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Dev -> Master for 1.1.0 release #158

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Jun 25, 2024
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11dd9b6
Set a default docker registry outside of profile scope
JoseEspinosa May 12, 2023
43c2b11
Add dev to changelog version and document last change
JoseEspinosa May 12, 2023
20387d3
Merge pull request #95 from JoseEspinosa/quay_fix
JoseEspinosa May 12, 2023
672a671
Change uniclust30 to uniref30 path
athbaltzis May 16, 2023
b7f59db
Update CHANGELOG
athbaltzis May 16, 2023
cc4145d
Merge pull request #97 from athbaltzis/dev
JoseEspinosa May 16, 2023
a9aa8a7
Update colabfold container to python 3.10 and fix bug for multimers
athbaltzis May 17, 2023
42dc8c8
Update docker registry
athbaltzis May 17, 2023
6b6fd50
Revert default docker.registry
athbaltzis May 17, 2023
6418f2a
Update container in MMSEQS_COLABFOLDSEARCH
athbaltzis May 17, 2023
005f84d
Update container for RUN_ALPHAFOLD2 module
athbaltzis May 17, 2023
16a0119
Change file read type to any
athbaltzis May 18, 2023
6198d7e
Fix bug with filename collision
athbaltzis May 18, 2023
3393d17
Update RUN_ALPHAFOLD2_MSA and RUN_ALPHAFOLD2_PRED containers
athbaltzis May 18, 2023
23f5fb7
Update container paths and revert type of file read for alphafold dbs
athbaltzis May 19, 2023
aeb394a
Add dockerfiles
athbaltzis May 19, 2023
868c81f
Fix linting
athbaltzis May 19, 2023
85574af
Fix linting
athbaltzis May 19, 2023
86acba0
Fix lintint 3rd attempt
athbaltzis May 19, 2023
e83e255
Fix linting 4th attempt
athbaltzis May 19, 2023
671760c
Update CHANGELOG
athbaltzis May 19, 2023
b1d40d5
Add quay.io source for singularity pulls
athbaltzis May 19, 2023
1080e2b
Merge pull request #100 from athbaltzis/dev
athbaltzis May 19, 2023
2fef3ea
Update gpu flag for colabfold
athbaltzis May 20, 2023
a357972
Merge pull request #101 from athbaltzis/dev
JoseEspinosa May 22, 2023
e071acd
Update COLABFOLD_BATCH dockerfile
athbaltzis Jun 1, 2023
c97eedd
Update alphafold2 full_dbs parameter description
athbaltzis Jun 1, 2023
03a53c6
Put white bg to metro map png
athbaltzis Jun 1, 2023
66507e1
Update CHANGELOG
athbaltzis Jun 1, 2023
7f45653
Update colabfold output name pattern
athbaltzis Jun 2, 2023
6e27484
Rename figs
athbaltzis Jun 2, 2023
40fd35e
Update README.md
athbaltzis Jun 2, 2023
a531ba7
Merge pull request #105 from athbaltzis/dev
athbaltzis Jun 2, 2023
f7a2a5f
Add singularity.registry = 'quay.io' and bump nxf version to 23.04.0
JoseEspinosa Jun 14, 2023
c0d8978
Update nf-core containers declaration
JoseEspinosa Jun 14, 2023
e80a8bb
Fix lint and update changelog
JoseEspinosa Jun 14, 2023
27a1e3a
Use nxf version 23.04.0 in ci
JoseEspinosa Jun 14, 2023
888c890
Merge pull request #106 from JoseEspinosa/updates
JoseEspinosa Jun 14, 2023
1424009
Change double quotes for single quotes to avoid expansion
JoseEspinosa Jun 29, 2023
262e86d
Update changelog
JoseEspinosa Jun 29, 2023
da6cd06
Adapt command for POSIX portability
JoseEspinosa Jun 30, 2023
36cb7ca
Merge pull request #109 from JoseEspinosa/fixes
JoseEspinosa Jun 30, 2023
fb29546
Template update for nf-core/tools version 2.9
nf-core-bot Jun 30, 2023
0750e43
Merge branch 'TEMPLATE' of https://github.com/nf-core/proteinfold int…
JoseEspinosa Jul 3, 2023
4e95501
Remove old params not longer used by nf-validation
JoseEspinosa Jul 3, 2023
f314eb8
Modify methodsDescriptionText in WorkflowColabfold and WorkflowEsmfold
JoseEspinosa Jul 3, 2023
57e38b0
Fix lints
JoseEspinosa Jul 3, 2023
33cb52d
Remove tracedir according to current template
JoseEspinosa Jul 3, 2023
3a2e413
Update assets/multiqc_config.yml
JoseEspinosa Jul 11, 2023
ba11c1c
Update assets/multiqc_config.yml
JoseEspinosa Jul 11, 2023
dc38fd3
Fix nf-core lint
JoseEspinosa Jul 11, 2023
1e2b200
Merge branch 'merge-template-2.9' of https://github.com/JoseEspinosa/…
JoseEspinosa Jul 11, 2023
3acccff
Merge pull request #111 from JoseEspinosa/merge-template-2.9
JoseEspinosa Jul 11, 2023
6b99a1f
Add file-path and mimetype to schema paths
JoseEspinosa Jul 21, 2023
4a7c6b2
Use nf-validation plugin for parameter validation
JoseEspinosa Jul 21, 2023
949b7dc
Add input schema
JoseEspinosa Jul 21, 2023
190781a
Replace input_check by nf-validation
JoseEspinosa Jul 21, 2023
2e2121a
Make lint happy
JoseEspinosa Jul 21, 2023
3e5e182
Update changelog
JoseEspinosa Jul 21, 2023
a7f7281
Remove unused validationSchemaIgnoreParams
JoseEspinosa Jul 21, 2023
e888c1c
Making lint happy
JoseEspinosa Jul 21, 2023
236d405
Merge pull request #112 from JoseEspinosa/updates
JoseEspinosa Jul 24, 2023
8bb50bf
Update paths to test dbs
JoseEspinosa Sep 6, 2023
7c20277
Update changelog
JoseEspinosa Sep 6, 2023
6cc42c5
Fix indent
JoseEspinosa Sep 7, 2023
d983660
Update changelog
JoseEspinosa Sep 7, 2023
bbc2265
Merge pull request #114 from JoseEspinosa/updates
JoseEspinosa Sep 7, 2023
4883de3
Template update for nf-core/tools version 2.10
nf-core-bot Sep 25, 2023
06a1538
Merge branch 'TEMPLATE' of https://github.com/nf-core/proteinfold int…
JoseEspinosa Sep 26, 2023
0a8f8a8
Add dump_parameters to the other subworkflows
JoseEspinosa Sep 26, 2023
aae18b5
Update changelog
JoseEspinosa Sep 26, 2023
e9fad86
Merge pull request #117 from JoseEspinosa/merge_temp_2.10
JoseEspinosa Sep 27, 2023
8f2cbe3
Fix zenodo link
JoseEspinosa Sep 27, 2023
146c357
Merge pull request #118 from JoseEspinosa/fixes
JoseEspinosa Sep 27, 2023
8b701b0
Fix "Argument list too long" issue
JoseEspinosa Sep 29, 2023
a9ef4a8
Fix changelog msg
JoseEspinosa Sep 29, 2023
59d43d9
Format changelog
JoseEspinosa Sep 29, 2023
6d71c38
Escape properly bash command
JoseEspinosa Sep 29, 2023
37ff17f
Merge pull request #119 from JoseEspinosa/fixes
JoseEspinosa Sep 29, 2023
bc45cd6
Call gunzip by file to avoid too argument error
JoseEspinosa Oct 3, 2023
91868d1
Merge pull request #120 from JoseEspinosa/fixes
JoseEspinosa Oct 3, 2023
28e9b48
Template update for nf-core/tools version 2.11
nf-core-bot Dec 19, 2023
e484f62
Template update for nf-core/tools version 2.11.1
nf-core-bot Dec 20, 2023
ccde84d
Template update for nf-core/tools version 2.12
nf-core-bot Jan 29, 2024
33f224c
Merge branch 'TEMPLATE' of https://github.com/nf-core/proteinfold int…
JoseEspinosa Jan 30, 2024
940b5b7
Make prettier happy
JoseEspinosa Jan 30, 2024
ba04e5f
Make prettier happy
JoseEspinosa Jan 30, 2024
104fc22
Fix schema
JoseEspinosa Jan 30, 2024
d164612
[automated] Fix linting with Prettier
nf-core-bot Jan 30, 2024
6b27456
Merge pull request #127 from JoseEspinosa/merging-template-2.12
JoseEspinosa Jan 30, 2024
ed8c87c
Template update for nf-core/tools version 2.13
nf-core-bot Feb 20, 2024
4707da1
First iteration towards lib removal
JoseEspinosa Feb 29, 2024
ae8d735
Clean alphafold2 workflow
JoseEspinosa Feb 29, 2024
d9834c0
Clean colabfold workflow
JoseEspinosa Feb 29, 2024
d1982dd
Clean esmfold
JoseEspinosa Feb 29, 2024
e678a6c
Clean prepare_esmfold_dbs
JoseEspinosa Feb 29, 2024
7945ca7
Fix stub section
JoseEspinosa Feb 29, 2024
619ac8d
Update main
JoseEspinosa Feb 29, 2024
bba9830
Update subworkflows
JoseEspinosa Feb 29, 2024
8b19f9a
Update missing subworkflows
JoseEspinosa Feb 29, 2024
e184460
Add take to prepare subworkflow
JoseEspinosa Feb 29, 2024
896cf72
Fix colabfold workflow
JoseEspinosa Feb 29, 2024
1538206
Template update for nf-core/tools version 2.13.1
nf-core-bot Feb 29, 2024
2d8bcae
Remove prints
JoseEspinosa Feb 29, 2024
d779379
Remove lib folder
JoseEspinosa Feb 29, 2024
8ca4342
Update changelog
JoseEspinosa Feb 29, 2024
544fccf
Make lint happy
JoseEspinosa Feb 29, 2024
b60cf11
Fix lint
JoseEspinosa Feb 29, 2024
b2f4a1e
Fix lint
JoseEspinosa Feb 29, 2024
289e962
Fix error
JoseEspinosa Feb 29, 2024
4d2dc6b
Make nf-core lint happy
JoseEspinosa Feb 29, 2024
663fa13
Fix changelog
JoseEspinosa Mar 1, 2024
835e2fd
Merge pull request #132 from JoseEspinosa/fixes
JoseEspinosa Mar 1, 2024
3876d2b
Merge branch 'TEMPLATE' of https://github.com/nf-core/proteinfold int…
JoseEspinosa Mar 5, 2024
06d37a4
Remove dumpsoftwareversions from modules.json
JoseEspinosa Mar 6, 2024
6d9e34d
Remove template updated files from files unchanged
JoseEspinosa Mar 6, 2024
0cffa6d
Fix error introduced by the template merge
JoseEspinosa Mar 6, 2024
8d4448f
Remove duplicated line
JoseEspinosa Mar 6, 2024
45b44b8
Merge pull request #134 from JoseEspinosa/merging-template-2.13.1
JoseEspinosa Mar 6, 2024
c57f9cf
Update alphafold standard container
JoseEspinosa Mar 18, 2024
f5d4bf1
Update dockerfile alphafold standard
JoseEspinosa Mar 19, 2024
def38fd
Update docker image for af2 msa for testing
JoseEspinosa Mar 19, 2024
400ce19
Update alphafold dockerfiles
JoseEspinosa Mar 20, 2024
d54e571
Use dev image for split mode (prediction step)
JoseEspinosa Mar 20, 2024
1bdff57
Merge pull request #136 from JoseEspinosa/fixes
JoseEspinosa Mar 22, 2024
030dd34
Add error to modules that can not use conda
JoseEspinosa Mar 22, 2024
d319d8e
Update changelog
JoseEspinosa Mar 22, 2024
dbbab38
Merge pull request #138 from JoseEspinosa/fixes
JoseEspinosa Apr 2, 2024
848afa9
Include esmfold small test
JoseEspinosa Apr 2, 2024
d824025
Add the esmfold test to ci
JoseEspinosa Apr 2, 2024
a6ddabd
Merge pull request #139 from JoseEspinosa/fixes
bjlang Apr 2, 2024
adc4224
fix name of mmseq output channel db_indexed
ziadbkh Apr 8, 2024
13b873e
Merge pull request #143 from ziadbkh/master
JoseEspinosa Apr 8, 2024
3ece71e
Force value channels to run all samples
JoseEspinosa Apr 18, 2024
4e4ba3f
Nicely align comments
JoseEspinosa Apr 18, 2024
65201c8
Update changelog
JoseEspinosa Apr 18, 2024
a487545
Merge remote-tracking branch 'upstream/dev' into updates
JoseEspinosa Apr 18, 2024
cf30828
Update subworkflows/local/prepare_alphafold2_dbs.nf
JoseEspinosa Apr 18, 2024
65bf8e9
Update link parameters name in schema, nextflow config, etc.
JoseEspinosa Apr 18, 2024
067d572
Merge branch 'updates' of https://github.com/JoseEspinosa/nf-core-pro…
JoseEspinosa Apr 18, 2024
df3400f
Merge pull request #146 from JoseEspinosa/updates
JoseEspinosa Apr 18, 2024
f55ae96
Update aria2
JoseEspinosa Apr 18, 2024
0dff3c9
Update mmseqs_createindex
JoseEspinosa Apr 18, 2024
4a10983
Update rest of modules
JoseEspinosa Apr 18, 2024
ce52af0
Merge branch 'dev' of https://github.com/JoseEspinosa/nf-core-protein…
JoseEspinosa Apr 18, 2024
f743963
Some plumbing after modules update
JoseEspinosa Apr 19, 2024
c93df6c
Make prettier happy
JoseEspinosa Apr 19, 2024
89ae64b
test
JoseEspinosa Apr 19, 2024
9a30c96
Get rid of first to force value channel
JoseEspinosa Apr 23, 2024
acdadb7
Update CHANGELOG
JoseEspinosa Apr 23, 2024
788bbfc
Merge pull request #149 from JoseEspinosa/dev
JoseEspinosa Apr 24, 2024
785f0c3
Add test for alphafold download
JoseEspinosa Apr 24, 2024
6f25a65
Add test for colabfold download
JoseEspinosa Apr 24, 2024
3cf462c
Update nextflow config
JoseEspinosa Apr 24, 2024
c212c42
Add download test to ci
JoseEspinosa Apr 24, 2024
9579b6d
Update changelog
JoseEspinosa Apr 24, 2024
51830a4
Update CHANGELOG.md
JoseEspinosa Apr 24, 2024
f274102
Merge pull request #151 from JoseEspinosa/updates
JoseEspinosa Apr 24, 2024
5627018
Add skip_multiqc parameter
JoseEspinosa Apr 24, 2024
0ccb5d4
Add skip_multiqc to alphafold2 workflow
JoseEspinosa Apr 24, 2024
5babe67
Add skip_multiqc to colabfold workflow
JoseEspinosa Apr 24, 2024
075aefe
Add skip_multiqc to esmfold workflow
JoseEspinosa Apr 24, 2024
7f56c7d
Update changelog
JoseEspinosa Apr 24, 2024
631fe4f
Make linting happy
JoseEspinosa Apr 24, 2024
7c4cf7a
Merge pull request #152 from JoseEspinosa/updates
JoseEspinosa Apr 24, 2024
4ad7b7f
Change link protocol from ftp to https
JoseEspinosa Apr 29, 2024
eaf453b
Merge branch 'updates' of https://github.com/JoseEspinosa/nf-core-pro…
JoseEspinosa Apr 30, 2024
daf52db
Update paths to Colabfold uniref30
JoseEspinosa Apr 30, 2024
7afeb60
Update docker file
JoseEspinosa May 2, 2024
ae58cec
clean dockerfiler
JoseEspinosa May 2, 2024
05adf28
Update images for colabfold
JoseEspinosa May 6, 2024
e991c4e
Template update for nf-core/tools version 2.14.0
nf-core-bot May 8, 2024
fbc85e1
Template update for nf-core/tools version 2.14.1
nf-core-bot May 9, 2024
edaa689
Update dockerfile
JoseEspinosa May 14, 2024
a94aa7c
Merge branch 'TEMPLATE' of https://github.com/nf-core/proteinfold int…
JoseEspinosa May 14, 2024
0b7bccd
Add pipelines_testdata_base_path param
JoseEspinosa May 14, 2024
68c065f
Update changelog
JoseEspinosa May 14, 2024
1207ebb
rm CUSTOM_DUMPSOFTWAREVERSIONS from modules.config
JoseEspinosa May 14, 2024
e9e2798
Revert testing leak
JoseEspinosa May 14, 2024
5040419
Fix tyop
JoseEspinosa May 14, 2024
76767a2
:'(
JoseEspinosa May 14, 2024
1fba293
Merge pull request #155 from JoseEspinosa/merge_template_2.14.1
JoseEspinosa May 15, 2024
399c1eb
Merge remote-tracking branch 'upstream/dev' into updates
JoseEspinosa May 15, 2024
dc1df3f
rm cp as is file is named directly by colabfold
JoseEspinosa May 15, 2024
5296b65
Retrieving files without copying as now the id is used by colabfold f…
JoseEspinosa May 15, 2024
2548c8d
Fix typo
JoseEspinosa May 16, 2024
af58d8e
Fix LD_LIBRARY_PATH
JoseEspinosa May 30, 2024
d53b9ab
Update changelog
JoseEspinosa May 30, 2024
0c48bd6
Make lint happy
JoseEspinosa May 30, 2024
d979d3f
Fix schema
JoseEspinosa May 30, 2024
8126d0e
Merge pull request #156 from JoseEspinosa/updates
JoseEspinosa May 31, 2024
8e7f23b
Bump version 1.1.0 on changelog
JoseEspinosa May 31, 2024
e24b6e5
Bump version 1.1.0 to images
JoseEspinosa May 31, 2024
2bef5e7
Bump version 1.1.0 to readme
JoseEspinosa May 31, 2024
b29d676
Some minor corrections
JoseEspinosa May 31, 2024
2bec617
Bump v1.1.0 to multiqc config
JoseEspinosa Jun 1, 2024
4308842
Merge pull request #157 from JoseEspinosa/bump_v1.1.0
JoseEspinosa Jun 3, 2024
b9e4c13
Update mgnify fasta
JoseEspinosa Jun 3, 2024
d33e481
Merge pull request #159 from JoseEspinosa/updates
JoseEspinosa Jun 3, 2024
2642202
Publish pdb_seqres when from prepare_alphafold2_dbs
JoseEspinosa Jun 4, 2024
f3be7a5
Publish pdb_seqres when downloaded using prepare_alphafold2_dbs
JoseEspinosa Jun 4, 2024
6a02035
Merge branch 'updates' of https://github.com/JoseEspinosa/nf-core-pro…
JoseEspinosa Jun 4, 2024
a9fc87e
Add previous PR and update parameter table
JoseEspinosa Jun 4, 2024
adf0118
Simplify CI by using matrix of parameterers
JoseEspinosa Jun 4, 2024
1f86e49
Update README
JoseEspinosa Jun 4, 2024
17b3f2f
Modify contributing as suggested in review
JoseEspinosa Jun 4, 2024
028733b
Fix several comments of tests config files
JoseEspinosa Jun 4, 2024
f303668
Apply review suggestions to usage
JoseEspinosa Jun 4, 2024
0fffa5f
Align comments of subworkflows
JoseEspinosa Jun 4, 2024
ff82923
Create channels instead of using just file method
JoseEspinosa Jun 4, 2024
b641a37
Create channels instead of using just file method
JoseEspinosa Jun 5, 2024
3b092aa
Add meta to aria2 call
JoseEspinosa Jun 5, 2024
ded727e
Force value channel for bfd
JoseEspinosa Jun 7, 2024
dd38311
Create channels instead of just using file method
JoseEspinosa Jun 10, 2024
83b0b6b
Update docs
JoseEspinosa Jun 10, 2024
9857ca2
Make lint happy
JoseEspinosa Jun 10, 2024
f5bdad2
Make nf-core lint happy
JoseEspinosa Jun 10, 2024
48a0a3f
Add uniref30_alphafold2_link parameter to changelog
JoseEspinosa Jun 10, 2024
0637765
Merge branch 'updates' of https://github.com/JoseEspinosa/nf-core-pro…
JoseEspinosa Jun 10, 2024
6f083ce
Make lint happy
JoseEspinosa Jun 11, 2024
58fa8a9
Merge pull request #160 from JoseEspinosa/updates
JoseEspinosa Jun 11, 2024
a0c132d
Modify path to esmfold db in test_full
JoseEspinosa Jun 11, 2024
c3c748a
Merge pull request #161 from JoseEspinosa/updates
JoseEspinosa Jun 12, 2024
9065362
Fix file staging
JoseEspinosa Jun 17, 2024
ebe7b0a
Merge remote-tracking branch 'upstream/dev' into fixes
JoseEspinosa Jun 17, 2024
1e8fc3a
Merge pull request #162 from JoseEspinosa/fixes
JoseEspinosa Jun 17, 2024
2b3c03a
Fix full test and update release date
JoseEspinosa Jun 19, 2024
9ecebf2
Fix changelog
JoseEspinosa Jun 19, 2024
8a1b1a4
Merge pull request #163 from JoseEspinosa/fixes
JoseEspinosa Jun 19, 2024
4f89eb7
Always upload logs after trying to launch AWS megatests
adamrtalbot Jun 20, 2024
3c642ac
Fix tyop
JoseEspinosa Jun 20, 2024
71ac60e
Merge remote-tracking branch 'upstream/dev' into fixes
JoseEspinosa Jun 20, 2024
2286292
Merge pull request #164 from JoseEspinosa/fixes
JoseEspinosa Jun 20, 2024
d2d5ff6
Merge pull request #165 from nf-core/always-upload-logs-after-megatest
JoseEspinosa Jun 21, 2024
11f7a93
Discriminate between num_recycles of esmfold and colabfold (default v…
JoseEspinosa Jun 21, 2024
ae73c37
Update readme
JoseEspinosa Jun 21, 2024
12fb738
Add mention to AWS Open Data Sponsorship Program
JoseEspinosa Jun 21, 2024
cf94e83
Merge remote-tracking branch 'upstream/dev' into fixes
JoseEspinosa Jun 21, 2024
e30e250
Update changelog
JoseEspinosa Jun 21, 2024
564e06a
Merge pull request #166 from JoseEspinosa/fixes
JoseEspinosa Jun 21, 2024
0c64479
Update date
JoseEspinosa Jun 21, 2024
b6281b3
Merge pull request #167 from JoseEspinosa/updates
JoseEspinosa Jun 21, 2024
0def5c7
Final prerelease updates
JoseEspinosa Jun 25, 2024
5926d82
Update CHANGELOG.md
JoseEspinosa Jun 25, 2024
9e62090
Apply suggestions review
JoseEspinosa Jun 25, 2024
38e5520
Merge pull request #168 from JoseEspinosa/updates
JoseEspinosa Jun 25, 2024
8608879
Use stable version of tools for download CI
JoseEspinosa Jun 25, 2024
867d245
Merge remote-tracking branch 'upstream/dev' into updates
JoseEspinosa Jun 25, 2024
c993517
Get rid of leak
JoseEspinosa Jun 25, 2024
6f66cb0
Merge pull request #169 from JoseEspinosa/updates
JoseEspinosa Jun 25, 2024
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4 changes: 4 additions & 0 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -37,6 +37,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- [[#148](https://github.com/nf-core/proteinfold/issues/148)] - Update Colabfold DBs.
- [[PR #159](https://github.com/nf-core/proteinfold/pull/159)] - Update `mgnify` paths to new available version.
- [[PR ##163](https://github.com/nf-core/proteinfold/pull/163)] - Fix full test CI.
- [[#150]](https://github.com/nf-core/proteinfold/issues/150)] - Add thanks to the AWS Open Data Sponsorship program in `README.md`.
- [[PR ##166](https://github.com/nf-core/proteinfold/pull/166)] - Create 2 different parameters for Colabfold and ESMfold number of recycles.

### Parameters

@@ -57,6 +59,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
| `--uniclust30_path` | `--uniref30_alphafold2_path` |
| `--uniref30` | `--uniref30_colabfold_link` |
| `--uniref30_path` | `--uniref30_colabfold_path` |
| `--num_recycle` | `--num_recycles_colabfold` |
| | `--num_recycles_esmfold` |
| | `--uniref30_alphafold2_link` |
| | `--esmfold_db` |
| | `--esmfold_model_preset` |
10 changes: 5 additions & 5 deletions README.md
Original file line number Diff line number Diff line change
@@ -95,7 +95,7 @@ The pipeline takes care of downloading the databases and parameters required by
--mode colabfold \
--colabfold_server local \
--colabfold_db <null (default) | PATH> \
--num_recycle 3 \
--num_recycles_colabfold 3 \
--use_amber <true/false> \
--colabfold_model_preset "AlphaFold2-ptm" \
--use_gpu <true/false> \
@@ -113,7 +113,7 @@ The pipeline takes care of downloading the databases and parameters required by
--colabfold_server webserver \
--host_url <custom MMSeqs2 API Server URL> \
--colabfold_db <null (default) | PATH> \
--num_recycle 3 \
--num_recycles_colabfold 3 \
--use_amber <true/false> \
--colabfold_model_preset "AlphaFold2-ptm" \
--use_gpu <true/false> \
@@ -133,7 +133,7 @@ The pipeline takes care of downloading the databases and parameters required by
--mode esmfold \
--esmfold_model_preset <monomer/multimer> \
--esmfold_db <null (default) | PATH> \
--num_recycles 4 \
--num_recycles_esmfold 4 \
--use_gpu <true/false> \
-profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```
@@ -154,10 +154,10 @@ For more details about the output files and reports, please refer to the

nf-core/proteinfold was originally written by Athanasios Baltzis ([@athbaltzis](https://github.com/athbaltzis)), Jose Espinosa-Carrasco ([@JoseEspinosa](https://github.com/JoseEspinosa)), Luisa Santus ([@luisas](https://github.com/luisas)) and Leila Mansouri ([@l-mansouri](https://github.com/l-mansouri)) from [The Comparative Bioinformatics Group](https://www.crg.eu/en/cedric_notredame) at [The Centre for Genomic Regulation, Spain](https://www.crg.eu/) under the umbrella of the [BovReg project](https://www.bovreg.eu/) and Harshil Patel ([@drpatelh](https://github.com/drpatelh)) from [Seqera Labs, Spain](https://seqera.io/).

We thank the following people for their extensive assistance in the development of this pipeline:

Many thanks to others who have helped out and contributed along the way too, including (but not limited to): Norman Goodacre and Waleed Osman from Interline Therapeutics ([@interlinetx](https://github.com/interlinetx)), Martin Steinegger ([@martin-steinegger](https://github.com/martin-steinegger)) and Raoul J.P. Bonnal ([@rjpbonnal](https://github.com/rjpbonnal))

We would also like to thanks to the AWS Open Data Sponsorship Program for generously providing the resources necessary to host the data utilized in the testing, development, and deployment of nf-core proteinfold.

## Contributions and Support

If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).
6 changes: 3 additions & 3 deletions docs/usage.md
Original file line number Diff line number Diff line change
@@ -234,7 +234,7 @@ nextflow run nf-core/proteinfold \
--mode colabfold \
--colabfold_server local \
--colabfold_db <null (default) | DB_PATH> \
--num_recycle 3 \
--num_recycles_colabfold 3 \
--use_amber <true/false> \
--colabfold_model_preset "AlphaFold2-ptm" \
--use_gpu <true/false> \
@@ -252,7 +252,7 @@ nextflow run nf-core/proteinfold \
--colabfold_server webserver \
--host_url <custom MMSeqs2 API Server URL> \
--colabfold_db <null (default) | DB_PATH> \
--num_recycle 3 \
--num_recycles_colabfold 3 \
--use_amber <true/false> \
--colabfold_model_preset "AlphaFold2-ptm" \
--use_gpu <true/false> \
@@ -407,7 +407,7 @@ nextflow run nf-core/proteinfold \
--outdir <OUTDIR> \
--mode esmfold
--esmfold_db <null (default) | DB_PATH> \
--num_recycles 4 \
--num_recycles_esmfold 4 \
--esmfold_model_preset <monomer/multimer> \
--use_gpu <true/false> \
-profile <docker>
4 changes: 2 additions & 2 deletions main.nf
Original file line number Diff line number Diff line change
@@ -144,7 +144,7 @@ workflow NFCORE_PROTEINFOLD {
PREPARE_COLABFOLD_DBS.out.params,
PREPARE_COLABFOLD_DBS.out.colabfold_db,
PREPARE_COLABFOLD_DBS.out.uniref30,
params.num_recycle
params.num_recycles_colabfold
)
ch_multiqc = COLABFOLD.out.multiqc_report
ch_versions = ch_versions.mix(COLABFOLD.out.versions)
@@ -172,7 +172,7 @@ workflow NFCORE_PROTEINFOLD {
ESMFOLD (
ch_versions,
PREPARE_ESMFOLD_DBS.out.params,
params.num_recycle
params.num_recycles_esmfold
)
ch_multiqc = ESMFOLD.out.multiqc_report
ch_versions = ch_versions.mix(ESMFOLD.out.versions)
4 changes: 2 additions & 2 deletions nextflow.config
Original file line number Diff line number Diff line change
@@ -50,7 +50,7 @@ params {
// Colabfold parameters
colabfold_server = "webserver"
colabfold_model_preset = "alphafold2_ptm" // {'auto', 'alphafold2', 'alphafold2_ptm', 'alphafold2_multimer_v1', 'alphafold2_multimer_v2', 'alphafold2_multimer_v3'}
num_recycle = 3
num_recycles_colabfold = 3
use_amber = true
colabfold_db = null
db_load_mode = 0
@@ -69,7 +69,7 @@ params {
// Esmfold parameters
esmfold_db = null
esmfold_model_preset = "monomer"
num_recycles = 4
num_recycles_esmfold = 4

// Esmfold links
esmfold_3B_v1 = null
6 changes: 3 additions & 3 deletions nextflow_schema.json
Original file line number Diff line number Diff line change
@@ -130,10 +130,10 @@
],
"fa_icon": "fas fa-stream"
},
"num_recycle": {
"num_recycles_colabfold": {
"type": "integer",
"default": 3,
"description": "Number of recycles",
"description": "Number of recycles for Colabfold",
"fa_icon": "fas fa-recycle"
},
"use_amber": {
@@ -180,7 +180,7 @@
"description": "Specifies the PARAMS path used by 'esmfold' mode",
"fa_icon": "fas fa-folder-open"
},
"num_recycles": {
"num_recycles_esmfold": {
"type": "integer",
"default": 4,
"description": "Specifies the number of recycles used by Esmfold",
8 changes: 4 additions & 4 deletions workflows/colabfold.nf
Original file line number Diff line number Diff line change
@@ -45,7 +45,7 @@ workflow COLABFOLD {
ch_colabfold_params // channel: path(colabfold_params)
ch_colabfold_db // channel: path(colabfold_db)
ch_uniref30 // channel: path(uniref30)
num_recycle // int: Number of recycles for esmfold
num_recycles // int: Number of recycles for esmfold

main:
ch_multiqc_files = Channel.empty()
@@ -72,7 +72,7 @@ workflow COLABFOLD {
ch_colabfold_params,
[],
[],
num_recycle
num_recycles
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
} else {
@@ -82,7 +82,7 @@ workflow COLABFOLD {
ch_colabfold_params,
[],
[],
num_recycle
num_recycles
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
}
@@ -122,7 +122,7 @@ workflow COLABFOLD {
ch_colabfold_params,
ch_colabfold_db,
ch_uniref30,
num_recycle
num_recycles
)
ch_versions = ch_versions.mix(COLABFOLD_BATCH.out.versions)
}
6 changes: 3 additions & 3 deletions workflows/esmfold.nf
Original file line number Diff line number Diff line change
@@ -41,7 +41,7 @@ workflow ESMFOLD {
take:
ch_versions // channel: [ path(versions.yml) ]
ch_esmfold_params // directory: /path/to/esmfold/params/
ch_num_recycle // int: Number of recycles for esmfold
ch_num_recycles // int: Number of recycles for esmfold

main:
ch_multiqc_files = Channel.empty()
@@ -64,14 +64,14 @@ workflow ESMFOLD {
RUN_ESMFOLD(
MULTIFASTA_TO_SINGLEFASTA.out.input_fasta,
ch_esmfold_params,
ch_num_recycle
ch_num_recycles
)
ch_versions = ch_versions.mix(RUN_ESMFOLD.out.versions)
} else {
RUN_ESMFOLD(
ch_fasta,
ch_esmfold_params,
ch_num_recycle
ch_num_recycles
)
ch_versions = ch_versions.mix(RUN_ESMFOLD.out.versions)
}