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version 3.1#37

Code

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glormph merged 19 commits intomasterlehtiolab/ddamsproteomics:masterfrom devlehtiolab/ddamsproteomics:devCopy head branch name to clipboardFeb 3, 2025

+872-232

Commits

Commits on Nov 5, 2024

• Bug fix, was not importing sys and using it in mods.py

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  d72160c

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Commits on Jan 28, 2025

• Started on sage in DDA workflow, runs through percolator now

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  f69dd0b

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Commits on Jan 30, 2025

• Sage now working throughout

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  0ae7818

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Commits on Jan 31, 2025

• Add msgf/sage to param schema so they end up in report

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  197f1d4

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• Adapt tests to sage/msgf - runs fine locally

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  5f14dc9

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• Fix tims scan nr issue (percolator needs integers, psmtable/mzmllookup have the msconvert result instead

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  36e5b89

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• Lower sage memory for testing (github)

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  0f6006e

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• 4GB mem wasnt enough for sage tests

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  4f77a1e

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• Luciphor should crash pipeline if it crashes, not go through pipe/grep/notcrash

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  3a055f7

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• Volcano plots back, had prev messed up the existence checker for those

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  c28e1e5

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• Also output PCA for sets, even if DEqMS / groups have been used

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  a3ae693

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• New palette for isobaric plots

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  1de5c7a

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• Crash early with message when not all sets are in the total proteome PSMs table

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  3f423a1

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• Remove channels feature, to remove channels which are empty instead of --keepnapsms

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Commits on Feb 3, 2025

• Upgrade msstitch to get extra column for msgfperco: explainedioncurrentratio. Also upgrade msgf, openms

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  91c4421

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• Error when remove_channels has an incorrect set name specified

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  4fec297

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• Small cleanup/fix

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  e9858ce

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• Add tables of PSM stats to report overview part

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  f7160f3

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• Changelog, version bump, doc update

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