Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / nf-core/metapep issues and pull requests

#99 - Changelog cleanup

Pull Request - State: open - Opened by tillenglert about 1 year ago - 2 comments

#98 - Forgot to add test_all to nextflow.config

Pull Request - State: closed - Opened by tillenglert about 1 year ago - 1 comment

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

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

#96 - Feature/chunk size rework

Pull Request - State: closed - Opened by tillenglert about 1 year ago - 3 comments

#95 - Fix typo in peptide lengths

Pull Request - State: closed - Opened by tillenglert about 1 year ago - 1 comment

#94 - Overview figure update

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 3 comments

#93 - Check and expand Ci tests

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 9 comments

#92 - Bugfix/peptide length check

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment

#91 - Feature/allow allpep lengths

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment

#90 - Script headers

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment

#89 - Bugfix peptide Lengths and include log instead of tsv

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 2 comments

#88 - Update Citations

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 2 comments

#87 - Template update nf-core tools 2.9

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment

#86 - Adjusted used resource request labels

Pull Request - State: closed - Opened by skrakau over 1 year ago - 1 comment

#85 - Add log file to outdir/logs/ instead of a tsv for the unified model lengths

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 4 comments

#84 - Multiqc

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 5 comments

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

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

#82 - Add label retry to download proteins process

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment

#81 - Remove subsampling for now

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 2 comments

#80 - Add tests

Pull Request - State: closed - Opened by skrakau over 1 year ago - 2 comments

#79 - Make versions of pandas and other tools match in all modules

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment

#78 - New Parameters for pandas memory usage and chunk sizes

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 2 comments

#77 - Delete push to docker hub workflows

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment

#76 - Subworkflow input check remodeling

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 4 comments

#75 - Peptide length additional checks

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 3 comments

#74 - Peptide lengths can only be set over all alleles

Issue - State: closed - Opened by tillenglert over 1 year ago - 1 comment
Labels: bug

#73 - Update Epytope version to 3.3.1

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 5 comments

#72 - Remove assets/weights.tsv and update usage.md

Pull Request - State: closed - Opened by skrakau over 1 year ago - 2 comments

#71 - `INPUT_CHECK` subworkflow restructure

Issue - State: closed - Opened by tillenglert over 1 year ago - 3 comments
Labels: enhancement

#70 - Supported allele check and show

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 4 comments

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

Pull Request - State: closed - Opened by nf-core-bot over 1 year ago - 3 comments

#68 - Tests for MHCflurry and MHCnuggets

Issue - State: open - Opened by tillenglert over 1 year ago
Labels: enhancement

#66 - Look into `polars` python library as alternative for `pandas`

Issue - State: open - Opened by tillenglert over 1 year ago
Labels: enhancement

#65 - Bugfix/datamodel figure

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment

#64 - Docs/update datamodel figure

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 2 comments

#63 - test_mouse fails on github actions (PR on dev)

Issue - State: closed - Opened by tillenglert over 1 year ago - 2 comments
Labels: bug, duplicate

#62 - Feat/update prodigal

Pull Request - State: closed - Opened by tillenglert over 1 year ago
Labels: enhancement

#61 - Update docs - more detailed description about data model

Pull Request - State: closed - Opened by skrakau over 1 year ago - 1 comment

#60 - MultiQC

Issue - State: closed - Opened by skrakau over 1 year ago
Labels: bug

#59 - Update relational data model figure

Issue - State: closed - Opened by skrakau over 1 year ago - 4 comments
Labels: documentation, enhancement

#58 - Sort input for GENERATE_PROTEIN_AND_ENTITY_IDS to ensure deterministi…

Pull Request - State: closed - Opened by skrakau over 1 year ago - 1 comment
Labels: enhancement

#57 - Use meta map for allele_id and allele_name

Issue - State: open - Opened by tillenglert over 1 year ago - 1 comment
Labels: enhancement

#56 - Doc/docs update

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment
Labels: documentation

#55 - Epitopeprediction update

Pull Request - State: closed - Opened by tillenglert over 1 year ago - 1 comment
Labels: enhancement

#54 - Change head to nf-core

Issue - State: closed - Opened by skrakau over 1 year ago - 1 comment
Labels: bug

#53 - Add documentation about internally used data model

Issue - State: closed - Opened by skrakau over 1 year ago - 1 comment
Labels: documentation, enhancement

#52 - Use Pandas float_precision param when reading floats

Pull Request - State: closed - Opened by skrakau over 1 year ago - 2 comments

#51 - Make association of entity_ids and microbiome_ids deterministic

Issue - State: closed - Opened by skrakau over 1 year ago
Labels: enhancement

#50 - Pre-filter peptides prior prediction

Issue - State: open - Opened by skrakau over 1 year ago
Labels: enhancement

#49 - Update to new Pandas 2.0 release

Issue - State: open - Opened by skrakau over 1 year ago
Labels: enhancement

#48 - Check supported models and handle warnings

Issue - State: closed - Opened by skrakau over 1 year ago - 3 comments
Labels: enhancement

#47 - Update containers

Pull Request - State: closed - Opened by skrakau over 1 year ago - 1 comment

#46 - Add more documentation and control taxid input more thoroughly

Pull Request - State: closed - Opened by tillenglert almost 2 years ago - 3 comments

#45 - Enable multiple weights for bins

Pull Request - State: closed - Opened by tillenglert almost 2 years ago - 2 comments

#44 - Optimize COLLECT_STATS process

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 2 comments

#43 - Add full-size test

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 1 comment

#42 - Fix CI tests using GitHub secrets

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 1 comment

#41 - Clean up CI tests

Issue - State: closed - Opened by skrakau almost 2 years ago - 1 comment
Labels: enhancement

#40 - Bugfix/bin processing

Pull Request - State: closed - Opened by tillenglert almost 2 years ago - 2 comments

#39 - Fix CI tests using NCBI secrets

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 1 comment

#38 - Erroneous processing of entities - changed with co-assembly feature

Issue - State: closed - Opened by skrakau almost 2 years ago
Labels: bug

#37 - Current version doesn't work with syfpeithi and mouse alleles

Issue - State: closed - Opened by skrakau almost 2 years ago - 1 comment
Labels: bug

#36 - Add custom script for efficient TSV file concatenation (2)

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 1 comment

#35 - Add custom script for efficient TSV file concatenation

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 1 comment

#34 - Caching issue of `PREDICT_EPITOPES` results

Issue - State: closed - Opened by skrakau almost 2 years ago - 1 comment
Labels: bug

#33 - Binned score distribution

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 1 comment

#32 - Optimize `prepare_score_distribution.py`

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 1 comment

#31 - Merging template updates 2.7.2

Pull Request - State: closed - Opened by skrakau almost 2 years ago - 2 comments

#30 - Co-assembly input: Resolve redundant protein prediction

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

#29 - Add data model figure and included in output.md

Pull Request - State: closed - Opened by skrakau almost 2 years ago

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

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

#27 - 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

#26 - Optimize prep entity binding ratios - chunkwise

Pull Request - State: closed - Opened by skrakau about 2 years ago - 1 comment

#25 - Optimize prep entity binding ratios2

Pull Request - State: closed - Opened by skrakau about 2 years ago

#24 - Optimize generate_peptides.py

Pull Request - State: closed - Opened by skrakau about 2 years ago - 1 comment

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

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

#22 - 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

#21 - Chunk-wise processing of peptides and optimized pandas operations

Pull Request - State: closed - Opened by skrakau about 2 years ago - 3 comments

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

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

#19 - Merging template 2.4 updates

Pull Request - State: closed - Opened by skrakau over 2 years ago - 1 comment

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

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

#17 - Integrate epitopeprediction

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

#16 - Merging template updates

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

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

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

#14 - 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

#13 - Update modules

Pull Request - State: closed - Opened by AntoniaSchuster over 2 years ago - 1 comment

#12 - Update documentation

Pull Request - State: closed - Opened by AntoniaSchuster over 2 years ago - 1 comment

#11 - Merge template update 2.3

Pull Request - State: closed - Opened by AntoniaSchuster over 2 years ago - 1 comment

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

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

#9 - Write documentation

Issue - State: closed - Opened by AntoniaSchuster almost 3 years ago
Labels: documentation

#8 - Add schematic representation of data model

Issue - State: closed - Opened by skrakau almost 3 years ago
Labels: enhancement

#7 - Update module prodigal

Pull Request - State: closed - Opened by AntoniaSchuster almost 3 years ago - 2 comments

#6 - add publish_dir for multiqc to modules.config

Pull Request - State: closed - Opened by AntoniaSchuster almost 3 years ago - 2 comments

#5 - Change pipeline version to 1.0dev

Pull Request - State: closed - Opened by AntoniaSchuster almost 3 years ago - 1 comment

#4 - Merge dsl2 template

Pull Request - State: closed - Opened by AntoniaSchuster almost 3 years ago - 2 comments

#3 - Fix generation of dict_proteinId_assemblyIds for Entrez download

Pull Request - State: closed - Opened by skrakau almost 3 years ago - 1 comment

#2 - Avoid redundant processing of co-assemblies

Pull Request - State: closed - Opened by AntoniaSchuster almost 3 years ago - 4 comments

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

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