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

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

[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.

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