Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Fix uppercase model preset "alphaFold2-ptm" #175

Merged
merged 4 commits into from
Aug 7, 2024
Merged

Fix uppercase model preset "alphaFold2-ptm" #175

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
4 commits
Select commit Hold shift + click to select a range
bfd3c76
Fix uppercase model preset
JoseEspinosa Aug 6, 2024
4769bee
Update changelog
JoseEspinosa Aug 6, 2024
4ca5fdc
Fix instances of alphafold2_ptm
JoseEspinosa Aug 6, 2024
02babc4
Fix condition to run MULTIFASTA_TO_CSV when executing colabfold serve…
JoseEspinosa Aug 7, 2024
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
2 changes: 2 additions & 0 deletions CHANGELOG.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0

### Enhancements & fixes

- [[PR #175](https://github.com/nf-core/proteinfold/pull/175)] - Fix typo in some instances of model preset `alphafold2_ptm`.

## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30

### Enhancements & fixes
Expand Down
4 changes: 2 additions & 2 deletions README.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -97,7 +97,7 @@ The pipeline takes care of downloading the databases and parameters required by
--colabfold_db <null (default) | PATH> \
--num_recycles_colabfold 3 \
--use_amber <true/false> \
--colabfold_model_preset "AlphaFold2-ptm" \
--colabfold_model_preset "alphafold2_ptm" \
--use_gpu <true/false> \
--db_load_mode 0
-profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
Expand All @@ -115,7 +115,7 @@ The pipeline takes care of downloading the databases and parameters required by
--colabfold_db <null (default) | PATH> \
--num_recycles_colabfold 3 \
--use_amber <true/false> \
--colabfold_model_preset "AlphaFold2-ptm" \
--colabfold_model_preset "alphafold2_ptm" \
--use_gpu <true/false> \
-profile <docker/singularity/podman/shifter/charliecloud/conda/institute>
```
Expand Down
4 changes: 2 additions & 2 deletions docs/usage.md
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -236,7 +236,7 @@ nextflow run nf-core/proteinfold \
--colabfold_db <null (default) | DB_PATH> \
--num_recycles_colabfold 3 \
--use_amber <true/false> \
--colabfold_model_preset "AlphaFold2-ptm" \
--colabfold_model_preset "alphafold2_ptm" \
--use_gpu <true/false> \
--db_load_mode 0 \
-profile <docker/singularity/.../institute>
Expand All @@ -254,7 +254,7 @@ nextflow run nf-core/proteinfold \
--colabfold_db <null (default) | DB_PATH> \
--num_recycles_colabfold 3 \
--use_amber <true/false> \
--colabfold_model_preset "AlphaFold2-ptm" \
--colabfold_model_preset "alphafold2_ptm" \
--use_gpu <true/false> \
-profile <docker/singularity/.../institute>
```
Expand Down
2 changes: 1 addition & 1 deletion workflows/colabfold.nf
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -91,7 +91,7 @@ workflow COLABFOLD {
//
// MODULE: Run mmseqs
//
if (params.colabfold_model_preset != 'AlphaFold2-ptm') {
if (params.colabfold_model_preset != 'alphafold2_ptm' && params.colabfold_model_preset != 'alphafold2') {
MULTIFASTA_TO_CSV(
ch_fasta
)
Expand Down