Ecosyste.ms: Issues

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GitHub / nf-core/proteinfold issues and pull requests

#120 - Call gunzip by file to avoid too argument error

Pull Request - State: closed - Opened by JoseEspinosa 9 months ago - 1 comment

#119 - Fix "Argument list too long" issue

Pull Request - State: closed - Opened by JoseEspinosa 9 months ago - 1 comment

#118 - Fix zenodo link

Pull Request - State: closed - Opened by JoseEspinosa 9 months ago - 1 comment

#117 - Merge template v2.10

Pull Request - State: closed - Opened by JoseEspinosa 9 months ago - 3 comments

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

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

#115 - Throw message error when profile conda is used

Issue - State: open - Opened by JoseEspinosa 10 months ago
Labels: enhancement

#114 - Update paths to test dbs

Pull Request - State: closed - Opened by JoseEspinosa 10 months ago - 1 comment

#113 - DBs for esmfold full test was empty

Issue - State: closed - Opened by JoseEspinosa 12 months ago - 1 comment
Labels: enhancement

#112 - Use nf-validation plugin for parameter and samplesheet validation

Pull Request - State: closed - Opened by JoseEspinosa 12 months ago - 2 comments

#111 - Merge template 2.9

Pull Request - State: closed - Opened by JoseEspinosa about 1 year ago - 4 comments

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

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

#109 - Fix DOWNLOAD_PDBMMCIF

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

#108 - DOWNLOAD_PDBMMCIF process breaks

Issue - State: open - Opened by JoseEspinosa about 1 year ago
Labels: bug

#107 - Add checksums validation for DBs files

Issue - State: open - Opened by JoseEspinosa about 1 year ago - 1 comment
Labels: enhancement

#106 - Add singularity.registry = 'quay.io' and bump NF version to 23.04.0

Pull Request - State: closed - Opened by JoseEspinosa about 1 year ago - 2 comments

#104 - Add background to tubemap svg

Issue - State: open - Opened by robsyme about 1 year ago
Labels: bug

#103 - DB paths not being resolved properly

Issue - State: open - Opened by drpatelh about 1 year ago - 1 comment
Labels: bug

#102 - Could not load dynamic library 'libcuda.so.1'

Issue - State: closed - Opened by Nicobouch about 1 year ago - 1 comment
Labels: bug

#101 - Update gpu flag for colabfold

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

#100 - Update containers for local modules

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

#99 - colabfold - No module named 'openmm'

Issue - State: closed - Opened by Nicobouch about 1 year ago - 5 comments
Labels: bug

#98 - Add OpenFold workflow

Issue - State: open - Opened by athbaltzis about 1 year ago
Labels: enhancement

#97 - Change uniclust30 to uniref30 path when using the full BFD database in Alphafold2

Pull Request - State: closed - Opened by athbaltzis about 1 year ago - 2 comments

#96 - PDBMMCIF download error

Issue - State: closed - Opened by Nicobouch about 1 year ago - 8 comments
Labels: bug

#95 - Set a default docker registry outside of profile scope

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

#94 - Update modules

Pull Request - State: closed - Opened by JoseEspinosa about 1 year ago - 2 comments

#93 - Update CHANGELOG

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

#92 - Add ESMFold workflow to the pipeline

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

#91 - Updated the Colabfold (version 1.5.2) and AlphaFold (version 2.3.2) containers

Pull Request - State: closed - Opened by l-mansouri about 1 year ago - 2 comments

#90 - Nf core template merge 2.8

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

#89 - Issue with excessive symlinking and update in the documentation

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

#88 - Issue with excessive symlinking

Issue - State: closed - Opened by multimeric about 1 year ago - 8 comments
Labels: bug

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

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

#86 - Integrate Jalview for the visualisation of AlphaFold2 and Colabfold results

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

#85 - Update ColabFold version

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

#84 - Update AlphaFold2 version

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

#83 - Add ESMFold workflow

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

#82 - update paths

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

#81 - Support multiline fasta for colabfold multimer predictions

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

#80 - Nvidia gpu profile

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

#79 - Bump version 1.1.0dev

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

#78 - Update dev after release

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

#77 - Fix linting issues with black

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

#76 - Update images for release

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

#75 - Changes proposed by the reviews before the initial release

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

#74 - Initial release (1.0.0 - - White Silver Reebok)

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

#73 - Pre-release PR

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

#72 - Update README

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

#71 - Update changelog

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

#70 - Update usage and docs

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

#69 - Merge template v2.7.2

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

#68 - Update documentation with recommendations for distributed file systems

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

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

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

#66 - Standardization before release

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

#65 - Merge template v2.7.1

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

#64 - Merging template updates v2.7.1

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

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

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

#62 - Bug fixes towards the first release

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

#61 - Restructure in only two modes and add DB configs

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

#60 - Update ci and aws full tests and their configs

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

#59 - Update AF2_split to 2.2.4

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

#58 - Populate multiqc report, remove custom config and bug fixes

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

#57 - Add colabfold_db dir to test_colabfold_webserver.config

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

#56 - colabfold: alphafold params based on model type

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

#54 - Update AlphaFold2 to the latest version (v.2.2.4)

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

#53 - First iteration towards the creation of the mmseqs modules

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

#52 - Create an institutional config for the pipeline and get rid of custom config

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

#51 - remove wrong suffix from colabfold local dirs

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

#50 - wrong path for local colabfold_db directories envdb and uniref30

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

#49 - when colabfold_db is initialized no params directory is created

Issue - State: closed - Opened by rjpbonnal over 1 year ago - 5 comments
Labels: bug

#47 - ColabSearch input db oder is inverted

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

#46 - Colabsearch when linking files multiple versions of versions.yml are present

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

#45 - creates the versions.yml in the process folder

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

#44 - colabfold, MMSEQS_TSV2EXPROFILEDB creation of versions.yml in the wrong place

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

#43 - uniclust30 contains subdirectories and file must operate accordingly

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

#42 - alphafold/uniclust30 contains a subdirectory which is not linked at runtime

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

#41 - Fix bug with illegal characters (0) in pdb_seqres database

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

#40 - Fix the path issues when using af2_db and colabfold_db params

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

#39 - Parse failed with pdb_seqres.txt

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

#38 - modified modules to add version reporting

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

#37 - Bug when manually specifying the path to AF2 dbs and params

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

#36 - Get rid of custom configuration

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

#35 - Populate multiqc report

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

#34 - Update and restructure modules

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

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

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

#32 - Add Omegafold workflow

Issue - State: open - Opened by kenibrewer almost 2 years ago
Labels: enhancement

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

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

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

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

#28 - Files missing for pdb_mmcif after download

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

#27 - Download failing due to ssl verification

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

#26 - Add AF2 Split

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

#25 - Rearrange the way DBs are downloaded

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

#24 - Add modules version reporting

Issue - State: closed - Opened by JoseEspinosa about 2 years ago
Labels: enhancement

#22 - Create a local aria2 module

Issue - State: closed - Opened by JoseEspinosa about 2 years ago
Labels: enhancement