From 9edbb0a70abd7ed96aab8572300c3abb6ea97633 Mon Sep 17 00:00:00 2001 From: tdanhorn Date: Wed, 24 Jan 2024 17:15:02 -0700 Subject: [PATCH 1/5] Fix `--three_prime_clip_r{1,2} parameter` documentation (bug #1382) --- nextflow_schema.json | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nextflow_schema.json b/nextflow_schema.json index a7f7ed7065..b70486246b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -158,7 +158,7 @@ "default": 0, "fa_icon": "fas fa-cut", "description": "Remove bp from the 3' end of read 1", - "help_text": "This may remove some unwanted bias from the 3'. Corresponds to the FastP flag `--three_prime_clip_r1`.", + "help_text": "This may remove some unwanted bias from the 3'. Corresponds to the FastP flag `--trim_tail1`.", "hidden": true }, "three_prime_clip_r2": { @@ -166,7 +166,7 @@ "default": 0, "fa_icon": "fas fa-cut", "description": "Remove bp from the 3' end of read 2", - "help_text": "This may remove some unwanted bias from the 3' end. Corresponds to the FastP flag `--three_prime_clip_r2`.", + "help_text": "This may remove some unwanted bias from the 3' end. Corresponds to the FastP flag `--trim_tail2`.", "hidden": true }, "trim_nextseq": { From ac0227e76bc59378ac0e713b528c9c51d1004abc Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 25 Jan 2024 07:20:03 +0000 Subject: [PATCH 2/5] [automated] Fix linting with Prettier --- .devcontainer/devcontainer.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4ecfbfe335..4a9bc5c79d 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.linting.pylintPath": "/opt/conda/bin/pylint", }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] - } - } + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], + }, + }, } From d3127e0f85b74f1685c6d30e9d456a634227ff5e Mon Sep 17 00:00:00 2001 From: Thomas Date: Mon, 5 Feb 2024 17:12:13 -0700 Subject: [PATCH 3/5] Update CHANGELOG.md with #1383 --- CHANGELOG.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 766c417dc8..08c9393b4a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -31,7 +31,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1351](https://github.com/nf-core/sarek/pull/1351) - Fix params name for test profiles (`bcftools_annotations`) - [#1357](https://github.com/nf-core/sarek/pull/1364) - Fixed bug where samples were dropped while reconstituting BAM files - [#1373](https://github.com/nf-core/sarek/pull/1373) - Add `chr` prefix to NCBench bed file & enable trimming -- [#1373](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix +- [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix +- [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation ### Removed From 0c83a2ca5966918abdeb6cf9c0937c36a71493c9 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 6 Feb 2024 10:19:43 +0100 Subject: [PATCH 4/5] Apply suggestions from code review --- .devcontainer/devcontainer.json | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index 4a9bc5c79d..4ecfbfe335 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -18,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint", + "python.linting.pylintPath": "/opt/conda/bin/pylint" }, // Add the IDs of extensions you want installed when the container is created. - "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], - }, - }, + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] + } + } } From e5f48b76efe57387439521bd011f894b468a21ec Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 6 Feb 2024 10:57:11 +0100 Subject: [PATCH 5/5] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 08c9393b4a..e9f84ae74d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -33,6 +33,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#1373](https://github.com/nf-core/sarek/pull/1373) - Add `chr` prefix to NCBench bed file & enable trimming - [#1381](https://github.com/nf-core/sarek/pull/1381) - Swap NGSCheckMate bed file for GATK.GRCh37 to one without the `chr` prefix - [#1383](https://github.com/nf-core/sarek/pull/1383) - Fix `--three_prime_clip_r{1,2}` parameter documentation +- [#1390](https://github.com/nf-core/sarek/pull/1390) - Fix badges in README ### Removed