Dev#3

Open

ziadbkh wants to merge 230 commits intomasterfrom

dev

Commits on Apr 19, 2024

add gadi config
ziadbkh
committed

Commits on May 12, 2024

Commits on May 13, 2024

update
ziadbkh
committed

Commits on May 20, 2024

Commits on Aug 6, 2024

Commits on Aug 8, 2024

Bump to version 1.1.0dev

athbaltzis
authored and
ziadbkh
committed
Update CHANGELOG

athbaltzis
authored and
ziadbkh
committed
Add accelerator directive to GPU processes

robsyme
authored and
ziadbkh
committed
Add gpu to COLABFOLD_BATCH

robsyme
authored and
ziadbkh
committed
Accelerator null instead of zero

robsyme
authored and
ziadbkh
committed
If statement for accelerator

robsyme
authored and
ziadbkh
committed
Changelog fix

robsyme
authored and
ziadbkh
committed
Deal with multiline fasta for colabfold multimers

athbaltzis
authored and
ziadbkh
committed
Update CHANGELOG

athbaltzis
authored and
ziadbkh
committed
Reduce pdb_mmcif excessive symlinking

athbaltzis
authored and
ziadbkh
committed
Update documentation

athbaltzis
authored and
ziadbkh
committed
update paths

FriederikeHanssen
authored and
ziadbkh
committed
Update modules.json

athbaltzis
authored and
ziadbkh
committed
Update modules.json

athbaltzis
authored and
ziadbkh
committed
Make prettier happy

athbaltzis
authored and
ziadbkh
committed
Update CHANGELOG.md

athbaltzis
authored and
ziadbkh
committed
Update dbs.config

athbaltzis
authored and
ziadbkh
committed
Template update for nf-core/tools version 2.8

nf-core-bot
authored and
ziadbkh
committed
Run prettier

athbaltzis
authored and
ziadbkh
committed
Update .github/workflows/awsfulltest.yml

authored and
ziadbkh
committed
Added changes to run with new versions of colabfold (v.1.5.2) and alphafold (v.2.3.2)

Leila Mansouri
authored and
ziadbkh
committed
Added changes to run with new versions of colabfold (v.1.5.2) and alphafold (v.2.3.2)

l-mansouri
authored and
ziadbkh
committed
Added changes to run with new versions of colabfold (v.1.5.2) and alphafold (v.2.3.2)

l-mansouri
authored and
ziadbkh
committed
changed params name in the stub run

Leila Mansouri
authored and
ziadbkh
committed
specified where to fetch the ubuntu docker containers

Leila Mansouri
authored and
ziadbkh
committed
changed container names to be consisten with pipeline realease version

l-mansouri
authored and
ziadbkh
committed
updated the name of the containers to the nf-core ones

l-mansouri
authored and
ziadbkh
committed
updated the name of the containers to the nf-core ones

l-mansouri
authored and
ziadbkh
committed
updated redfundant path

l-mansouri
authored and
ziadbkh
committed
Update modules/local/combine_uniprot.nf

authored and
ziadbkh
committed
Update modules/local/multifasta_to_csv.nf

authored and
ziadbkh
committed
Create esmfold module and workflow

athbaltzis
authored and
ziadbkh
committed
Add WorkflowEsmofld.groovy

athbaltzis
authored and
ziadbkh
committed
Add modules_esmfold config and fix arguments

athbaltzis
authored and
ziadbkh
committed
Update nextflow_schema and nextflow.config

athbaltzis
authored and
ziadbkh
committed
Create ESMFOLD workflow

athbaltzis
authored and
ziadbkh
committed
Add test profiles for esmfold

athbaltzis
authored and
ziadbkh
committed
Add ESMFOLD workflow to the main and fix bugs

athbaltzis
authored and
ziadbkh
committed
Update nextflow_schema

athbaltzis
authored and
ziadbkh
committed
Update metromap

athbaltzis
authored and
ziadbkh
committed
Update README and docs

athbaltzis
authored and
ziadbkh
committed
Add colabfold server warning

athbaltzis
authored and
ziadbkh
committed
Add Citation

athbaltzis
authored and
ziadbkh
committed
Fix plddt tsv and update output docs

athbaltzis
authored and
ziadbkh
committed
Update AWS mega tests paths

athbaltzis
authored and
ziadbkh
committed
Update paths to docker images

athbaltzis
authored and
ziadbkh
committed
Fix prettier issues

athbaltzis
authored and
ziadbkh
committed
Fix prettier issues

athbaltzis
authored and
ziadbkh
committed
Update CHANGELOG

athbaltzis
authored and
ziadbkh
committed
Update paths to containers in local modules from dockerhub to quay

athbaltzis
authored and
ziadbkh
committed
Align lines

athbaltzis
authored and
ziadbkh
committed
Update README.md

authored and
ziadbkh
committed
Update README.md

authored and
ziadbkh
committed
Update CHANGELOG.md

authored and
ziadbkh
committed
Update README.md

authored and
ziadbkh
committed
Update nextflow.config

authored and
ziadbkh
committed
Update workflows/esmfold.nf

authored and
ziadbkh
committed
Update subworkflows/local/prepare_esmfold_dbs.nf

authored and
ziadbkh
committed
Fix prettier

athbaltzis
authored and
ziadbkh
committed
Fix indent

athbaltzis
authored and
ziadbkh
committed
Simplify prepare_esmfold

athbaltzis
authored and
ziadbkh
committed
Update subworkflows/local/prepare_esmfold_dbs.nf

authored and
ziadbkh
committed
Update workflows/esmfold.nf

authored and
ziadbkh
committed
Update workflows/esmfold.nf

authored and
ziadbkh
committed
Update workflows/esmfold.nf

authored and
ziadbkh
committed
Update conf/dbs.config

authored and
ziadbkh
committed
Update CHANGELOG

athbaltzis
authored and
ziadbkh
committed
Update local module

JoseEspinosa
authored and
ziadbkh
committed
Get rid of quay in config containers

JoseEspinosa
authored and
ziadbkh
committed
Update nf-core modules

JoseEspinosa
authored and
ziadbkh
committed
Fix typo

JoseEspinosa
authored and
ziadbkh
committed
Fix indent

JoseEspinosa
authored and
ziadbkh
committed
Make changelog version order descendent

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Remove untar patch

JoseEspinosa
authored and
ziadbkh
committed
Set a default docker registry outside of profile scope

JoseEspinosa
authored and
ziadbkh
committed
Add dev to changelog version and document last change

JoseEspinosa
authored and
ziadbkh
committed
Change uniclust30 to uniref30 path

athbaltzis
authored and
ziadbkh
committed
Update CHANGELOG

athbaltzis
authored and
ziadbkh
committed
Update colabfold container to python 3.10 and fix bug for multimers

athbaltzis
authored and
ziadbkh
committed
Update docker registry

athbaltzis
authored and
ziadbkh
committed
Revert default docker.registry

athbaltzis
authored and
ziadbkh
committed
Update container in MMSEQS_COLABFOLDSEARCH

athbaltzis
authored and
ziadbkh
committed
Update container for RUN_ALPHAFOLD2 module

athbaltzis
authored and
ziadbkh
committed
Change file read type to any

athbaltzis
authored and
ziadbkh
committed
Fix bug with filename collision

athbaltzis
authored and
ziadbkh
committed
Update RUN_ALPHAFOLD2_MSA and RUN_ALPHAFOLD2_PRED containers

athbaltzis
authored and
ziadbkh
committed
Update container paths and revert type of file read for alphafold dbs

athbaltzis
authored and
ziadbkh
committed
Add dockerfiles

athbaltzis
authored and
ziadbkh
committed
Fix linting

athbaltzis
authored and
ziadbkh
committed
Fix linting

athbaltzis
authored and
ziadbkh
committed
Fix lintint 3rd attempt

athbaltzis
authored and
ziadbkh
committed
Fix linting 4th attempt

athbaltzis
authored and
ziadbkh
committed
Update CHANGELOG

athbaltzis
authored and
ziadbkh
committed
Add quay.io source for singularity pulls

athbaltzis
authored and
ziadbkh
committed
Update gpu flag for colabfold

athbaltzis
authored and
ziadbkh
committed
Update COLABFOLD_BATCH dockerfile

athbaltzis
authored and
ziadbkh
committed
Update alphafold2 full_dbs parameter description

athbaltzis
authored and
ziadbkh
committed
Put white bg to metro map png

athbaltzis
authored and
ziadbkh
committed
Update CHANGELOG

athbaltzis
authored and
ziadbkh
committed
Update colabfold output name pattern

athbaltzis
authored and
ziadbkh
committed
Rename figs

athbaltzis
authored and
ziadbkh
committed
Update README.md

authored and
ziadbkh
committed
Add singularity.registry = 'quay.io' and bump nxf version to 23.04.0

JoseEspinosa
authored and
ziadbkh
committed
Update nf-core containers declaration

JoseEspinosa
authored and
ziadbkh
committed
Fix lint and update changelog

JoseEspinosa
authored and
ziadbkh
committed
Use nxf version 23.04.0 in ci

JoseEspinosa
authored and
ziadbkh
committed
Change double quotes for single quotes to avoid expansion

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Adapt command for POSIX portability

JoseEspinosa
authored and
ziadbkh
committed
Template update for nf-core/tools version 2.9

nf-core-bot
authored and
ziadbkh
committed
Remove old params not longer used by nf-validation

JoseEspinosa
authored and
ziadbkh
committed
Modify methodsDescriptionText in WorkflowColabfold and WorkflowEsmfold

JoseEspinosa
authored and
ziadbkh
committed
Fix lints

JoseEspinosa
authored and
ziadbkh
committed
Remove tracedir according to current template

JoseEspinosa
authored and
ziadbkh
committed
Fix nf-core lint

JoseEspinosa
authored and
ziadbkh
committed
Update assets/multiqc_config.yml

authored and
ziadbkh
committed
Update assets/multiqc_config.yml

authored and
ziadbkh
committed
Add file-path and mimetype to schema paths

JoseEspinosa
authored and
ziadbkh
committed
Use nf-validation plugin for parameter validation

JoseEspinosa
authored and
ziadbkh
committed
Add input schema

JoseEspinosa
authored and
ziadbkh
committed
Replace input_check by nf-validation

JoseEspinosa
authored and
ziadbkh
committed
Make lint happy

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Remove unused validationSchemaIgnoreParams

JoseEspinosa
authored and
ziadbkh
committed
Making lint happy

JoseEspinosa
authored and
ziadbkh
committed
Update paths to test dbs

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Fix indent

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Template update for nf-core/tools version 2.10

nf-core-bot
authored and
ziadbkh
committed
Add dump_parameters to the other subworkflows

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Fix zenodo link

JoseEspinosa
authored and
ziadbkh
committed
Fix "Argument list too long" issue

JoseEspinosa
authored and
ziadbkh
committed
Fix changelog msg

JoseEspinosa
authored and
ziadbkh
committed
Format changelog

JoseEspinosa
authored and
ziadbkh
committed
Escape properly bash command

JoseEspinosa
authored and
ziadbkh
committed
Call gunzip by file to avoid too argument error

JoseEspinosa
authored and
ziadbkh
committed
Template update for nf-core/tools version 2.11

nf-core-bot
authored and
ziadbkh
committed
Template update for nf-core/tools version 2.11.1

nf-core-bot
authored and
ziadbkh
committed
Template update for nf-core/tools version 2.12

nf-core-bot
authored and
ziadbkh
committed
Make prettier happy

JoseEspinosa
authored and
ziadbkh
committed
Make prettier happy

JoseEspinosa
authored and
ziadbkh
committed
Fix schema

JoseEspinosa
authored and
ziadbkh
committed
[automated] Fix linting with Prettier

nf-core-bot
authored and
ziadbkh
committed
First iteration towards lib removal

JoseEspinosa
authored and
ziadbkh
committed
Clean alphafold2 workflow

JoseEspinosa
authored and
ziadbkh
committed
Clean colabfold workflow

JoseEspinosa
authored and
ziadbkh
committed
Clean esmfold

JoseEspinosa
authored and
ziadbkh
committed
Clean prepare_esmfold_dbs

JoseEspinosa
authored and
ziadbkh
committed
Fix stub section

JoseEspinosa
authored and
ziadbkh
committed
Update main

JoseEspinosa
authored and
ziadbkh
committed
Update subworkflows

JoseEspinosa
authored and
ziadbkh
committed
Update missing subworkflows

JoseEspinosa
authored and
ziadbkh
committed
Add take to prepare subworkflow

JoseEspinosa
authored and
ziadbkh
committed
Fix colabfold workflow

JoseEspinosa
authored and
ziadbkh
committed
Remove prints

JoseEspinosa
authored and
ziadbkh
committed
Remove lib folder

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Make lint happy

JoseEspinosa
authored and
ziadbkh
committed
Fix lint

JoseEspinosa
authored and
ziadbkh
committed
Fix lint

JoseEspinosa
authored and
ziadbkh
committed
Fix error

JoseEspinosa
authored and
ziadbkh
committed
Make nf-core lint happy

JoseEspinosa
authored and
ziadbkh
committed
Fix changelog

JoseEspinosa
authored and
ziadbkh
committed
Template update for nf-core/tools version 2.13

nf-core-bot
authored and
ziadbkh
committed
Template update for nf-core/tools version 2.13.1

nf-core-bot
authored and
ziadbkh
committed
Remove dumpsoftwareversions from modules.json

JoseEspinosa
authored and
ziadbkh
committed
Remove template updated files from files unchanged

JoseEspinosa
authored and
ziadbkh
committed
Fix error introduced by the template merge

JoseEspinosa
authored and
ziadbkh
committed
Remove duplicated line

JoseEspinosa
authored and
ziadbkh
committed
Update alphafold standard container

JoseEspinosa
authored and
ziadbkh
committed
Update dockerfile alphafold standard

JoseEspinosa
authored and
ziadbkh
committed
Update docker image for af2 msa for testing

JoseEspinosa
authored and
ziadbkh
committed
Update alphafold dockerfiles

JoseEspinosa
authored and
ziadbkh
committed
Use dev image for split mode (prediction step)

JoseEspinosa
authored and
ziadbkh
committed
Add error to modules that can not use conda

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Force value channels to run all samples

JoseEspinosa
authored and
ziadbkh
committed
Nicely align comments

JoseEspinosa
authored and
ziadbkh
committed
Update changelog

JoseEspinosa
authored and
ziadbkh
committed
Include esmfold small test

JoseEspinosa
authored and
ziadbkh
committed
Add the esmfold test to ci

JoseEspinosa
authored and
ziadbkh
committed
Update link parameters name in schema, nextflow config, etc.

JoseEspinosa
authored and
ziadbkh
committed
Update subworkflows/local/prepare_alphafold2_dbs.nf

authored and
ziadbkh
committed
add gadi config
ziadbkh
committed
add visualisation
ziadbkh
committed
fix tower report
ziadbkh
committed
add plots
ziadbkh
committed
add figs to report
ziadbkh
committed
update
ziadbkh
committed
add visulaisation report
ziadbkh
committed
fix split msa
ziadbkh
committed
fix split esm-fold nofile channel
ziadbkh
committed
reports-update
ziadbkh
committed
add plots
ziadbkh
committed
new report
ziadbkh
committed
updated alphafold template with info on the left & navigation on the right

minh-biocommons
authored and
ziadbkh
committed
adding foldseek module
ziadbkh
committed
adding some commits from nf-core repo
ziadbkh
committed
update
ziadbkh
committed
few fixes for pull
ziadbkh
committed
fix readme
ziadbkh
committed
minor fixes
ziadbkh
committed

Comments

Commits

Commits on Apr 19, 2024

Commits on May 12, 2024

Commits on May 13, 2024

Commits on May 20, 2024

Commits on Jul 1, 2024

Commits on Jul 2, 2024

Commits on Jul 19, 2024

Commits on Jul 24, 2024

Commits on Aug 6, 2024

Commits on Aug 8, 2024