Updated CHANGELOG.md

CHANGELOG.md

@@ -10,12 +10,13 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [[#177](https://github.com/nf-core/proteinfold/issues/177)] - Fix typo in some instances of model preset `alphafold2_ptm`.
 - [[PR #178](https://github.com/nf-core/proteinfold/pull/178)] - Enable running multiple modes in parallel.
 - [[#179](https://github.com/nf-core/proteinfold/issues/179)] - Produce an interactive html report for the predicted structures.
-- [[#180](https://github.com/nf-core/proteinfold/issues/180)] - Implement Fooldseek.
+- [[#180](https://github.com/nf-core/proteinfold/issues/180)] - Implement Foldseek.
 - [[#188](https://github.com/nf-core/proteinfold/issues/188)] - Fix colabfold image to run in gpus.
 - [[PR ##205](https://github.com/nf-core/proteinfold/pull/205)] - Change input schema from `sequence,fasta` to `id,fasta`.
 - [[PR #210](https://github.com/nf-core/proteinfold/pull/210)] - Moving post-processing logic to a subworkflow, change wave images pointing to oras to point to https and refactor module to match nf-core folder structure.
 - [[#214](https://github.com/nf-core/proteinfold/issues/214)] - Fix colabfold image to run in cpus after [#188](https://github.com/nf-core/proteinfold/issues/188) fix.
 - [[#235](https://github.com/nf-core/proteinfold/issues/235)] - Update samplesheet to new version (switch from `sequence` column to `id`).
+- [[#239](https://github.com/nf-core/proteinfold/issues/239)] - Update alphafold2 standard mode Dockerfile.
 
 ## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30
 

dockerfiles/Dockerfile_nfcore-proteinfold_alphafold2_standard

@@ -66,9 +66,9 @@ RUN wget -q -P /app/alphafold/alphafold/common/ \
 RUN pip3 install --upgrade pip --no-cache-dir \
     && pip3 install -r /app/alphafold/requirements.txt --no-cache-dir \
     && pip3 install --upgrade --no-cache-dir \
-      jax==0.4.26 \
-      jaxlib==0.4.26+cuda12.cudnn89 \
-      -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
+    jax==0.4.26 \
+    jaxlib==0.4.26+cuda12.cudnn89 \
+    -f https://storage.googleapis.com/jax-releases/jax_cuda_releases.html
 
 RUN sed -i "s|alphafold/common/stereo_chemical_props.txt|/app/alphafold/alphafold/common/stereo_chemical_props.txt|g" /app/alphafold/alphafold/common/residue_constants.py
 
@@ -87,5 +87,5 @@ WORKDIR /app/alphafold
 RUN echo $'#!/bin/bash\n\
 ldconfig\n\
 python /app/alphafold/run_alphafold.py "$@"' > /app/run_alphafold.sh \
-  && chmod +x /app/run_alphafold.sh
+    && chmod +x /app/run_alphafold.sh
 ENTRYPOINT ["/app/run_alphafold.sh"]