Bump v1.1.0

CHANGELOG.md

@@ -3,7 +3,7 @@
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
-## 1.1.0dev - [date]
+## [[1.1.0](https://github.com/nf-core/proteinfold/releases/tag/1.1.0)] - 2025-06-07
 
 ### Enhancements & fixes
 

README.md

@@ -55,7 +55,7 @@ nextflow run nf-core/proteinfold \
    --outdir <OUTDIR>
 ```
 
-The pipeline takes care of downloading the required databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`]
+The pipeline takes care of downloading the databases and parameters required by AlphaFold2, Colabfold or ESMFold. In case you have already downloaded the required files, you can skip this step by providing the path to the databases in parameters using the corresponding parameter [`--alphafold2_db`], [`--colabfold_db`] or [`--esmfold_db`]
 
 - Typical command to run AlphaFold2 mode:
 

assets/multiqc_config.yml

@@ -1,7 +1,7 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/proteinfold/tree/dev" target="_blank">nf-core/proteinfold</a>
+  This report has been generated by the <a href="https://github.com/nf-core/proteinfold/releases/tag/1.1.0" target="_blank">nf-core/proteinfold</a>
   analysis pipeline. For information about how to interpret these results, please see the
-  <a href="https://nf-co.re/proteinfold/dev/docs/output" target="_blank">documentation</a>.
+  <a href="https://nf-co.re/proteinfold/1.1.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-core-proteinfold-methods-description":
     order: -1000

modules/local/colabfold_batch.nf

@@ -7,7 +7,7 @@ process COLABFOLD_BATCH {
         error("Local COLABFOLD_BATCH module does not support Conda. Please use Docker / Singularity / Podman instead.")
     }
 
-    container "nf-core/proteinfold_colabfold:dev"
+    container "nf-core/proteinfold_colabfold:1.1.0"
 
     input:
     tuple val(meta), path(fasta)

modules/local/download_pdbmmcif.nf

@@ -2,6 +2,7 @@
  * Download PDB MMCIF database
  */
 process DOWNLOAD_PDBMMCIF {
+    tag "${source_url_pdb_mmcif}--${source_url_pdb_obsolete}"
     label 'process_low'
     label 'error_retry'
 

modules/local/mmseqs_colabfoldsearch.nf

@@ -7,7 +7,7 @@ process MMSEQS_COLABFOLDSEARCH {
         error("Local MMSEQS_COLABFOLDSEARCH module does not support Conda. Please use Docker / Singularity / Podman instead.")
     }
 
-    container "nf-core/proteinfold_colabfold:dev"
+    container "nf-core/proteinfold_colabfold:1.1.0"
 
     input:
     tuple val(meta), path(fasta)

modules/local/run_alphafold2.nf

@@ -10,7 +10,7 @@ process RUN_ALPHAFOLD2 {
         error("Local RUN_ALPHAFOLD2 module does not support Conda. Please use Docker / Singularity / Podman instead.")
     }
 
-    container "nf-core/proteinfold_alphafold2_standard:dev"
+    container "nf-core/proteinfold_alphafold2_standard:1.1.0"
 
     input:
     tuple val(meta), path(fasta)

modules/local/run_alphafold2_msa.nf

@@ -10,7 +10,7 @@ process RUN_ALPHAFOLD2_MSA {
         error("Local RUN_ALPHAFOLD2_MSA module does not support Conda. Please use Docker / Singularity / Podman instead.")
     }
 
-    container "nf-core/proteinfold_alphafold2_msa:dev"
+    container "nf-core/proteinfold_alphafold2_msa:1.1.0"
 
     input:
     tuple val(meta), path(fasta)

modules/local/run_alphafold2_pred.nf

@@ -10,7 +10,7 @@ process RUN_ALPHAFOLD2_PRED {
         error("Local RUN_ALPHAFOLD2_PRED module does not support Conda. Please use Docker / Singularity / Podman instead.")
     }
 
-    container "nf-core/proteinfold_alphafold2_split:dev"
+    container "nf-core/proteinfold_alphafold2_split:1.1.0"
 
     input:
     tuple val(meta), path(fasta)

nextflow.config

@@ -322,7 +322,7 @@ manifest {
     description     = """Protein 3D structure prediction pipeline"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '1.1.0dev'
+    version         = '1.1.0'
     doi             = '10.5281/zenodo.7629996'
 }