PaulBrack Yamato issues

PaulBrack / Yamato

SWATH-QC metrics

Apache License 2.0

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Bump Newtonsoft.Json from 12.0.3 to 13.0.2 in /MzqcGenerator

#173 dependabot[bot] opened 1 year ago
0
Bump Newtonsoft.Json from 12.0.3 to 13.0.2 in /SwaMe

#172 dependabot[bot] opened 1 year ago
0
Bump Newtonsoft.Json from 12.0.3 to 13.0.1 in /SwaMe

#171 dependabot[bot] closed 1 year ago
1
Bump Newtonsoft.Json from 12.0.3 to 13.0.1 in /MzqcGenerator

#170 dependabot[bot] closed 1 year ago
1
If some swaths have sizes and others do not, should the SwathSizeDifference metric be zero, non-zero, or not output?

#169 Ozzard opened 3 years ago
0
Chromatogram metric generator inserts in reverse order except at the first element if retention times collide

#168 Ozzard opened 3 years ago
0
Interquartile range is usually underestimated by InterQuartileRangeCalculator

#167 Ozzard closed 3 years ago
2
StartTimestamp and MissingScans now also printed to mzQC

#166 marinaPauw opened 4 years ago
0
Prevent some simple race conditions when calculating BasePeaks

#165 Ozzard closed 4 years ago
3
Repeatability issues for SwaMe.PeakWidths

#164 marinaPauw opened 4 years ago
0
Trouble generating report file

#163 mwalzer closed 4 years ago
7
Improve scan queuing and processing with a custom queue that only stalls the XML parser for the minimum possible time

#162 Ozzard closed 4 years ago
0
Split out MzmlParser

#161 Ozzard closed 4 years ago
0
Enable pipes on stdin and stdout

#160 Ozzard closed 4 years ago
0
Move controlled vocabulary work into its own project + minor bugfix

#159 Ozzard closed 4 years ago
0
Update to most recent dependencies as at 2020-05-18

#158 Ozzard closed 4 years ago
0
Use better ontology references

#157 Ozzard closed 4 years ago
0
Fixing rt grouper bug

#156 marinaPauw closed 4 years ago
0
Update Dockerfiles for new .Net Core version and new file location

#155 Ozzard opened 4 years ago
0
SwaMe.Desktop - defaults on GUI do not correspond to defaults on console

#154 marinaPauw opened 4 years ago
0
SwaMe.Desktop expects IRT to be run and unhandled exception occurs as it looks for the launchsettings.json file

#153 marinaPauw opened 4 years ago
0
Fix #151: use exceptions for file format errors in CSVs

#152 Ozzard closed 4 years ago
0
Application exit status should be 1 on failures, 0 on success

#151 Ozzard closed 4 years ago
0
Add a production Nlog.config and update Nlog version

#150 Ozzard closed 4 years ago
0
When caching to disk, two jobs running on the same node should not use the same namespace for temporary files

#149 Ozzard closed 4 years ago
3
Either put a hint in the docs for the cache-to-disk option that it caches in the temp directory, or allow the user to specify the path

#148 Ozzard closed 4 years ago
2
The all-in-one SwaMe.Console on Linux does not respect a NLog.console in the same directory

#147 Ozzard closed 4 years ago
5
Revise log levels to reflect a user's perception of severity.

#146 Ozzard closed 4 years ago
0
What copyright should SwaMe.Console show?

#145 Ozzard opened 4 years ago
1
At present, this QC tool cannot provide faster QC indication for SCIEX 6600 files than can Skyline with a simple R or Ruby script

#144 Ozzard closed 4 years ago
2
Add desktop client

#143 PaulBrack closed 4 years ago
0
Provide a "production mode" that gives no logging or debug output on successful execution, but good error detail on failure

#142 Ozzard closed 4 years ago
1
Send all logging output to stderr, not stdout

#141 Ozzard closed 4 years ago
2
When showing help, show current defaults for all options *or* do not default

#140 Ozzard opened 4 years ago
0
Allow the user to specify an output file path and name for at least the mzQC file, and ideally all files

#139 Ozzard closed 4 years ago
4
Ensure all metrics available from Yamato/SwaMe/Prognosticator are available in a single mzQC output file

#138 Ozzard closed 4 years ago
2
When publishing standalone Linux binaries, publish the "publish" directory not the base directory

#137 Ozzard closed 4 years ago
3
Fix #134: test for readability by opening read-only

#136 Ozzard closed 4 years ago
0
Respect the current directory at program run time for file paths

#135 Ozzard closed 4 years ago
2
When testing file readability for input files, open read-only not read-write

#134 Ozzard closed 4 years ago
0
mwalzer docker action

#133 mwalzer closed 4 years ago
0
If statement to enable using a csv/tsv file as input for iRT

#132 marinaPauw closed 4 years ago
0
Added check to make sure there is an "id" and "cycle" in the wiff mzML

#131 marinaPauw closed 4 years ago
0
Should be able to deal with mzML files that were created from wiffs that do not have an "id" feature.

#130 marinaPauw opened 4 years ago
0
RC1 - Option 'z, cacheSpectraToDisk' has no value

#129 mwalzer closed 4 years ago
1
Option 'z, cacheSpectraToDisk' does not evaluate as positive if present but not set to true

#128 mwalzer closed 4 years ago
3
RC1 - Can't load file

#127 mwalzer closed 4 years ago
8
AvgMzRange corrected

#126 marinaPauw closed 4 years ago
0
Number of RT columns expected corrected to 15

#125 marinaPauw closed 4 years ago
0
MzQC files now separately output into the directory created for that file

#124 marinaPauw closed 4 years ago
0