusion Native Barcoding 96 Expansion barcodes (ONT)

Issue - State: closed - Opened by menickname almost 4 years ago - 6 comments

#82 - Seqkit backend and other improvements

Pull Request - State: closed - Opened by bsipos over 4 years ago - 2 comments

#81 - ncov2019 protocol version 3

Issue - State: closed - Opened by MaestSi over 4 years ago - 1 comment

#80 - Call snakemake with --cores argument

Pull Request - State: closed - Opened by jameshadfield over 4 years ago

#79 - improve display when no fastq data is available for a sample

Pull Request - State: closed - Opened by jameshadfield over 4 years ago

#76 - Scale 'unassigned' barcode bar to be per sample

Issue - State: open - Opened by rambaut over 4 years ago - 1 comment
Labels: enhancement

#75 - Include a coverage heat-map above amplicon graphic for each sample

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

#74 - Show coverage plot in summary panel

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

#73 - Fastqs with the same name in different folders are excluded from analysis

Issue - State: closed - Opened by MaestSi over 4 years ago - 9 comments
Labels: bug

#72 - Add --cores argument to snakemake calls

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

#71 - Improve read lengths histogram x-axis domain

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

#70 - Export Reads fails when there are unprocessed FASTQs on disk

Issue - State: open - Opened by jameshadfield over 4 years ago
Labels: bug

#69 - error in running the examples EBOV dataset

Issue - State: closed - Opened by micheledellab over 4 years ago - 11 comments

#68 - Allow fastqs to be gzipped

Pull Request - State: closed - Opened by jameshadfield over 4 years ago

#67 - Show coverage % in barchart at top

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

#66 - Front end memory issues when reaching millions of reads.

Issue - State: closed - Opened by rambaut over 4 years ago - 1 comment
Labels: bug

#65 - No data showing when using remote browser

Issue - State: closed - Opened by Psy-Fer over 4 years ago - 3 comments

#64 - Support for fastq.gz

Issue - State: closed - Opened by mattdmem over 4 years ago - 2 comments
Labels: enhancement

#63 - RAMPART & MinKNOW Barcoding

Issue - State: closed - Opened by mattdmem over 4 years ago - 2 comments

#62 - Reference heatmap needs improvement with light theme

Issue - State: open - Opened by jameshadfield over 4 years ago

#61 - Allow FASTQs to be in subfolders

Issue - State: closed - Opened by jameshadfield over 4 years ago - 1 comment

#60 - Export reads Error

Issue - State: closed - Opened by Zhu-Ying over 4 years ago - 2 comments

#59 - Remote browser fix

Pull Request - State: closed - Opened by iiSeymour over 4 years ago

#58 - Update installation.md

Pull Request - State: closed - Opened by rmp over 4 years ago - 1 comment

#57 - Update installation.md

Pull Request - State: closed - Opened by rmp over 4 years ago

#56 - Keep the reference colours consistent between runs and/or have some control over reference colour.

Issue - State: open - Opened by aineniamh over 4 years ago - 6 comments
Labels: enhancement

#55 - Improve documentation of config args to post processing scripts

Issue - State: open - Opened by aineniamh over 4 years ago - 2 comments
Labels: enhancement

#54 - Panel in UI to show currently running processing scripts

Issue - State: open - Opened by rambaut over 4 years ago - 2 comments
Labels: enhancement, high priority

#53 - Implement read filtering

Pull Request - State: closed - Opened by jameshadfield over 4 years ago

#52 - Reinstate UI for barcode-sample mapping/labelling.

Issue - State: closed - Opened by rambaut almost 5 years ago
Labels: enhancement

#51 - Filters panel for UI

Issue - State: closed - Opened by rambaut almost 5 years ago
Labels: enhancement

#50 - Amplicon caller in annotation script

Issue - State: open - Opened by rambaut almost 5 years ago
Labels: enhancement

#49 - Responsive design for iPads/Phones/MinION Mk1C etc touchscreen

Issue - State: open - Opened by rambaut almost 5 years ago
Labels: enhancement

#48 - Jump to sample if you click on a sample name

Issue - State: open - Opened by rambaut almost 5 years ago - 1 comment
Labels: enhancement

#47 - Generate reports as PDF or similar

Issue - State: open - Opened by rambaut almost 5 years ago
Labels: enhancement, high priority

#46 - Don't show coverage by reference if only one reference

Issue - State: open - Opened by rambaut almost 5 years ago
Labels: bug

#45 - Implemented the ability of parse_paf.py to cope with multiple mapping…

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

#44 - Resizing or zooming page using cmd – +/- doesn't resize components

Issue - State: closed - Opened by rambaut almost 5 years ago
Labels: bug

#43 - Optional reading of .bed files

Issue - State: open - Opened by rambaut about 5 years ago
Labels: enhancement

#42 - Command line/config option to specify number of references shown

Issue - State: closed - Opened by rambaut about 5 years ago - 1 comment
Labels: enhancement

#41 - If barcodeNames are specified then show the sample even if no reads are mapped

Issue - State: closed - Opened by rambaut about 5 years ago - 1 comment

#40 - Wrapping of sample names

Issue - State: closed - Opened by rambaut about 5 years ago
Labels: bug

#39 - Artifactual peak in read length histogram

Issue - State: open - Opened by rambaut about 5 years ago - 1 comment
Labels: bug, low priority

#38 - Heatmap colour scale reversed.

Issue - State: closed - Opened by rambaut about 5 years ago

#37 - Option to show absolute number of reference matches in heatmap

Issue - State: closed - Opened by rambaut about 5 years ago

#35 - Dynamic inclusion of references in the reference heatmap chart

Issue - State: closed - Opened by rambaut about 5 years ago - 1 comment
Labels: enhancement

#34 - Include an 'unmapped' row in the reference mapping heatmap chart

Issue - State: closed - Opened by rambaut about 5 years ago
Labels: enhancement

#33 - Dynamically pick colour range for different samples

Issue - State: closed - Opened by rambaut over 5 years ago - 2 comments
Labels: bug

#32 - Visualise genetic distance from reference

Issue - State: closed - Opened by rambaut over 5 years ago - 5 comments
Labels: enhancement

#31 - Bin reads from sample including any filters.

Issue - State: closed - Opened by rambaut over 5 years ago - 4 comments
Labels: enhancement

#30 - Add filters on to reads by clicking on UI components.

Issue - State: open - Opened by rambaut over 5 years ago
Labels: enhancement

#29 - More colours needed

Issue - State: closed - Opened by rambaut over 5 years ago - 1 comment
Labels: enhancement

#28 - Add modularity

Issue - State: open - Opened by rambaut over 5 years ago
Labels: enhancement

#27 - Dig-down display into each channel

Issue - State: closed - Opened by rambaut over 5 years ago - 1 comment
Labels: enhancement

#26 - Create a double clickable start button

Issue - State: open - Opened by rambaut over 5 years ago
Labels: enhancement

#25 - Create sample setup front end.

Issue - State: closed - Opened by rambaut over 5 years ago - 2 comments
Labels: enhancement

#24 - Adapt RAMPART's demuxing to use qcat.

Issue - State: closed - Opened by rambaut over 5 years ago - 3 comments
Labels: enhancement

#22 - 🇬🇭

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

#21 - Paths in config file should be relative to config file

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

#20 - Axis with log option toggle by clicking

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

#19 - Coverage plots with log axes

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

#18 - Daemon process should be able to resume

Issue - State: closed - Opened by rambaut over 6 years ago - 1 comment
Labels: enhancement, daemon