From 8e7f23b48ee9ff19a3a7f8f814fb84f7d8c1a082 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 31 May 2024 16:13:02 +0200 Subject: [PATCH 1/5] Bump version 1.1.0 on changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From e24b6e5d154b04a1a2b7e64a58eadc1d3701d3ab Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 31 May 2024 16:14:24 +0200 Subject: [PATCH 2/5] Bump version 1.1.0 to images --- modules/local/colabfold_batch.nf | 2 +- modules/local/mmseqs_colabfoldsearch.nf | 2 +- modules/local/run_alphafold2.nf | 2 +- modules/local/run_alphafold2_msa.nf | 2 +- modules/local/run_alphafold2_pred.nf | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) 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/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) From 2bef5e7be09076f64599ac20cf9ac154037e2472 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 31 May 2024 16:14:54 +0200 Subject: [PATCH 3/5] Bump version 1.1.0 to readme --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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' } From b29d6760b1a833ff1b2846ee54b6217ddeac9a5c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Fri, 31 May 2024 16:15:36 +0200 Subject: [PATCH 4/5] Some minor corrections --- README.md | 2 +- modules/local/download_pdbmmcif.nf | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) 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/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' From 2bec61707cd19d0b402f2ab7cdd958abf02c099c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Sat, 1 Jun 2024 08:48:18 +0200 Subject: [PATCH 5/5] Bump v1.1.0 to multiqc config --- assets/multiqc_config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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