From 80104ff1f3c3e85212d9453b3e8f7a8d1349394c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 25 Jun 2024 14:47:35 +0200 Subject: [PATCH 1/5] bump version 1.2.0dev --- CHANGELOG.md | 4 ++++ assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index d050b531..c4694bf2 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,6 +3,10 @@ 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). +## v1.2.0dev - [date] + +### Enhancements & fixes + ## [[1.1.0](https://github.com/nf-core/proteinfold/releases/tag/1.1.0)] - 2025-06-25 ### Credits diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index ae9db7c7..f6acb16a 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/nextflow.config b/nextflow.config index 7ca395f2..c2bb0528 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 = '1.1.0' + version = '1.2.0dev' doi = '10.5281/zenodo.7629996' } From 1fd4e42641f278c851295020b1049b3fc14ada31 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 29 Jul 2024 17:07:59 +0200 Subject: [PATCH 2/5] Fix multiqc report --- modules.json | 39 +++++++++++++++++++++------- modules/nf-core/multiqc/main.nf | 2 +- modules/nf-core/multiqc/multiqc.diff | 14 ++++++++++ 3 files changed, 44 insertions(+), 11 deletions(-) create mode 100644 modules/nf-core/multiqc/multiqc.diff diff --git a/modules.json b/modules.json index a4910d41..a695761f 100644 --- a/modules.json +++ b/modules.json @@ -8,33 +8,46 @@ "aria2": { "branch": "master", "git_sha": "7d0ccc097c60d23a195099b326a5882e135c7949", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/aria2/aria2.diff" }, "gunzip": { "branch": "master", "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mmseqs/createindex": { "branch": "master", "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "mmseqs/tsv2exprofiledb": { "branch": "master", "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": ["modules"] + "installed_by": [ + "modules" + ], + "patch": "modules/nf-core/multiqc/multiqc.diff" }, "untar": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["modules"], + "installed_by": [ + "modules" + ], "patch": "modules/nf-core/untar/untar.diff" } } @@ -44,20 +57,26 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": ["subworkflows"] + "installed_by": [ + "subworkflows" + ] } } } } } -} +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 47ac352f..bef8f50b 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -7,7 +7,7 @@ process MULTIQC { 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" input: - path multiqc_files, stageAs: "?/*" + path multiqc_files path(multiqc_config) path(extra_multiqc_config) path(multiqc_logo) diff --git a/modules/nf-core/multiqc/multiqc.diff b/modules/nf-core/multiqc/multiqc.diff new file mode 100644 index 00000000..d0efc03a --- /dev/null +++ b/modules/nf-core/multiqc/multiqc.diff @@ -0,0 +1,14 @@ +Changes in module 'nf-core/multiqc' +--- modules/nf-core/multiqc/main.nf ++++ modules/nf-core/multiqc/main.nf +@@ -7,7 +7,7 @@ + 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" + + input: +- path multiqc_files, stageAs: "?/*" ++ path multiqc_files + path(multiqc_config) + path(extra_multiqc_config) + path(multiqc_logo) + +************************************************************ From 58258e6d9d0a483b7cf919392970455b733c351c Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 29 Jul 2024 22:43:39 +0200 Subject: [PATCH 3/5] Bump version 1.1.1 --- CHANGELOG.md | 6 +++++- assets/multiqc_config.yml | 4 ++-- nextflow.config | 2 +- 3 files changed, 8 insertions(+), 4 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index c4694bf2..2fbddadb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,9 @@ 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). -## v1.2.0dev - [date] +## [[1.1.1](https://github.com/nf-core/proteinfold/releases/tag/1.1.1)] - 2025-07-30 + +- Minor patch release to fix multiqc report. ### Enhancements & fixes @@ -24,6 +26,8 @@ Special thanks to the following for their contributions to the release: Thank you to everyone else that has contributed by reporting bugs, enhancements or in any other way, shape or form. +## [[1.1.0](https://github.com/nf-core/proteinfold/releases/tag/1.1.0)] - 2025-06-21 + ### Enhancements & fixes - [[#80](https://github.com/nf-core/proteinfold/pull/80)] - Add `accelerator` directive to GPU processes when `params.use_gpu` is true. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index f6acb16a..3b58e3d0 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/nextflow.config b/nextflow.config index c2bb0528..7a0c5c4e 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 = '1.2.0dev' + version = '1.1.1' doi = '10.5281/zenodo.7629996' } From e640616b67d0dc4102c389694c5bdbf3fc440511 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Mon, 29 Jul 2024 22:46:06 +0200 Subject: [PATCH 4/5] Make lint happy --- modules.json | 38 ++++++++++---------------------------- 1 file changed, 10 insertions(+), 28 deletions(-) diff --git a/modules.json b/modules.json index a695761f..cdb36bb6 100644 --- a/modules.json +++ b/modules.json @@ -8,46 +8,34 @@ "aria2": { "branch": "master", "git_sha": "7d0ccc097c60d23a195099b326a5882e135c7949", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/aria2/aria2.diff" }, "gunzip": { "branch": "master", "git_sha": "5c460c5a4736974abde2843294f35307ee2b0e5e", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mmseqs/createindex": { "branch": "master", "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "mmseqs/tsv2exprofiledb": { "branch": "master", "git_sha": "151460db852d636979d9ff3ee631e2268060d4c3", - "installed_by": [ - "modules" - ] + "installed_by": ["modules"] }, "multiqc": { "branch": "master", "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/multiqc/multiqc.diff" }, "untar": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "modules" - ], + "installed_by": ["modules"], "patch": "modules/nf-core/untar/untar.diff" } } @@ -57,26 +45,20 @@ "utils_nextflow_pipeline": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfcore_pipeline": { "branch": "master", "git_sha": "92de218a329bfc9a9033116eb5f65fd270e72ba3", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] }, "utils_nfvalidation_plugin": { "branch": "master", "git_sha": "5caf7640a9ef1d18d765d55339be751bb0969dfa", - "installed_by": [ - "subworkflows" - ] + "installed_by": ["subworkflows"] } } } } } -} \ No newline at end of file +} From 117257c56b8dd5ce6eb49ac39ff0a8de71629d93 Mon Sep 17 00:00:00 2001 From: JoseEspinosa Date: Tue, 30 Jul 2024 15:30:40 +0200 Subject: [PATCH 5/5] Update images to version 1.1.1 --- 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 +- modules/local/run_esmfold.nf | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/modules/local/colabfold_batch.nf b/modules/local/colabfold_batch.nf index 28f26274..5dab51fb 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:1.1.0" + container "nf-core/proteinfold_colabfold:1.1.1" input: tuple val(meta), path(fasta) diff --git a/modules/local/mmseqs_colabfoldsearch.nf b/modules/local/mmseqs_colabfoldsearch.nf index 17aae127..c2140c5b 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:1.1.0" + container "nf-core/proteinfold_colabfold:1.1.1" input: tuple val(meta), path(fasta) diff --git a/modules/local/run_alphafold2.nf b/modules/local/run_alphafold2.nf index 13136369..cb3527d3 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:1.1.0" + container "nf-core/proteinfold_alphafold2_standard:1.1.1" input: tuple val(meta), path(fasta) diff --git a/modules/local/run_alphafold2_msa.nf b/modules/local/run_alphafold2_msa.nf index e983ed92..fdc67e88 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:1.1.0" + container "nf-core/proteinfold_alphafold2_msa:1.1.1" input: tuple val(meta), path(fasta) diff --git a/modules/local/run_alphafold2_pred.nf b/modules/local/run_alphafold2_pred.nf index ddb1e6c3..92b5d2a5 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:1.1.0" + container "nf-core/proteinfold_alphafold2_split:1.1.1" input: tuple val(meta), path(fasta) diff --git a/modules/local/run_esmfold.nf b/modules/local/run_esmfold.nf index 5f7a25ce..66c5bbc7 100644 --- a/modules/local/run_esmfold.nf +++ b/modules/local/run_esmfold.nf @@ -6,7 +6,7 @@ process RUN_ESMFOLD { error("Local RUN_ESMFOLD module does not support Conda. Please use Docker / Singularity / Podman instead.") } - container "nf-core/proteinfold_esmfold:1.1.0" + container "nf-core/proteinfold_esmfold:1.1.1" input: tuple val(meta), path(fasta)