nfcore/quantms v1.2.0 - Thimphu

Added Feature

• #275 BigBio Added support for bruker data in DIA branch @daichengxin @ypriverol @jspaezp.
• #275 BigBio And speed-up to DIA-NN pipeline @jspaezp.
• #275 BigBio Support for library-base search in DIA-NN pipeline @jspaezp.
• #300 BigBio Major refactoring of LFQ-DDA MBR algorithm @jpfeuffer @ypriverol @timosachsenberg.
• #279 BigBio Support for SAGE search engine @jpfeuffer @timosachsenberg @ypriverol.
• #122 BigBio Update openms 3.1.0 by @ypriverol @timosachsenberg

Changed

• #314 Update for pmultiqc to pmultiqc=0.0.23 @WangHong007 @daichengxin
• #308 Update for openms to openms=3.1.0
• Update for sdrf-pipelines to sdrf-pipelines=0.0.24
• Update for msstats to msstats=4.2.1

Fixed

• #316 Fixed jar path selection of luciphoradapter and msgf+
• Fixed bug where modification masses were not calculated correctly in DIA-NN conversion.
• Fixed multiple bugs Pull Request #293 BigBio, #279 BigBio, #265 BigBio, #260 BigBio, #257 BigBio

### Additional changes

• Post 1.1.1 release workup by @fabianegli in #100
• Merging template update 2.9 by @jpfeuffer in #108
• Important! Template update for nf-core/tools v2.9 by @nf-core-bot in #103
• Update diann_convert.py by @daichengxin in #121
• Minor changes by @ypriverol in #124
• Multiple changes before the release. by @ypriverol in #125
• Use https instead of http for shields.io resources by @fabianegli in #126
• Mypy found issue fixes by @fabianegli in #127
• More fixes for type annotations by @fabianegli in #128
• More fixes for type annotations by @fabianegli in #129
• set release date and release version by @fabianegli in #131
• Version 1.2 [PLEASE DO NOT MERGE YET] by @ypriverol in #120

Full Changelog: 1.1.1...1.2.0

nf-core/quantms v1.1.1 - Berlin-Bern

What's Changed

• Add release date and Zenodo DOI for version 1.1.0 by @ypriverol @fabianegli in #85
• Upgrade Comet to latest 20223010 version by @ypriverol in #88
• [Feature] micromambaci by @jpfeuffer in #89
• [FEATURE] update dev profile by @jpfeuffer in #91
• [Doc] mztab columns by @jpfeuffer in #92
• Update container logic by @sminot in #93

New Contributors

• @sminot made their first contribution in #93

Full Changelog: 1.1.0...1.1.1

nf-core/quantms v1.1.0 - Berlin

These release includes the following major changes:

• Bugfixes and speed increases in the OpenMS tools due to version update to 2.9.1
• Improvements in logging by adding many more process.ids
• Large restructuring of DIA branch to increase parallelizability
• Better error handling in MSstats step plus new parameter to filter for MSstats' adjusted p-value in the plots
• More efficient parsing of mzML statistics in a separate step
• A clearer distinction between per-run and experiment-wide FDRs with one parameter for each
• More test profiles including larger "full" tests

What's Changed

• [Feature] New release cycle for 1.1 by @jpfeuffer in #35
• [Testing] Add test profile as alias to test_lfq by @jpfeuffer in #36
• Important! Template update for nf-core/tools v2.4 by @nf-core-bot in #44
• Add mimetype to input parameter in schema by @drpatelh in #45
• Major changes in the quantms package by @ypriverol in #47
• [Fix] links due to server change by @jpfeuffer in #54
• Dev by @fabianegli in #55
• reproduce conda channel setup failure by @fabianegli in #56
• Important! Template update for nf-core/tools v2.5.1 by @nf-core-bot in #53
• Tetsrun by @fabianegli in #59
• Important! Template update for nf-core/tools v2.6 by @nf-core-bot in #60
• Sync dev by @jpfeuffer in #69
• Merging-template by @jpfeuffer in #70
• Important! Template update for nf-core/tools v2.7.2 by @nf-core-bot in #66
• Major PR with integration changes. by @ypriverol in #72
• small fixing for review PR #48 by @ypriverol in #74
• Contribution to v1 1 by @fabianegli in #76
• More changes for review 1.1 release by @ypriverol in #77
• small format changes by @ypriverol in #78
• changes for link module preprocess_expdesign.nf by @ypriverol in #79
• Prepare for release by @fabianegli in #80
• Dev by @ypriverol in #81
• consensusID remove process_medium by @ypriverol in #82
• [Release] 1.1 by @ypriverol in #48

New Contributors

• @nf-core-bot made their first contribution in #44
• @drpatelh made their first contribution in #45
• @fabianegli made their first contribution in #55

Full Changelog: 1.0...1.1.0

nf-core/quantms v1.0 - Havana

[1.0] nfcore/quantms - [05/02/2022] - Havana

Initial release of nf-core/quantms, created with the nf-core template.

Added

• New pipeline for DDA-LFQ data analysis
• New pipeline for DDA-ISO data analysis
• New datasets for DDA-LFQ and DDA-ISO data analysis
• Documentation added for DDA pipeline
• First pipeline for DIA-LFQ data analysis

Fixed

• This is the first release - no reported issues

Dependencies

The pipeline is using Nextflow DSL2, each process will be run with its own Biocontainer. This means that on occasion it is entirely possible for the pipeline to be using different versions of the same tool. However, the overall software dependency changes compared to the last release have been listed below for reference.

Dependency	Version
thermorawfileparser	1.3.4
comet	2021010
msgf+	2022.01.07
openms	2.8.0
sdrf-pipelines	0.0.21
percolator	3.5
pmultiqc	0.0.11
luciphor	2020_04_03
dia-nn	1.8.1
msstats	4.2.0
msstatstmt	2.2.0

Deprecated

New Contributors

• @ypriverol made their first contribution in #2
• @jpfeuffer made their first contribution in #12
• @daichengxin made their first contribution in #15

Full Changelog: https://github.com/nf-core/quantms/commits/1.0