From c50abf45d52acd661c5dc64f9c4d8e2ccafefd3b Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 13 Jul 2023 14:06:51 +0200 Subject: [PATCH 1/8] fix multiqc_config.yml links --- nf_core/pipeline-template/assets/multiqc_config.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml index 570ed3d8e5..34fd83424b 100644 --- a/nf_core/pipeline-template/assets/multiqc_config.yml +++ b/nf_core/pipeline-template/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the {{ name }} + This report has been generated by the {{ name }} analysis pipeline.{% if branded %} For information about how to interpret these results, please see the - documentation.{% endif %} + documentation.{% endif %} report_section_order: "{{ name_noslash }}-methods-description": order: -1000 From 71191dadddaeb1b0f54fe6f21d64aa1d36eee6eb Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 13 Jul 2023 14:27:26 +0200 Subject: [PATCH 2/8] remove version from multiqc_config.yml and adapt linting accordingly --- nf_core/lint/multiqc_config.py | 4 ++-- nf_core/pipeline-template/assets/multiqc_config.yml | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/lint/multiqc_config.py b/nf_core/lint/multiqc_config.py index 9eff60091f..e6f0581f00 100644 --- a/nf_core/lint/multiqc_config.py +++ b/nf_core/lint/multiqc_config.py @@ -75,9 +75,9 @@ def multiqc_config(self): if "report_comment" not in mqc_yml: raise AssertionError() if mqc_yml["report_comment"].strip() != ( - f'This report has been generated by the nf-core/{self.pipeline_name} analysis pipeline. For information about how to ' - f'interpret these results, please see the documentation.' ): raise AssertionError() diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml index 34fd83424b..70bf5f9ecb 100644 --- a/nf_core/pipeline-template/assets/multiqc_config.yml +++ b/nf_core/pipeline-template/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > This report has been generated by the {{ name }} analysis pipeline.{% if branded %} For information about how to interpret these results, please see the - documentation.{% endif %} + documentation.{% endif %} report_section_order: "{{ name_noslash }}-methods-description": order: -1000 From 02455fc4048bccc78a0bd5511f58b654e00f1263 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 13 Jul 2023 14:29:56 +0200 Subject: [PATCH 3/8] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 426225685a..74c2323866 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Template +- Remove pipeline version from `multiqc_config.yml`links and adapt linting accordingly ([]()) + ### Linting ### Modules From c62367b7cd558b50bcac434791f1ed7ba34b091a Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 13 Jul 2023 14:57:27 +0200 Subject: [PATCH 4/8] add the version back --- nf_core/lint/multiqc_config.py | 4 ++-- nf_core/pipeline-template/assets/multiqc_config.yml | 4 ++-- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/nf_core/lint/multiqc_config.py b/nf_core/lint/multiqc_config.py index e6f0581f00..d6da077d2f 100644 --- a/nf_core/lint/multiqc_config.py +++ b/nf_core/lint/multiqc_config.py @@ -75,9 +75,9 @@ def multiqc_config(self): if "report_comment" not in mqc_yml: raise AssertionError() if mqc_yml["report_comment"].strip() != ( - f'This report has been generated by the nf-core/{self.pipeline_name} analysis pipeline. For information about how to ' - f'interpret these results, please see the documentation.' ): raise AssertionError() diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml index 70bf5f9ecb..6c62dde529 100644 --- a/nf_core/pipeline-template/assets/multiqc_config.yml +++ b/nf_core/pipeline-template/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the {{ name }} + This report has been generated by the {{ name }} analysis pipeline.{% if branded %} For information about how to interpret these results, please see the - documentation.{% endif %} + documentation.{% endif %} report_section_order: "{{ name_noslash }}-methods-description": order: -1000 From ed4babf185c05a9d7dbda0813cf16b611bbb38bd Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 13 Jul 2023 14:58:22 +0200 Subject: [PATCH 5/8] update changelog --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 74c2323866..1e2305b336 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,7 +4,7 @@ ### Template -- Remove pipeline version from `multiqc_config.yml`links and adapt linting accordingly ([]()) +- Fix links in `multiqc_config.yml` ([#2372](https://github.com/nf-core/tools/pull/2372)) ### Linting From b670f3a1ac93933d60363791a13028db48b62fb6 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 18 Jul 2023 10:52:33 +0200 Subject: [PATCH 6/8] version in multipqc_config.yml is dev if the version is x.x.xdev --- nf_core/lint/multiqc_config.py | 1 + nf_core/pipeline-template/assets/multiqc_config.yml | 6 ++++++ 2 files changed, 7 insertions(+) diff --git a/nf_core/lint/multiqc_config.py b/nf_core/lint/multiqc_config.py index d6da077d2f..4877b41194 100644 --- a/nf_core/lint/multiqc_config.py +++ b/nf_core/lint/multiqc_config.py @@ -72,6 +72,7 @@ def multiqc_config(self): # Check that the minimum plugins exist and are coming first in the summary try: version = self.nf_config.get("manifest.version", "").strip(" '\"") + version = "dev" if "dev" in version else version if "report_comment" not in mqc_yml: raise AssertionError() if mqc_yml["report_comment"].strip() != ( diff --git a/nf_core/pipeline-template/assets/multiqc_config.yml b/nf_core/pipeline-template/assets/multiqc_config.yml index 6c62dde529..9423ee53f7 100644 --- a/nf_core/pipeline-template/assets/multiqc_config.yml +++ b/nf_core/pipeline-template/assets/multiqc_config.yml @@ -1,7 +1,13 @@ report_comment: > + {% if 'dev' in version -%} + This report has been generated by the {{ name }} + analysis pipeline.{% if branded %} For information about how to interpret these results, please see the + documentation.{% endif %} + {%- else %} This report has been generated by the {{ name }} analysis pipeline.{% if branded %} For information about how to interpret these results, please see the documentation.{% endif %} + {% endif %} report_section_order: "{{ name_noslash }}-methods-description": order: -1000 From 8fcb465f0228a46c9a59a48d570901c7ea4dc7f6 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 18 Jul 2023 11:40:05 +0200 Subject: [PATCH 7/8] bump-version will use dev in multiqc_config.yml if the new version is x.x.xdev --- nf_core/bump_version.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/nf_core/bump_version.py b/nf_core/bump_version.py index b462ee1377..0bf3b10c42 100644 --- a/nf_core/bump_version.py +++ b/nf_core/bump_version.py @@ -45,14 +45,19 @@ def bump_pipeline_version(pipeline_obj, new_version): ], ) # multiqc_config.yaml + multiqc_new_version = "dev" if "dev" in new_version else new_version update_file_version( Path("assets", "multiqc_config.yml"), pipeline_obj, [ + ( + "/dev/", + f"/{multiqc_new_version}/", + ), ( rf"{re.escape(current_version)}", - f"{new_version}", - ) + f"{multiqc_new_version}", + ), ], ) From 19a19f69e02817bd95cb405380ebcc93014a8afe Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Tue, 18 Jul 2023 11:49:40 +0200 Subject: [PATCH 8/8] remove last / from bump-version pattern --- nf_core/bump_version.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/bump_version.py b/nf_core/bump_version.py index 0bf3b10c42..5f4616edfb 100644 --- a/nf_core/bump_version.py +++ b/nf_core/bump_version.py @@ -51,8 +51,8 @@ def bump_pipeline_version(pipeline_obj, new_version): pipeline_obj, [ ( - "/dev/", - f"/{multiqc_new_version}/", + "/dev", + f"/{multiqc_new_version}", ), ( rf"{re.escape(current_version)}",