diff --git a/CHANGELOG.md b/CHANGELOG.md index b5322d63..a4fdd7de 100644 --- a/CHANGELOG.md +++ b/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 diff --git a/README.md b/README.md index 39704e7d..622a21a4 100644 --- a/README.md +++ b/README.md @@ -55,7 +55,7 @@ nextflow run nf-core/proteinfold \ --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: diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f6acb16a..ae9db7c7 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/proteinfold + This report has been generated by the nf-core/proteinfold analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-proteinfold-methods-description": order: -1000 diff --git a/modules/local/colabfold_batch.nf b/modules/local/colabfold_batch.nf index 5b1c5467..28f26274 100644 --- a/modules/local/colabfold_batch.nf +++ b/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) diff --git a/modules/local/download_pdbmmcif.nf b/modules/local/download_pdbmmcif.nf index fef63755..98ef831e 100644 --- a/modules/local/download_pdbmmcif.nf +++ b/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' diff --git a/modules/local/mmseqs_colabfoldsearch.nf b/modules/local/mmseqs_colabfoldsearch.nf index c6a2c9b0..17aae127 100644 --- a/modules/local/mmseqs_colabfoldsearch.nf +++ b/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) diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf index 5607712d..86d728d7 100644 --- a/modules/local/run_alphafold2.nf +++ b/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) diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf index 6c9bfcf8..401a6aa5 100644 --- a/modules/local/run_alphafold2_msa.nf +++ b/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) diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf index ee9983c5..ddb1e6c3 100644 --- a/modules/local/run_alphafold2_pred.nf +++ b/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) diff --git a/nextflow.config b/nextflow.config index d191605b..d39fccd2 100644 --- a/nextflow.config +++ b/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' }