What’s Changed

• Add release date and Zenodo DOI for version 1.1.0 by @ypriverol @fabianegli in https://github.com/nf-core/quantms/pull/85
• Upgrade Comet to latest 20223010 version by @ypriverol in https://github.com/nf-core/quantms/pull/88
• [Feature] micromambaci by @jpfeuffer in https://github.com/nf-core/quantms/pull/89
• [FEATURE] update dev profile by @jpfeuffer in https://github.com/nf-core/quantms/pull/91
• [Doc] mztab columns by @jpfeuffer in https://github.com/nf-core/quantms/pull/92
• Update container logic by @sminot in https://github.com/nf-core/quantms/pull/93

New Contributors

• @sminot made their first contribution in https://github.com/nf-core/quantms/pull/93

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

New Contributors

• @nf-core-bot made their first contribution in https://github.com/nf-core/quantms/pull/44
• @drpatelh made their first contribution in https://github.com/nf-core/quantms/pull/45
• @fabianegli made their first contribution in https://github.com/nf-core/quantms/pull/55

Full Changelog: https://github.com/nf-core/quantms/compare/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 https://github.com/nf-core/quantms/pull/2
• @jpfeuffer made their first contribution in https://github.com/nf-core/quantms/pull/12
• @daichengxin made their first contribution in https://github.com/nf-core/quantms/pull/15

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