nf-core/diaproteomics issues and pull requests

#161 - Important! Template update for nf-core/tools v2.13

Pull Request - State: open - Opened by nf-core-bot 7 months ago

#160 - Important! Template update for nf-core/tools v2.12

Pull Request - State: closed - Opened by nf-core-bot 8 months ago - 1 comment

#159 - Important! Template update for nf-core/tools v2.11.1

Pull Request - State: closed - Opened by nf-core-bot 10 months ago - 1 comment

#158 - Important! Template update for nf-core/tools v2.11

Pull Request - State: closed - Opened by nf-core-bot 10 months ago - 1 comment

#157 - Important! Template update for nf-core/tools v2.10

Pull Request - State: closed - Opened by nf-core-bot about 1 year ago - 1 comment

#156 - Important! Template update for nf-core/tools v2.9

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#155 - Important! Template update for nf-core/tools v2.8

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 1 comment

#154 - Important! Template update for nf-core/tools v2.7.2

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#153 - Important! Template update for nf-core/tools v2.7.1

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#152 - Since this wwas merged with quantms - consider closing all open issues and archiving this?

Issue - State: open - Opened by apeltzer almost 2 years ago - 1 comment
Labels: enhancement

#151 - Important! Template update for nf-core/tools v2.6

Pull Request - State: closed - Opened by nf-core-bot almost 2 years ago - 1 comment

#150 - Important! Template update for nf-core/tools v2.5.1

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 1 comment

#149 - Important! Template update for nf-core/tools v2.5

Pull Request - State: closed - Opened by nf-core-bot about 2 years ago - 2 comments

#148 - do not have the irt_sheet.tsv

Issue - State: closed - Opened by nuan604 about 2 years ago - 5 comments
Labels: bug

#147 - Add mimetype to input parameter in schema

Pull Request - State: open - Opened by drpatelh over 2 years ago

#146 - Important! Template update for nf-core/tools v2.4

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#145 - Important! Template update for nf-core/tools v2.3.2

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#144 - Important! Template update for nf-core/tools v2.3.1

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#143 - Important! Template update for nf-core/tools v2.3

Pull Request - State: closed - Opened by nf-core-bot over 2 years ago - 1 comment

#142 - Important! Template update for nf-core/tools v2.2

Pull Request - State: closed - Opened by nf-core-bot almost 3 years ago - 1 comment

#141 - Important! Template update for nf-core/tools v2.1

Pull Request - State: closed - Opened by nf-core-bot about 3 years ago - 1 comment

#140 - Important! Template update for nf-core/tools v2.0.1

Pull Request - State: closed - Opened by nf-core-bot about 3 years ago - 1 comment

#139 - Important! Template update for nf-core/tools v2.0

Pull Request - State: closed - Opened by KevinMenden about 3 years ago - 1 comment

#138 - Removed redundant parameters and added descriptions.

Pull Request - State: closed - Opened by ksantone over 3 years ago - 1 comment

#137 - Removed redundant parameters and added to descriptions.

Pull Request - State: closed - Opened by ksantone over 3 years ago - 1 comment

#136 - Updated on dev (there will still probably be other issues).

Pull Request - State: closed - Opened by ksantone over 3 years ago - 1 comment

#135 - Updated changes to schema properly (schema build succeeded thus far).

Pull Request - State: closed - Opened by ksantone over 3 years ago - 2 comments

#134 - Updates to schema for parameters additions.

Pull Request - State: closed - Opened by ksantone over 3 years ago - 1 comment

#133 - Dockerfile - alias mamba so that nf-core lint passes

Pull Request - State: closed - Opened by ewels over 3 years ago - 1 comment

#132 - Use mamba to build the environment instead of conda

Pull Request - State: closed - Opened by ewels over 3 years ago - 1 comment

#131 - Remove code duplication in ci actions workflow

Pull Request - State: closed - Opened by ewels over 3 years ago - 2 comments

#130 - Modified Dockerfile to account for changes in DIAlignR.

Pull Request - State: closed - Opened by ksantone over 3 years ago - 1 comment

#129 - Modified Dockerfile to account for changes in DIAlignR.

Pull Request - State: closed - Opened by ksantone over 3 years ago - 1 comment

#128 - Modified Dockerfile to account for changes in DIAlignR.

Pull Request - State: closed - Opened by ksantone over 3 years ago - 1 comment

#127 - Modified Dockerfile to account for changes in DIAlignR.

Pull Request - State: closed - Opened by ksantone over 3 years ago - 1 comment

#126 - Template update 1.14

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#125 - Important! Template update for nf-core/tools v1.14

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago

#124 - Introduce zip decompression into the pipeline

Issue - State: open - Opened by Leon-Bichmann over 3 years ago
Labels: enhancement

#123 - Prepare for 1.2.4 release "Kalalau trail"

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 4 comments

#122 - reset to 1.2.4

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#121 - reset to dev

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#120 - prepare for 1.2.4 - "Kalalau Trail"

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#119 - no ms1 in test_full to reduce memory

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#118 - Raise memory for FDR estimation

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#117 - Update README

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#116 - Update Readme

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#115 - more mztab fixes

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#114 - Strip out MultiQC boilerplate code + some more tidying

Pull Request - State: closed - Opened by ewels over 3 years ago - 2 comments

#113 - typo

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#112 - more fixes

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#111 - fixes

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#110 - Prepare for DIAproteomics Release 1.2.3 (Mt. Elbrus South Route)

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 7 comments

#109 - Preparing for 1.2.3 release with mzTab output

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 10 comments

#108 - add better error messages using ifEmpty statements

Issue - State: open - Opened by Leon-Bichmann over 3 years ago - 1 comment
Labels: enhancement

#107 - add lucidchart reference

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#106 - Schema fixes

Pull Request - State: closed - Opened by ewels over 3 years ago - 3 comments

#105 - Important! Template update for nf-core/tools v1.13.3

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago

#104 - Important! Template update for nf-core/tools v1.13.2

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago

#103 - Merging template updates

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 8 comments

#102 - Important! Template update for nf-core/tools v1.13.1

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago

#101 - Important! Template update for nf-core/tools v1.13

Pull Request - State: closed - Opened by nf-core-bot over 3 years ago - 1 comment

#100 - DIAPROTEOMICS: Convert all usage parameters to JSON schema documentation

Issue - State: open - Opened by apeltzer over 3 years ago
Labels: enhancement

#99 - adapt chromatogram indexing memory requirements

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#98 - update DIAlignR once more

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#97 - lowmem batchsize

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#96 - add readOptions to FileCacher

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#95 - update DIAlignR

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#94 - bump-version to 1.2.2

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#93 - Prepare for release 1.2.2

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 3 comments

#92 - update DIAlignR to speed branch and introduce sqMass compression

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#91 - update full test profile

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#90 - string true/false to bool params

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#89 - update version to 1.2.1

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment

#88 - chromatogram_indexing at low memory

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#87 - restructure + more comments to code

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#86 - bump-version 1.2.0

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#85 - Preparing for release 1.2.1

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago - 2 comments

#84 - RT alignment between libraries

Issue - State: closed - Opened by Leon-Bichmann over 3 years ago - 1 comment
Labels: bug

#83 - fix: swap x and y of linear model

Pull Request - State: closed - Opened by Leon-Bichmann over 3 years ago

#82 - remove duplicate dropping

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago - 1 comment

#81 - Library generation from DDA doesn't merge libraries entirely

Issue - State: closed - Opened by Leon-Bichmann almost 4 years ago
Labels: bug

#80 - msstats pdf optional

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#79 - rm parallel in else case

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#78 - reset to dev

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#77 - fix parallelization param and Changelog

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#76 - quick fix: pqp lib_used

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago - 1 comment

#75 - Bug: Adapt for pqp lib file format

Issue - State: closed - Opened by Leon-Bichmann almost 4 years ago - 1 comment
Labels: bug

#74 - add further input check of batches and number of entries

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago - 1 comment

#73 - Include an exception when multiple libraries and irts are used for the same batch

Issue - State: closed - Opened by Leon-Bichmann almost 4 years ago
Labels: enhancement

#72 - Preparing for 1.2.0

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago - 1 comment

#71 - Preparing for 1.2.0

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago - 2 comments

#70 - Important! Template update for nf-core/tools v1.12.1

Pull Request - State: closed - Opened by nf-core-bot almost 4 years ago

#69 - BiocParallel can fail in some cases

Issue - State: closed - Opened by Leon-Bichmann almost 4 years ago - 2 comments
Labels: bug

#68 - fix plots

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#67 - fix plots

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#66 - add min_upper_edge_dist param

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#65 - update DIAlignr and biocparallel

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#64 - Add biocparallel to the conda environment

Pull Request - State: closed - Opened by lkuchenb almost 4 years ago

#63 - projectDir/baseDir

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

#62 - reformatted output to publishDir

Pull Request - State: closed - Opened by Leon-Bichmann almost 4 years ago

GitHub / nf-core/diaproteomics issues and pull requests