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While looking for multiple hits per MS2 spectrum (in DIA for example), top_hits should be turned off (set to 0). Unfortunately this currently results in a crash during the FDR calculations with the er…
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Facing issues with running the FeatureLinkerUnlabeledKD tool with consensusXML files.
When the module is run with the featureXML files from the MetaboliteAdductDecharger step, it appears to run wi…
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### Description of the bug
```
nf-core/quantms execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 8.
The full error message was…
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Hi there,
I found there are three parameters, "prot_prior", "pep_emission", and "pep_spurious_emission" in the Epifany node configuration, that are automatically being grid searched if the values a…
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When running SpectraST using the OpenMS Thirdparty Unix binary, it works, however it does not correctly annotate RT metavalues.
In fact for my data it annotates the same value as m/z for retention …
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Hi,
I am using OpenMS component to analyze protein mass spectrometry, at some steps I always encounter the following report:
`QIODevice::read (QNetworkReplyHttpImpl): device not open`
For example i…
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My pipeline fails when using Lys-C as a digestion enzyme, ```NT=Lys-C;AC=MS:1001309 ``` or ```NT=Lys-C/P;AC=MS_1001310```. It works with trypsin ```NT=Trypsin;AC=MS_1001251```. My command is:
```
n…
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Greetings,
What is the license of these files: src/tests/class_tests/openms/data/PepNovoOutfile.out, ./src/tests/class_tests/openms/data/PepNovoOutfile_version_file.txt .
The whole directory sha…
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### Description of the bug
```
ERROR ~ Error executing process > 'NFCORE_QUANTMS:QUANTMS:LFQ:PROTEOMICSLFQ (PXD002854-serum.sdrf_openms_design)'
Caused by:
Process `NFCORE_QUANTMS:QUANTMS:LFQ:…
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- [x] It is not even building for PRs
- [x] Boost Debug is still on.
- [x] Names between travis and gh actions do not match (pr123 vs pr-123).
- [ ] Suffix for pyopenms builds missing.
- [x] CMake…