From 4faf200b6ee8b08a4d8ebd26a3393fcfaa998103 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 14 Oct 2024 10:33:21 +0200 Subject: [PATCH 01/30] bump pipeline version also in `.nf-core.yml` --- nf_core/pipelines/bump_version.py | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py index 18aa869328..c6a2f59f33 100644 --- a/nf_core/pipelines/bump_version.py +++ b/nf_core/pipelines/bump_version.py @@ -107,6 +107,18 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None: ) ], ) + # .nf-core.yml - pipeline version + # update entry: version: 1.0.0dev, but not `nf_core_version`, or `bump_version` + update_file_version( + ".nf-core.yml", + pipeline_obj, + [ + ( + rf"$\s+(version:\s*){re.escape(current_version)}", + rf"\g<1>{new_version}", + ) + ], + ) def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None: From 84963ab8d9a3dfff85e9529c347d0e3d0cfd1bb3 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 14 Oct 2024 10:34:14 +0200 Subject: [PATCH 02/30] only log and write new contents, if pattern was actually found --- nf_core/pipelines/bump_version.py | 20 +++++++++++--------- 1 file changed, 11 insertions(+), 9 deletions(-) diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py index c6a2f59f33..fe5730a714 100644 --- a/nf_core/pipelines/bump_version.py +++ b/nf_core/pipelines/bump_version.py @@ -206,6 +206,7 @@ def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patt return replacements = [] + updated_version = False for pattern in patterns: found_match = False @@ -229,14 +230,15 @@ def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patt if found_match: content = "\n".join(newcontent) + "\n" + updated_version = True else: log.error(f"Could not find version number in {filename}: `{pattern}`") - - log.info(f"Updated version in '{filename}'") - for replacement in replacements: - stderr.print(f" [red] - {replacement[0].strip()}", highlight=False) - stderr.print(f" [green] + {replacement[1].strip()}", highlight=False) - stderr.print("\n") - - with open(fn, "w") as fh: - fh.write(content) + if updated_version: + log.info(f"Updated version in '{filename}'") + for replacement in replacements: + stderr.print(f" [red] - {replacement[0].strip()}", highlight=False) + stderr.print(f" [green] + {replacement[1].strip()}", highlight=False) + stderr.print("\n") + + with open(fn, "w") as fh: + fh.write(content) From 58a4487c6de5ee4d8c854f363054d77e9a86a5f5 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 14 Oct 2024 10:40:01 +0200 Subject: [PATCH 03/30] add some types --- nf_core/pipelines/bump_version.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py index fe5730a714..b5727decc1 100644 --- a/nf_core/pipelines/bump_version.py +++ b/nf_core/pipelines/bump_version.py @@ -205,8 +205,8 @@ def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patt log.warning(f"File not found: '{fn}'") return - replacements = [] - updated_version = False + replacements: List[Tuple[str, str]] = [] + updated_version: bool = False for pattern in patterns: found_match = False From 57dd319030a2d0f7148730495224cff4967cae08 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 14 Oct 2024 08:45:44 +0000 Subject: [PATCH 04/30] bump version to 3.0.3dev --- .gitpod.yml | 2 +- CHANGELOG.md | 14 ++++++++++++++ setup.py | 2 +- 3 files changed, 16 insertions(+), 2 deletions(-) diff --git a/.gitpod.yml b/.gitpod.yml index f92457278b..efe193f35f 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -1,4 +1,4 @@ -image: nfcore/gitpod:latest +image: nfcore/gitpod:dev tasks: - name: install current state of nf-core/tools and setup pre-commit command: | diff --git a/CHANGELOG.md b/CHANGELOG.md index 5ad584d68e..2f4b463351 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,5 +1,19 @@ # nf-core/tools: Changelog +## v3.0.3 + +### Template + +### Download + +### Linting + +### Modules + +### Subworkflows + +### General + ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] ### Template diff --git a/setup.py b/setup.py index 78b56fe384..11b3022494 100644 --- a/setup.py +++ b/setup.py @@ -2,7 +2,7 @@ from setuptools import find_packages, setup -version = "3.0.2" +version = "3.0.3dev" with open("README.md") as f: readme = f.read() From 50027db437414b33d7ee5572f64076e7b0113b51 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 14 Oct 2024 13:06:19 +0200 Subject: [PATCH 05/30] rewrite the logic in bump_version.py to handle yml files better --- nf_core/pipelines/bump_version.py | 153 ++++++++++++++++++------------ 1 file changed, 93 insertions(+), 60 deletions(-) diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py index b5727decc1..55fb82ad20 100644 --- a/nf_core/pipelines/bump_version.py +++ b/nf_core/pipelines/bump_version.py @@ -5,7 +5,7 @@ import logging import re from pathlib import Path -from typing import List, Tuple, Union +from typing import List, Optional, Tuple, Union import rich.console @@ -60,6 +60,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None: f"/releases/tag/{new_version}", ) ], + yaml_key=["report_comment"], ) if multiqc_current_version != "dev" and multiqc_new_version == "dev": update_file_version( @@ -71,6 +72,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None: "/tree/dev", ) ], + yaml_key=["report_comment"], ) if multiqc_current_version == "dev" and multiqc_new_version != "dev": update_file_version( @@ -82,6 +84,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None: f"/releases/tag/{multiqc_new_version}", ) ], + yaml_key=["report_comment"], ) update_file_version( Path("assets", "multiqc_config.yml"), @@ -92,6 +95,7 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None: f"/{multiqc_new_version}/", ), ], + yaml_key=["report_comment"], ) # nf-test snap files pipeline_name = pipeline_obj.nf_config.get("manifest.name", "").strip(" '\"") @@ -114,10 +118,12 @@ def bump_pipeline_version(pipeline_obj: Pipeline, new_version: str) -> None: pipeline_obj, [ ( - rf"$\s+(version:\s*){re.escape(current_version)}", - rf"\g<1>{new_version}", + current_version, + new_version, ) ], + required=False, + yaml_key=["template", "version"], ) @@ -159,10 +165,11 @@ def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None: # example: # NXF_VER: # - "20.04.0" - rf"- \"{re.escape(current_version)}\"", - f'- "{new_version}"', + current_version, + new_version, ) ], + yaml_key=["jobs", "test", "strategy", "matrix", "NXF_VER"], ) # README.md - Nextflow version badge @@ -183,62 +190,88 @@ def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None: ) -def update_file_version(filename: Union[str, Path], pipeline_obj: Pipeline, patterns: List[Tuple[str, str]]) -> None: - """Updates the version number in a requested file. +def update_file_version( + filename: Union[str, Path], + pipeline_obj: Pipeline, + patterns: List[Tuple[str, str]], + required: bool = True, + yaml_key: Optional[List[str]] = None, +) -> None: + fn: Path = pipeline_obj._fp(filename) - Args: - filename (str): File to scan. - pipeline_obj (nf_core.pipelines.lint.PipelineLint): A PipelineLint object that holds information - about the pipeline contents and build files. - pattern (str): Regex pattern to apply. - - Raises: - ValueError, if the version number cannot be found. - """ - # Load the file - fn = pipeline_obj._fp(filename) - content = "" - try: - with open(fn) as fh: - content = fh.read() - except FileNotFoundError: + if not fn.exists(): log.warning(f"File not found: '{fn}'") return - replacements: List[Tuple[str, str]] = [] - updated_version: bool = False - for pattern in patterns: - found_match = False - - newcontent = [] - for line in content.splitlines(): - # Match the pattern - matches_pattern = re.findall(rf"^.*{pattern[0]}.*$", line) - if matches_pattern: - found_match = True - - # Replace the match - newline = re.sub(pattern[0], pattern[1], line) - newcontent.append(newline) - - # Save for logging - replacements.append((line, newline)) - - # No match, keep line as it is - else: - newcontent.append(line) - - if found_match: - content = "\n".join(newcontent) + "\n" - updated_version = True - else: - log.error(f"Could not find version number in {filename}: `{pattern}`") - if updated_version: - log.info(f"Updated version in '{filename}'") - for replacement in replacements: - stderr.print(f" [red] - {replacement[0].strip()}", highlight=False) - stderr.print(f" [green] + {replacement[1].strip()}", highlight=False) - stderr.print("\n") - - with open(fn, "w") as fh: - fh.write(content) + if yaml_key: + update_yaml_file(fn, patterns, yaml_key, required) + else: + update_text_file(fn, patterns, required) + + +def update_yaml_file(fn: Path, patterns: List[Tuple[str, str]], yaml_key: List[str], required: bool): + import yaml + + with open(fn) as file: + yaml_content = yaml.safe_load(file) + + try: + target = yaml_content + for key in yaml_key[:-1]: + target = target[key] + + last_key = yaml_key[-1] + current_value = target[last_key] + + new_value = current_value + for pattern, replacement in patterns: + new_value = re.sub(pattern, replacement, new_value) + + if new_value != current_value: + target[last_key] = new_value + with open(fn, "w") as file: + yaml.dump(yaml_content, file) + log.info(f"Updated version in YAML file '{fn}'") + log_change(current_value, new_value) + except KeyError as e: + handle_error(f"Could not find key {e} in the YAML structure of {fn}", required) + + +def update_text_file(fn: Path, patterns: List[Tuple[str, str]], required: bool): + with open(fn) as file: + content = file.read() + + updated = False + for pattern, replacement in patterns: + new_content, count = re.subn(pattern, replacement, content) + if count > 0: + log_change(content, new_content) + content = new_content + updated = True + log.info(f"Updated version in '{fn}'") + log.debug(f"Replaced pattern '{pattern}' with '{replacement}' {count} times") + elif required: + handle_error(f"Could not find version number in {fn}: `{pattern}`", required) + + if updated: + with open(fn, "w") as file: + file.write(content) + + +def handle_error(message: str, required: bool): + if required: + raise ValueError(message) + else: + log.info(message) + + +def log_change(old_content: str, new_content: str): + old_lines = old_content.splitlines() + new_lines = new_content.splitlines() + + for old_line, new_line in zip(old_lines, new_lines): + if old_line != new_line: + stderr.print(f" [red] - {old_line.strip()}", highlight=False) + stderr.print(f" [green] + {new_line.strip()}", highlight=False) + + stderr.print("\n") From 41c4b95662ab4686aa39194d2ca5b427596e8815 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 14 Oct 2024 13:06:48 +0200 Subject: [PATCH 06/30] add test for version bump in `.nf-core.yml` --- tests/pipelines/test_bump_version.py | 17 +++++++++++++++-- 1 file changed, 15 insertions(+), 2 deletions(-) diff --git a/tests/pipelines/test_bump_version.py b/tests/pipelines/test_bump_version.py index 709e82427d..8d6032f23f 100644 --- a/tests/pipelines/test_bump_version.py +++ b/tests/pipelines/test_bump_version.py @@ -13,12 +13,25 @@ def test_bump_pipeline_version(self): """Test that making a release with the working example files works""" # Bump the version number - nf_core.pipelines.bump_version.bump_pipeline_version(self.pipeline_obj, "1.1") + nf_core.pipelines.bump_version.bump_pipeline_version(self.pipeline_obj, "1.1.0") new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir) # Check nextflow.config new_pipeline_obj.load_pipeline_config() - assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.1" + assert new_pipeline_obj.nf_config["manifest.version"].strip("'\"") == "1.1.0" + + # Check multiqc_config.yml + with open(new_pipeline_obj._fp("assets/multiqc_config.yml")) as fh: + multiqc_config = yaml.safe_load(fh) + + assert "report_comment" in multiqc_config + assert "/releases/tag/1.1.0" in multiqc_config["report_comment"] + + # Check .nf-core.yml + with open(new_pipeline_obj._fp(".nf-core.yml")) as fh: + nf_core_yml = yaml.safe_load(fh) + if nf_core_yml["template"]: + assert nf_core_yml["template"]["version"] == "1.1.0" def test_dev_bump_pipeline_version(self): """Test that making a release works with a dev name and a leading v""" From 78c92289febfc6c1fd404c4d728c131668cc72e8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Mon, 14 Oct 2024 13:09:02 +0200 Subject: [PATCH 07/30] Update CHANGELOG.md MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 2f4b463351..c3a4eaa71d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,6 +1,6 @@ # nf-core/tools: Changelog -## v3.0.3 +## v3.0.3dev ### Template From 9e3d2d1cff1cdebeebf0f56c083c419474fbfeb8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 14 Oct 2024 13:25:12 +0200 Subject: [PATCH 08/30] bump default nextflow version in test --- tests/pipelines/test_bump_version.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tests/pipelines/test_bump_version.py b/tests/pipelines/test_bump_version.py index 8d6032f23f..408be5020b 100644 --- a/tests/pipelines/test_bump_version.py +++ b/tests/pipelines/test_bump_version.py @@ -46,7 +46,7 @@ def test_dev_bump_pipeline_version(self): def test_bump_nextflow_version(self): # Bump the version number to a specific version, preferably one # we're not already on - version = "22.04.3" + version = "24.04.2" nf_core.pipelines.bump_version.bump_nextflow_version(self.pipeline_obj, version) new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir) new_pipeline_obj._load() From 6e5d73782c6406cf98ae1bcac444e4e02f70cce6 Mon Sep 17 00:00:00 2001 From: mashehu Date: Mon, 14 Oct 2024 14:09:27 +0200 Subject: [PATCH 09/30] remove outdated readme pattern --- nf_core/pipelines/bump_version.py | 15 +++++++-------- tests/pipelines/test_bump_version.py | 2 +- 2 files changed, 8 insertions(+), 9 deletions(-) diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py index 55fb82ad20..b091fce70e 100644 --- a/nf_core/pipelines/bump_version.py +++ b/nf_core/pipelines/bump_version.py @@ -180,12 +180,7 @@ def bump_nextflow_version(pipeline_obj: Pipeline, new_version: str) -> None: ( rf"nextflow%20DSL2-%E2%89%A5{re.escape(current_version)}-23aa62.svg", f"nextflow%20DSL2-%E2%89%A5{new_version}-23aa62.svg", - ), - ( - # example: 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=20.04.0`) - rf"1\.\s*Install\s*\[`Nextflow`\]\(https:\/\/www\.nextflow\.io\/docs\/latest\/getstarted\.html#installation\)\s*\(`>={re.escape(current_version)}`\)", - f"1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>={new_version}`)", - ), + ) ], ) @@ -225,14 +220,18 @@ def update_yaml_file(fn: Path, patterns: List[Tuple[str, str]], yaml_key: List[s new_value = current_value for pattern, replacement in patterns: - new_value = re.sub(pattern, replacement, new_value) + # check if current value is list + if isinstance(current_value, list): + new_value = [re.sub(pattern, replacement, item) for item in current_value] + else: + new_value = re.sub(pattern, replacement, current_value) if new_value != current_value: target[last_key] = new_value with open(fn, "w") as file: yaml.dump(yaml_content, file) log.info(f"Updated version in YAML file '{fn}'") - log_change(current_value, new_value) + log_change(str(current_value), str(new_value)) except KeyError as e: handle_error(f"Could not find key {e} in the YAML structure of {fn}", required) diff --git a/tests/pipelines/test_bump_version.py b/tests/pipelines/test_bump_version.py index 408be5020b..8af5c0e4d1 100644 --- a/tests/pipelines/test_bump_version.py +++ b/tests/pipelines/test_bump_version.py @@ -46,7 +46,7 @@ def test_dev_bump_pipeline_version(self): def test_bump_nextflow_version(self): # Bump the version number to a specific version, preferably one # we're not already on - version = "24.04.2" + version = "25.04.2" nf_core.pipelines.bump_version.bump_nextflow_version(self.pipeline_obj, version) new_pipeline_obj = nf_core.utils.Pipeline(self.pipeline_dir) new_pipeline_obj._load() From 634d7233a0d7f4e67b9f570b8659bdffcc35ad95 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 14 Oct 2024 12:11:07 +0000 Subject: [PATCH 10/30] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3a4eaa71d..1ceb2d6324 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,8 @@ ### General +- Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) + ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] ### Template From 8ae861d94b9ff9d8af5edd3d44df789c69da491a Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 14 Oct 2024 15:55:02 +0200 Subject: [PATCH 11/30] keep pipeline name in version.yml file Why going for pipeline when we have shortname? --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index adad7a6a0b..2a619e2e4a 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -47,7 +47,7 @@ workflow {{ short_name|upper }} { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + 'pipeline_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml', + name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + '{{ short_name }}_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } From db1687d7615b310c793a4f4e570fd08d8295b984 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 14 Oct 2024 13:56:28 +0000 Subject: [PATCH 12/30] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3a4eaa71d..1ff8468ccb 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -14,6 +14,8 @@ ### General +- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223)) + ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] ### Template From 8e2d899d8d9b462d3111b2301f0e9747a60d3675 Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Mon, 14 Oct 2024 15:56:40 +0200 Subject: [PATCH 13/30] Update nf_core/pipeline-template/workflows/pipeline.nf --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index 2a619e2e4a..dbf5f1f891 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -47,7 +47,7 @@ workflow {{ short_name|upper }} { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: {% if is_nfcore %}'nf_core_' {% else %} '' {% endif %} + '{{ short_name }}_software_' + {% if multiqc %} 'mqc_' {% else %} '' {% endif %} + 'versions.yml', + name: {% if is_nfcore %}'nf_core_' + {% else %}{% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% else %}{% endif %} + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } From 597a0ae54acbfca5e8f0758e6856d96ae4a1385b Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Mon, 14 Oct 2024 14:09:41 +0000 Subject: [PATCH 14/30] [automated] Update CHANGELOG.md --- CHANGELOG.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1ff8468ccb..c4da129906 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Template +- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223)) + ### Download ### Linting @@ -14,8 +16,6 @@ ### General -- Keep pipeline name in version.yml file ([#3223](https://github.com/nf-core/tools/pull/3223)) - ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] ### Template From 18cbf05530d40b71546e23e146d53719d852916a Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 15 Oct 2024 09:45:40 +0200 Subject: [PATCH 15/30] Update nf_core/pipeline-template/workflows/pipeline.nf MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit Co-authored-by: Júlia Mir Pedrol --- nf_core/pipeline-template/workflows/pipeline.nf | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/workflows/pipeline.nf b/nf_core/pipeline-template/workflows/pipeline.nf index dbf5f1f891..4dd8674c1b 100644 --- a/nf_core/pipeline-template/workflows/pipeline.nf +++ b/nf_core/pipeline-template/workflows/pipeline.nf @@ -47,7 +47,7 @@ workflow {{ short_name|upper }} { softwareVersionsToYAML(ch_versions) .collectFile( storeDir: "${params.outdir}/pipeline_info", - name: {% if is_nfcore %}'nf_core_' + {% else %}{% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% else %}{% endif %} + 'versions.yml', + name: {% if is_nfcore %}'nf_core_' + {% endif %} '{{ short_name }}_software_' {% if multiqc %} + 'mqc_' {% endif %} + 'versions.yml', sort: true, newLine: true ).set { ch_collated_versions } From e8eccd9007e92c91839de8844b144e63a4d4d21e Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 15 Oct 2024 09:50:00 +0200 Subject: [PATCH 16/30] Template: Fix Manifest DOI text - Add line break - Fix indentation --- nf_core/pipeline-template/nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 052a5d8b1f..90e620069a 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -286,7 +286,7 @@ validation { \033[0;35m ${manifest.name} ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ - afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} + afterText = """${manifest.doi ? "\n* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} * The nf-core framework https://doi.org/10.1038/s41587-020-0439-x From 7c5caac39c24d40c5339b5df7e22d6d41ba247dd Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 15 Oct 2024 07:52:05 +0000 Subject: [PATCH 17/30] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3a4eaa71d..310207fb54 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Template +- Fix Manifest DOI text ([#3224](https://github.com/nf-core/tools/pull/3224)) + ### Download ### Linting From 4deb397280e82edb482cd45d644d7a49235a1a2b Mon Sep 17 00:00:00 2001 From: Maxime U Garcia Date: Tue, 15 Oct 2024 09:53:56 +0200 Subject: [PATCH 18/30] Template: Do not assume pipeline name is url I'd rather we use {{ name }} that way we see in the script what we have. If we have manifest.name we assume that people are using a name that org/pipeline, which should work for nf-core pipeline, but might not work for all. --- nf_core/pipeline-template/nextflow.config | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/nf_core/pipeline-template/nextflow.config b/nf_core/pipeline-template/nextflow.config index 052a5d8b1f..3ddd062cf7 100644 --- a/nf_core/pipeline-template/nextflow.config +++ b/nf_core/pipeline-template/nextflow.config @@ -272,7 +272,7 @@ validation { defaultIgnoreParams = ["genomes"] help { enabled = true - command = "nextflow run $manifest.name -profile --input samplesheet.csv --outdir " + command = "nextflow run {{ name }} -profile --input samplesheet.csv --outdir " fullParameter = "help_full" showHiddenParameter = "show_hidden" {% if is_nfcore -%} @@ -283,7 +283,7 @@ validation { \033[0;34m |\\ | |__ __ / ` / \\ |__) |__ \033[0;33m} {\033[0m \033[0;34m | \\| | \\__, \\__/ | \\ |___ \033[0;32m\\`-._,-`-,\033[0m \033[0;32m`._,._,\'\033[0m -\033[0;35m ${manifest.name} ${manifest.version}\033[0m +\033[0;35m {{ name }} ${manifest.version}\033[0m -\033[2m----------------------------------------------------\033[0m- """ afterText = """${manifest.doi ? "* The pipeline\n" : ""}${manifest.doi.tokenize(",").collect { " https://doi.org/${it.trim().replace('https://doi.org/','')}"}.join("\n")}${manifest.doi ? "\n" : ""} @@ -291,7 +291,7 @@ validation { https://doi.org/10.1038/s41587-020-0439-x * Software dependencies - https://github.com/${manifest.name}/blob/master/CITATIONS.md + https://github.com/{{ name }}/blob/master/CITATIONS.md """{% endif %} }{% if is_nfcore %} summary { From 5487a622a176fd0bdfd1135f4c68a098a2014f48 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 15 Oct 2024 07:57:12 +0000 Subject: [PATCH 19/30] [automated] Update CHANGELOG.md --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index c3a4eaa71d..800f53dbce 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -4,6 +4,8 @@ ### Template +- Do not assume pipeline name is url ([#3225](https://github.com/nf-core/tools/pull/3225)) + ### Download ### Linting From 0efbd559cade59d2414d82d4b5938553e154ab22 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 15 Oct 2024 10:12:03 +0200 Subject: [PATCH 20/30] keep yaml item order --- nf_core/pipelines/bump_version.py | 7 +++++-- 1 file changed, 5 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py index b091fce70e..72246b8045 100644 --- a/nf_core/pipelines/bump_version.py +++ b/nf_core/pipelines/bump_version.py @@ -205,10 +205,13 @@ def update_file_version( def update_yaml_file(fn: Path, patterns: List[Tuple[str, str]], yaml_key: List[str], required: bool): - import yaml + from ruamel.yaml import YAML + + yaml = YAML() + yaml.preserve_quotes = True with open(fn) as file: - yaml_content = yaml.safe_load(file) + yaml_content = yaml.load(file) try: target = yaml_content From 30e3d5dfaaa427d77e83d28cb6a01874106fbe69 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 15 Oct 2024 10:21:55 +0200 Subject: [PATCH 21/30] add docstrings --- nf_core/pipelines/bump_version.py | 33 +++++++++++++++++++++++++++++-- 1 file changed, 31 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/bump_version.py b/nf_core/pipelines/bump_version.py index 72246b8045..3190ed70d4 100644 --- a/nf_core/pipelines/bump_version.py +++ b/nf_core/pipelines/bump_version.py @@ -8,6 +8,7 @@ from typing import List, Optional, Tuple, Union import rich.console +from ruamel.yaml import YAML import nf_core.utils from nf_core.utils import Pipeline @@ -192,6 +193,18 @@ def update_file_version( required: bool = True, yaml_key: Optional[List[str]] = None, ) -> None: + """ + Updates a file with a new version number. + + Args: + filename (str): The name of the file to update. + pipeline_obj (nf_core.utils.Pipeline): A `Pipeline` object that holds information + about the pipeline contents. + patterns (List[Tuple[str, str]]): A list of tuples containing the regex patterns to + match and the replacement strings. + required (bool, optional): Whether the file is required to exist. Defaults to `True`. + yaml_key (Optional[List[str]], optional): The YAML key to update. Defaults to `None`. + """ fn: Path = pipeline_obj._fp(filename) if not fn.exists(): @@ -205,11 +218,18 @@ def update_file_version( def update_yaml_file(fn: Path, patterns: List[Tuple[str, str]], yaml_key: List[str], required: bool): - from ruamel.yaml import YAML + """ + Updates a YAML file with a new version number. + Args: + fn (Path): The name of the file to update. + patterns (List[Tuple[str, str]]): A list of tuples containing the regex patterns to + match and the replacement strings. + yaml_key (List[str]): The YAML key to update. + required (bool): Whether the file is required to exist. + """ yaml = YAML() yaml.preserve_quotes = True - with open(fn) as file: yaml_content = yaml.load(file) @@ -240,6 +260,15 @@ def update_yaml_file(fn: Path, patterns: List[Tuple[str, str]], yaml_key: List[s def update_text_file(fn: Path, patterns: List[Tuple[str, str]], required: bool): + """ + Updates a text file with a new version number. + + Args: + fn (Path): The name of the file to update. + patterns (List[Tuple[str, str]]): A list of tuples containing the regex patterns to + match and the replacement strings. + required (bool): Whether the file is required to exist. + """ with open(fn) as file: content = file.read() From e06ca52e98057a5a1cebb5defcf71495dcafe632 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 15 Oct 2024 15:23:44 +0200 Subject: [PATCH 22/30] create: add toggle all shortcut --- nf_core/pipelines/create/__init__.py | 17 +++++++++++++---- 1 file changed, 13 insertions(+), 4 deletions(-) diff --git a/nf_core/pipelines/create/__init__.py b/nf_core/pipelines/create/__init__.py index 26e4d23283..6a610ccccb 100644 --- a/nf_core/pipelines/create/__init__.py +++ b/nf_core/pipelines/create/__init__.py @@ -1,14 +1,11 @@ """A Textual app to create a pipeline.""" import logging -from pathlib import Path import click -import yaml from textual.app import App -from textual.widgets import Button +from textual.widgets import Button, Switch -import nf_core from nf_core.pipelines.create import utils from nf_core.pipelines.create.basicdetails import BasicDetails from nf_core.pipelines.create.custompipeline import CustomPipeline @@ -46,6 +43,7 @@ class PipelineCreateApp(App[utils.CreateConfig]): BINDINGS = [ ("d", "toggle_dark", "Toggle dark mode"), ("q", "quit", "Quit"), + ("a", "toggle_all", "Toggle all"), ] SCREENS = { "welcome": WelcomeScreen(), @@ -105,3 +103,14 @@ def on_button_pressed(self, event: Button.Pressed) -> None: def action_toggle_dark(self) -> None: """An action to toggle dark mode.""" self.dark: bool = not self.dark + + def action_toggle_all(self) -> None: + """An action to toggle all Switches.""" + switches = self.query(Switch) + if not switches: + return # No Switches widgets found + # Determine the new state based on the first switch + new_state = not switches.first().value if switches.first() else True + for switch in switches: + switch.value = new_state + self.refresh() From 762be8059d034edb7a031ccf195667783fcb1f74 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Tue, 15 Oct 2024 13:25:15 +0000 Subject: [PATCH 23/30] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1ceb2d6324..a8a9227773 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -15,6 +15,7 @@ ### General - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) +- create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11] From 2b4ed85d80978e88a0fdcd8d6bbab5d8b33fa714 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 15 Oct 2024 16:03:02 +0200 Subject: [PATCH 24/30] fix test path in update-textual-snapshots --- .../workflows/update-textual-snapshots.yml | 2 +- CONTRIBUTING.md | 2 +- nf_core/utils.py | 2 +- .../test_basic_details_custom.svg | 250 ++++++++--------- .../test_basic_details_nfcore.svg | 256 ++++++++--------- .../test_create_app/test_choose_type.svg | 246 ++++++++--------- .../test_customisation_help.svg | 258 ++++++++--------- .../test_create_app/test_final_details.svg | 246 ++++++++--------- .../test_create_app/test_github_details.svg | 260 +++++++++--------- .../test_github_exit_message.svg | 252 ++++++++--------- .../test_create_app/test_github_question.svg | 238 ++++++++-------- .../test_create_app/test_type_custom.svg | 254 ++++++++--------- .../test_create_app/test_type_nfcore.svg | 252 ++++++++--------- .../test_type_nfcore_validation.svg | 254 ++++++++--------- .../test_create_app/test_welcome.svg | 250 ++++++++--------- 15 files changed, 1511 insertions(+), 1511 deletions(-) diff --git a/.github/workflows/update-textual-snapshots.yml b/.github/workflows/update-textual-snapshots.yml index fb936762f8..2adb1b8d81 100644 --- a/.github/workflows/update-textual-snapshots.yml +++ b/.github/workflows/update-textual-snapshots.yml @@ -46,7 +46,7 @@ jobs: - name: Run pytest to update snapshots id: pytest run: | - python3 -m pytest tests/test_create_app.py --snapshot-update --color=yes --durations=0 + python3 -m pytest tests/pipelines/test_create_app.py --snapshot-update --color=yes --durations=0 continue-on-error: true # indication that the run has finished diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index f9773296c1..ce36354331 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -153,7 +153,7 @@ Optionally followed by the description that you want to add to the changelog. - Update Textual snapshots: -If the Textual snapshots (run by `tests/test_crate_app.py`) fail, an HTML report is generated and uploaded as an artifact. +If the Textual snapshots (run by `tests/pipelines/test_crate_app.py`) fail, an HTML report is generated and uploaded as an artifact. If you are sure that these changes are correct, you can automatically update the snapshots form the PR by posting a comment with the magic words: ``` diff --git a/nf_core/utils.py b/nf_core/utils.py index 068da22def..87dd307e70 100644 --- a/nf_core/utils.py +++ b/nf_core/utils.py @@ -323,7 +323,7 @@ def fetch_wf_config(wf_path: Path, cache_config: bool = True) -> dict: # If we can, save a cached copy # HINT: during testing phase (in test_download, for example) we don't want - # to save configuration copy in $HOME, otherwise the tests/test_download.py::DownloadTest::test_wf_use_local_configs + # to save configuration copy in $HOME, otherwise the tests/pipelines/test_download.py::DownloadTest::test_wf_use_local_configs # will fail after the first attempt. It's better to not save temporary data # in others folders than tmp when doing tests in general if cache_path and cache_config: diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg index 0e16822902..f327dac799 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_custom.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-1305977867-matrix { + .terminal-1837969819-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1305977867-title { + .terminal-1837969819-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1305977867-r1 { fill: #c5c8c6 } -.terminal-1305977867-r2 { fill: #e3e3e3 } -.terminal-1305977867-r3 { fill: #989898 } -.terminal-1305977867-r4 { fill: #e1e1e1 } -.terminal-1305977867-r5 { fill: #4ebf71;font-weight: bold } -.terminal-1305977867-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-1305977867-r7 { fill: #1e1e1e } -.terminal-1305977867-r8 { fill: #008139 } -.terminal-1305977867-r9 { fill: #121212 } -.terminal-1305977867-r10 { fill: #e2e2e2 } -.terminal-1305977867-r11 { fill: #787878 } -.terminal-1305977867-r12 { fill: #454a50 } -.terminal-1305977867-r13 { fill: #7ae998 } -.terminal-1305977867-r14 { fill: #e2e3e3;font-weight: bold } -.terminal-1305977867-r15 { fill: #0a180e;font-weight: bold } -.terminal-1305977867-r16 { fill: #000000 } -.terminal-1305977867-r17 { fill: #fea62b;font-weight: bold } -.terminal-1305977867-r18 { fill: #a7a9ab } -.terminal-1305977867-r19 { fill: #e2e3e3 } + .terminal-1837969819-r1 { fill: #c5c8c6 } +.terminal-1837969819-r2 { fill: #e3e3e3 } +.terminal-1837969819-r3 { fill: #989898 } +.terminal-1837969819-r4 { fill: #e1e1e1 } +.terminal-1837969819-r5 { fill: #4ebf71;font-weight: bold } +.terminal-1837969819-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-1837969819-r7 { fill: #1e1e1e } +.terminal-1837969819-r8 { fill: #008139 } +.terminal-1837969819-r9 { fill: #121212 } +.terminal-1837969819-r10 { fill: #e2e2e2 } +.terminal-1837969819-r11 { fill: #787878 } +.terminal-1837969819-r12 { fill: #454a50 } +.terminal-1837969819-r13 { fill: #7ae998 } +.terminal-1837969819-r14 { fill: #e2e3e3;font-weight: bold } +.terminal-1837969819-r15 { fill: #0a180e;font-weight: bold } +.terminal-1837969819-r16 { fill: #000000 } +.terminal-1837969819-r17 { fill: #fea62b;font-weight: bold } +.terminal-1837969819-r18 { fill: #a7a9ab } +.terminal-1837969819-r19 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Basic details - - - - -GitHub organisationWorkflow name - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -nf-corePipeline Name -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -A short description of your pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Description -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -Name of the main author / authors - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Author(s) -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +nf-corePipeline Name +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +A short description of your pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Description +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +Name of the main author / authors + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Author(s) +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg index 02f4fc213e..6a4e424130 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_basic_details_nfcore.svg @@ -19,256 +19,256 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Basic details - - - - -GitHub organisationWorkflow name - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -nf-core                                   Pipeline Name -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -A short description of your pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Description -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -Name of the main author / authors - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Author(s) -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +nf-core                                   Pipeline Name +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +A short description of your pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Description +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +Name of the main author / authors + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Author(s) +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg index 73ba989e00..3eaceeb477 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_choose_type.svg @@ -19,251 +19,251 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Choose pipeline type - - - - -Choose "nf-core" if:Choose "Custom" if: - -● You want your pipeline to be part of the ● Your pipeline will never be part of  -nf-core communitynf-core -● You think that there's an outside chance ● You want full control over all features  -that it ever could be part of nf-corethat are included from the template  -(including those that are mandatory for  -nf-core). -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - nf-core  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Custom  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - -What's the difference? - -  Choosing "nf-core" effectively pre-selects the following template features: - -● GitHub Actions continuous-integration configuration files: -▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) -▪ Code formatting checks with Prettier -▪ Auto-fix linting functionality using @nf-core-bot -▪ Marking old issues as stale -● Inclusion of shared nf-core configuration profiles - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Choose pipeline type + + + + +Choose "nf-core" if:Choose "Custom" if: + +● You want your pipeline to be part of the ● Your pipeline will never be part of  +nf-core communitynf-core +● You think that there's an outside chance ● You want full control over all features  +that it ever could be part of nf-corethat are included from the template  +(including those that are mandatory for  +nf-core). +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + nf-core  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Custom  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + +What's the difference? + +  Choosing "nf-core" effectively pre-selects the following template features: + +● GitHub Actions continuous-integration configuration files: +▪ Pipeline test runs: Small-scale (GitHub) and large-scale (AWS) +▪ Code formatting checks with Prettier +▪ Auto-fix linting functionality using @nf-core-bot +▪ Marking old issues as stale +● Inclusion of shared nf-core configuration profiles + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index d469a47615..f86647d785 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,257 +19,257 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use a GitHub Create a GitHub  Show help  -▁▁▁▁▁▁▁▁        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add Github CI testsThe pipeline will  Show help  -▁▁▁▁▁▁▁▁include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI)  -testing▄▄ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use reference genomesThe pipeline will be  Hide help  -▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most  -common reference  -genome files from  -iGenomes - - -Nf-core pipelines are configured to use a copy of the most common reference  -genome files. - -By selecting this option, your pipeline will include a configuration file  -specifying the paths to these files. - -The required code to use these files will also be included in the template.  -When the pipeline user provides an appropriate genome key, the pipeline will -automatically download the required reference files. -▅▅ -For more information about reference genomes in nf-core pipelines, see the  - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add Github badgesThe README.md file of  Show help  -▁▁▁▁▁▁▁▁the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use a GitHub Create a GitHub  Show help  +▁▁▁▁▁▁▁▁        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add Github CI testsThe pipeline will  Show help  +▁▁▁▁▁▁▁▁include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing▄▄ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use reference genomesThe pipeline will be  Hide help  +▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + + +Nf-core pipelines are configured to use a copy of the most common reference  +genome files. + +By selecting this option, your pipeline will include a configuration file  +specifying the paths to these files. + +The required code to use these files will also be included in the template.  +When the pipeline user provides an appropriate genome key, the pipeline will +automatically download the required reference files. +▅▅ +For more information about reference genomes in nf-core pipelines, see the  + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add Github badgesThe README.md file of  Show help  +▁▁▁▁▁▁▁▁the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg index b34483176a..74c232f747 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_final_details.svg @@ -19,251 +19,251 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Final details - - - - -First version of the pipelinePath to the output directory where the  -pipeline will be created -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -1.0.0dev.                                          -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Finish  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Final details + + + + +First version of the pipelinePath to the output directory where the  +pipeline will be created +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +1.0.0dev.                                          +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Finish  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg index 9276d53489..77a293fb79 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_details.svg @@ -19,258 +19,258 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Create GitHub repository - -  Now that we have created a new pipeline locally, we can create a new GitHub repository and push    -  the code to it. - - - - -Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -for login. Show  -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -GitHub username••••••••••••                   -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - -The name of the organisation where the The name of the new GitHub repository -GitHub repo will be cretaed -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -nf-core                               mypipeline                             -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - -⚠️ You can't create a repository directly in the nf-core organisation. -Please create the pipeline repo to an organisation where you have access or use your user  -account. A core-team member will be able to transfer the repo to nf-core once the development -has started. - -💡 Your GitHub user account will be used by default if nf-core is given as the org name. - - -▔▔▔▔▔▔▔▔Private -Select to make the new GitHub repo private. -▁▁▁▁▁▁▁▁ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Create GitHub repository + +  Now that we have created a new pipeline locally, we can create a new GitHub repository and push    +  the code to it. + + + + +Your GitHub usernameYour GitHub personal access token▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +for login. Show  +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +GitHub username••••••••••••                   +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + +The name of the organisation where the The name of the new GitHub repository +GitHub repo will be cretaed +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +nf-core                               mypipeline                             +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + +⚠️ You can't create a repository directly in the nf-core organisation. +Please create the pipeline repo to an organisation where you have access or use your user  +account. A core-team member will be able to transfer the repo to nf-core once the development +has started. + +💡 Your GitHub user account will be used by default if nf-core is given as the org name. + + +▔▔▔▔▔▔▔▔Private +Select to make the new GitHub repo private. +▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg index f840f8849f..1be8c63f10 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_exit_message.svg @@ -19,254 +19,254 @@ font-weight: 700; } - .terminal-1075265190-matrix { + .terminal-995675175-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1075265190-title { + .terminal-995675175-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1075265190-r1 { fill: #c5c8c6 } -.terminal-1075265190-r2 { fill: #e3e3e3 } -.terminal-1075265190-r3 { fill: #989898 } -.terminal-1075265190-r4 { fill: #e1e1e1 } -.terminal-1075265190-r5 { fill: #4ebf71;font-weight: bold } -.terminal-1075265190-r6 { fill: #98e024 } -.terminal-1075265190-r7 { fill: #626262 } -.terminal-1075265190-r8 { fill: #9d65ff } -.terminal-1075265190-r9 { fill: #fd971f } -.terminal-1075265190-r10 { fill: #d2d2d2 } -.terminal-1075265190-r11 { fill: #82aaff } -.terminal-1075265190-r12 { fill: #eeffff } -.terminal-1075265190-r13 { fill: #18954b } -.terminal-1075265190-r14 { fill: #e2e2e2 } -.terminal-1075265190-r15 { fill: #969696;font-weight: bold } -.terminal-1075265190-r16 { fill: #7ae998 } -.terminal-1075265190-r17 { fill: #008139 } -.terminal-1075265190-r18 { fill: #fea62b;font-weight: bold } -.terminal-1075265190-r19 { fill: #a7a9ab } -.terminal-1075265190-r20 { fill: #e2e3e3 } + .terminal-995675175-r1 { fill: #c5c8c6 } +.terminal-995675175-r2 { fill: #e3e3e3 } +.terminal-995675175-r3 { fill: #989898 } +.terminal-995675175-r4 { fill: #e1e1e1 } +.terminal-995675175-r5 { fill: #4ebf71;font-weight: bold } +.terminal-995675175-r6 { fill: #98e024 } +.terminal-995675175-r7 { fill: #626262 } +.terminal-995675175-r8 { fill: #9d65ff } +.terminal-995675175-r9 { fill: #fd971f } +.terminal-995675175-r10 { fill: #d2d2d2 } +.terminal-995675175-r11 { fill: #82aaff } +.terminal-995675175-r12 { fill: #eeffff } +.terminal-995675175-r13 { fill: #18954b } +.terminal-995675175-r14 { fill: #e2e2e2 } +.terminal-995675175-r15 { fill: #969696;font-weight: bold } +.terminal-995675175-r16 { fill: #7ae998 } +.terminal-995675175-r17 { fill: #008139 } +.terminal-995675175-r18 { fill: #fea62b;font-weight: bold } +.terminal-995675175-r19 { fill: #a7a9ab } +.terminal-995675175-r20 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -HowTo create a GitHub repository - - - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - -  If you would like to create the GitHub repository later, you can do it manually by following  -  these steps: - - 1. Create a new GitHub repository - 2. Add the remote to your local repository: - - -cd <pipeline_directory> -git remote add origin git@github.com:<username>/<repo_name>.git - - - 3. Push the code to the remote: - - -git push --all origin - - -💡 Note the --all flag: this is needed to push all branches to the remote. - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Close  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +HowTo create a GitHub repository + + + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + +  If you would like to create the GitHub repository later, you can do it manually by following  +  these steps: + + 1. Create a new GitHub repository + 2. Add the remote to your local repository: + + +cd <pipeline_directory> +git remote add origin git@github.com:<username>/<repo_name>.git + + + 3. Push the code to the remote: + + +git push --all origin + + +💡 Note the --all flag: this is needed to push all branches to the remote. + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Close  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg index f302feaae2..8aad414e62 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_github_question.svg @@ -19,247 +19,247 @@ font-weight: 700; } - .terminal-3993718311-matrix { + .terminal-345103272-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3993718311-title { + .terminal-345103272-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3993718311-r1 { fill: #c5c8c6 } -.terminal-3993718311-r2 { fill: #e3e3e3 } -.terminal-3993718311-r3 { fill: #989898 } -.terminal-3993718311-r4 { fill: #e1e1e1 } -.terminal-3993718311-r5 { fill: #4ebf71;font-weight: bold } -.terminal-3993718311-r6 { fill: #7ae998 } -.terminal-3993718311-r7 { fill: #507bb3 } -.terminal-3993718311-r8 { fill: #dde6ed;font-weight: bold } -.terminal-3993718311-r9 { fill: #008139 } -.terminal-3993718311-r10 { fill: #001541 } -.terminal-3993718311-r11 { fill: #fea62b;font-weight: bold } -.terminal-3993718311-r12 { fill: #a7a9ab } -.terminal-3993718311-r13 { fill: #e2e3e3 } + .terminal-345103272-r1 { fill: #c5c8c6 } +.terminal-345103272-r2 { fill: #e3e3e3 } +.terminal-345103272-r3 { fill: #989898 } +.terminal-345103272-r4 { fill: #e1e1e1 } +.terminal-345103272-r5 { fill: #4ebf71;font-weight: bold } +.terminal-345103272-r6 { fill: #7ae998 } +.terminal-345103272-r7 { fill: #507bb3 } +.terminal-345103272-r8 { fill: #dde6ed;font-weight: bold } +.terminal-345103272-r9 { fill: #008139 } +.terminal-345103272-r10 { fill: #001541 } +.terminal-345103272-r11 { fill: #fea62b;font-weight: bold } +.terminal-345103272-r12 { fill: #a7a9ab } +.terminal-345103272-r13 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Create GitHub repository - - -  After creating the pipeline template locally, we can create a GitHub repository and push the  -  code to it. - -  Do you want to create a GitHub repository? - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Create GitHub repo  Finish without creating a repo  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Create GitHub repository + + +  After creating the pipeline template locally, we can create a GitHub repository and push the  +  code to it. + +  Do you want to create a GitHub repository? + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Create GitHub repo  Finish without creating a repo  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index 399989e478..c8537c6d17 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,255 +19,255 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use a GitHub Create a GitHub  Show help  -▁▁▁▁▁▁▁▁        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add Github CI testsThe pipeline will  Show help  -▁▁▁▁▁▁▁▁include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI)  -testing -▃▃ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use reference genomesThe pipeline will be  Show help  -▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most  -common reference  -genome files from  -iGenomes - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add Github badgesThe README.md file of  Show help  -▁▁▁▁▁▁▁▁the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add configuration The pipeline will  Show help  -▁▁▁▁▁▁▁▁        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -profiles containing  -custom parameters  -requried to run  -nf-core pipelines at  -different institutions - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use code lintersThe pipeline will  Show help  -▁▁▁▁▁▁▁▁include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -and CI tests to lint  -your code: pre-commit, -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use a GitHub Create a GitHub  Show help  +▁▁▁▁▁▁▁▁        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add Github CI testsThe pipeline will  Show help  +▁▁▁▁▁▁▁▁include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing +▃▃ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use reference genomesThe pipeline will be  Show help  +▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add Github badgesThe README.md file of  Show help  +▁▁▁▁▁▁▁▁the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add configuration The pipeline will  Show help  +▁▁▁▁▁▁▁▁        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +profiles containing  +custom parameters  +requried to run  +nf-core pipelines at  +different institutions + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use code lintersThe pipeline will  Show help  +▁▁▁▁▁▁▁▁include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +and CI tests to lint  +your code: pre-commit, +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg index eae7637189..c18bb31b8e 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore.svg @@ -19,254 +19,254 @@ font-weight: 700; } - 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+ - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use reference genomesThe pipeline will be  Show help  -▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most common -reference genome files  -from iGenomes - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use multiqcThe pipeline will  Show help  -▁▁▁▁▁▁▁▁include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -module which generates  -an HTML report for  -quality control. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use fastqcThe pipeline will  Show help  -▁▁▁▁▁▁▁▁include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -module which performs  -quality control  -analysis of input FASTQ -files. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use nf-schemaUse the nf-schema  Show help  -▁▁▁▁▁▁▁▁Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -this pipeline. - - - - - - - - - - - - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use reference genomesThe pipeline will be  Show help  +▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most common +reference genome files  +from iGenomes + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use multiqcThe pipeline will  Show help  +▁▁▁▁▁▁▁▁include the MultiQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which generates  +an HTML report for  +quality control. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use fastqcThe pipeline will  Show help  +▁▁▁▁▁▁▁▁include the FastQC ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +module which performs  +quality control  +analysis of input FASTQ +files. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use nf-schemaUse the nf-schema  Show help  +▁▁▁▁▁▁▁▁Nextflow plugin for ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +this pipeline. + + + + + + + + + + + + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index 2253bd9ab1..fd6f2532c8 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,255 +19,255 @@ font-weight: 700; } - .terminal-3773691015-matrix { + .terminal-3655041559-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3773691015-title { + .terminal-3655041559-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3773691015-r1 { fill: #c5c8c6 } -.terminal-3773691015-r2 { fill: #e3e3e3 } -.terminal-3773691015-r3 { fill: #989898 } -.terminal-3773691015-r4 { fill: #e1e1e1 } -.terminal-3773691015-r5 { fill: #4ebf71;font-weight: bold } -.terminal-3773691015-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-3773691015-r7 { fill: #1e1e1e } -.terminal-3773691015-r8 { fill: #0f4e2a } -.terminal-3773691015-r9 { fill: #7b3042 } -.terminal-3773691015-r10 { fill: #a7a7a7 } -.terminal-3773691015-r11 { fill: #787878 } -.terminal-3773691015-r12 { fill: #e2e2e2 } -.terminal-3773691015-r13 { fill: #b93c5b } -.terminal-3773691015-r14 { fill: #454a50 } -.terminal-3773691015-r15 { fill: #7ae998 } -.terminal-3773691015-r16 { fill: #e2e3e3;font-weight: bold } -.terminal-3773691015-r17 { fill: #000000 } -.terminal-3773691015-r18 { fill: #008139 } -.terminal-3773691015-r19 { fill: #fea62b;font-weight: bold } -.terminal-3773691015-r20 { fill: #a7a9ab } -.terminal-3773691015-r21 { fill: #e2e3e3 } + .terminal-3655041559-r1 { fill: #c5c8c6 } +.terminal-3655041559-r2 { fill: #e3e3e3 } +.terminal-3655041559-r3 { fill: #989898 } +.terminal-3655041559-r4 { fill: #e1e1e1 } +.terminal-3655041559-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3655041559-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-3655041559-r7 { fill: #1e1e1e } +.terminal-3655041559-r8 { fill: #0f4e2a } +.terminal-3655041559-r9 { fill: #7b3042 } +.terminal-3655041559-r10 { fill: #a7a7a7 } +.terminal-3655041559-r11 { fill: #787878 } +.terminal-3655041559-r12 { fill: #e2e2e2 } +.terminal-3655041559-r13 { fill: #b93c5b } +.terminal-3655041559-r14 { fill: #454a50 } +.terminal-3655041559-r15 { fill: #7ae998 } +.terminal-3655041559-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-3655041559-r17 { fill: #000000 } +.terminal-3655041559-r18 { fill: #008139 } +.terminal-3655041559-r19 { fill: #fea62b;font-weight: bold } +.terminal-3655041559-r20 { fill: #a7a9ab } +.terminal-3655041559-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Basic details - - - - -GitHub organisationWorkflow name - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -nf-core                                   Pipeline Name -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Must be lowercase without  -punctuation. - - - -A short description of your pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Description -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Author(s) -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +nf-core                                   Pipeline Name +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Must be lowercase without  +punctuation. + + + +A short description of your pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Description +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Author(s) +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg index af00bd0b7a..d9941b650d 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_welcome.svg @@ -19,253 +19,253 @@ font-weight: 700; } - .terminal-3664377378-matrix { + .terminal-2299823026-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3664377378-title { + .terminal-2299823026-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3664377378-r1 { fill: #c5c8c6 } -.terminal-3664377378-r2 { fill: #e3e3e3 } -.terminal-3664377378-r3 { fill: #989898 } -.terminal-3664377378-r4 { fill: #98e024 } -.terminal-3664377378-r5 { fill: #626262 } -.terminal-3664377378-r6 { fill: #9d65ff } -.terminal-3664377378-r7 { fill: #fd971f } -.terminal-3664377378-r8 { fill: #e1e1e1 } -.terminal-3664377378-r9 { fill: #4ebf71;font-weight: bold } -.terminal-3664377378-r10 { fill: #e1e1e1;text-decoration: underline; } -.terminal-3664377378-r11 { fill: #18954b } -.terminal-3664377378-r12 { fill: #e2e2e2 } -.terminal-3664377378-r13 { fill: #e2e2e2;text-decoration: underline; } -.terminal-3664377378-r14 { fill: #e2e2e2;font-weight: bold;font-style: italic; } -.terminal-3664377378-r15 { fill: #7ae998 } -.terminal-3664377378-r16 { fill: #008139 } -.terminal-3664377378-r17 { fill: #fea62b;font-weight: bold } -.terminal-3664377378-r18 { fill: #a7a9ab } -.terminal-3664377378-r19 { fill: #e2e3e3 } + .terminal-2299823026-r1 { fill: #c5c8c6 } +.terminal-2299823026-r2 { fill: #e3e3e3 } +.terminal-2299823026-r3 { fill: #989898 } +.terminal-2299823026-r4 { fill: #98e024 } +.terminal-2299823026-r5 { fill: #626262 } +.terminal-2299823026-r6 { fill: #9d65ff } +.terminal-2299823026-r7 { fill: #fd971f } +.terminal-2299823026-r8 { fill: #e1e1e1 } +.terminal-2299823026-r9 { fill: #4ebf71;font-weight: bold } +.terminal-2299823026-r10 { fill: #e1e1e1;text-decoration: underline; } +.terminal-2299823026-r11 { fill: #18954b } +.terminal-2299823026-r12 { fill: #e2e2e2 } +.terminal-2299823026-r13 { fill: #e2e2e2;text-decoration: underline; } +.terminal-2299823026-r14 { fill: #e2e2e2;font-weight: bold;font-style: italic; } +.terminal-2299823026-r15 { fill: #7ae998 } +.terminal-2299823026-r16 { fill: #008139 } +.terminal-2299823026-r17 { fill: #fea62b;font-weight: bold } +.terminal-2299823026-r18 { fill: #a7a9ab } +.terminal-2299823026-r19 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - -                                          ,--./,-. -          ___     __   __   __   ___     /,-._.--~\  -    |\ | |__  __ /  ` /  \ |__) |__         }  { -    | \| |       \__, \__/ |  \ |___     \`-._,-`-, -                                          `._,._,' - - - -Welcome to the nf-core pipeline creation wizard - -  This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. - -  The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    -  pipelines. - -💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with -the community as early as possible; ideally before you start on your pipeline! See the  -nf-core guidelines and the #new-pipelines Slack channel for more information. - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Let's go!  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - - - - - - - - - - - - - d Toggle dark mode  q Quit  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + +                                          ,--./,-. +          ___     __   __   __   ___     /,-._.--~\  +    |\ | |__  __ /  ` /  \ |__) |__         }  { +    | \| |       \__, \__/ |  \ |___     \`-._,-`-, +                                          `._,._,' + + + +Welcome to the nf-core pipeline creation wizard + +  This app will help you create a new Nextflow pipeline from the nf-core/tools pipeline template. + +  The template helps anyone benefit from nf-core best practices, and is a requirement for nf-core    +  pipelines. + +💡 If you want to add a pipeline to nf-core, please join on Slack and discuss your plans with +the community as early as possible; ideally before you start on your pipeline! See the  +nf-core guidelines and the #new-pipelines Slack channel for more information. + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Let's go!  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  From 3d673864958b799117f42a0f7ee9c60b581855d8 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 15 Oct 2024 16:55:08 +0200 Subject: [PATCH 25/30] add toggle all switch --- nf_core/pipelines/create/custompipeline.py | 18 ++++++++++++++++-- 1 file changed, 16 insertions(+), 2 deletions(-) diff --git a/nf_core/pipelines/create/custompipeline.py b/nf_core/pipelines/create/custompipeline.py index 5debcfee7f..e433db41ec 100644 --- a/nf_core/pipelines/create/custompipeline.py +++ b/nf_core/pipelines/create/custompipeline.py @@ -2,9 +2,9 @@ from textual import on from textual.app import ComposeResult -from textual.containers import Center, ScrollableContainer +from textual.containers import Center, Horizontal, ScrollableContainer from textual.screen import Screen -from textual.widgets import Button, Footer, Header, Markdown, Switch +from textual.widgets import Button, Footer, Header, Markdown, Static, Switch from nf_core.pipelines.create.utils import PipelineFeature @@ -22,7 +22,13 @@ def compose(self) -> ComposeResult: """ ) ) + yield Horizontal( + Switch(id="toggle_all", value=True), + Static("Toggle all features", classes="feature_title"), + classes="custom_grid", + ) yield ScrollableContainer(id="features") + yield Center( Button("Back", id="back", variant="default"), Button("Continue", id="continue", variant="success"), @@ -35,6 +41,7 @@ def on_mount(self) -> None: self.query_one("#features").mount( PipelineFeature(feature["help_text"], feature["short_description"], feature["description"], name) ) + self.query_one("#toggle_all", Switch).value = True @on(Button.Pressed, "#continue") def on_button_pressed(self, event: Button.Pressed) -> None: @@ -45,3 +52,10 @@ def on_button_pressed(self, event: Button.Pressed) -> None: if not this_switch.value: skip.append(this_switch.id) self.parent.TEMPLATE_CONFIG.__dict__.update({"skip_features": skip, "is_nfcore": False}) + + @on(Switch.Changed, "#toggle_all") + def on_toggle_all(self, event: Switch.Changed) -> None: + """Handle toggling all switches.""" + new_state = event.value + for feature in self.query("PipelineFeature"): + feature.query_one(Switch).value = new_state From 27c5e3b201c14d2e55e1b455d0909bd783ca8516 Mon Sep 17 00:00:00 2001 From: mashehu Date: Tue, 15 Oct 2024 16:57:09 +0200 Subject: [PATCH 26/30] update snapshots --- .../test_customisation_help.svg | 258 +++++++++--------- .../test_create_app/test_type_custom.svg | 255 ++++++++--------- .../test_type_nfcore_validation.svg | 255 ++++++++--------- 3 files changed, 385 insertions(+), 383 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg index f86647d785..07ab592d27 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_customisation_help.svg @@ -19,257 +19,257 @@ font-weight: 700; } - .terminal-1327302158-matrix { + .terminal-3477423502-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-1327302158-title { + .terminal-3477423502-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-1327302158-r1 { fill: #c5c8c6 } -.terminal-1327302158-r2 { fill: #e3e3e3 } -.terminal-1327302158-r3 { fill: #989898 } -.terminal-1327302158-r4 { fill: #e1e1e1 } -.terminal-1327302158-r5 { fill: #4ebf71;font-weight: bold } -.terminal-1327302158-r6 { fill: #1e1e1e } -.terminal-1327302158-r7 { fill: #507bb3 } -.terminal-1327302158-r8 { fill: #e2e2e2 } -.terminal-1327302158-r9 { fill: #808080 } -.terminal-1327302158-r10 { fill: #dde6ed;font-weight: bold } -.terminal-1327302158-r11 { fill: #001541 } -.terminal-1327302158-r12 { fill: #14191f } -.terminal-1327302158-r13 { fill: #0178d4 } -.terminal-1327302158-r14 { fill: #454a50 } -.terminal-1327302158-r15 { fill: #e2e3e3;font-weight: bold } -.terminal-1327302158-r16 { fill: #000000 } -.terminal-1327302158-r17 { fill: #e4e4e4 } -.terminal-1327302158-r18 { fill: #7ae998 } -.terminal-1327302158-r19 { fill: #0a180e;font-weight: bold } -.terminal-1327302158-r20 { fill: #008139 } -.terminal-1327302158-r21 { fill: #fea62b;font-weight: bold } -.terminal-1327302158-r22 { fill: #a7a9ab } -.terminal-1327302158-r23 { fill: #e2e3e3 } + .terminal-3477423502-r1 { fill: #c5c8c6 } +.terminal-3477423502-r2 { fill: #e3e3e3 } +.terminal-3477423502-r3 { fill: #989898 } +.terminal-3477423502-r4 { fill: #e1e1e1 } +.terminal-3477423502-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3477423502-r6 { fill: #1e1e1e } +.terminal-3477423502-r7 { fill: #e2e2e2 } +.terminal-3477423502-r8 { fill: #507bb3 } +.terminal-3477423502-r9 { fill: #808080 } +.terminal-3477423502-r10 { fill: #dde6ed;font-weight: bold } +.terminal-3477423502-r11 { fill: #001541 } +.terminal-3477423502-r12 { fill: #0178d4 } +.terminal-3477423502-r13 { fill: #454a50 } +.terminal-3477423502-r14 { fill: #e2e3e3;font-weight: bold } +.terminal-3477423502-r15 { fill: #000000 } +.terminal-3477423502-r16 { fill: #e4e4e4 } +.terminal-3477423502-r17 { fill: #14191f } +.terminal-3477423502-r18 { fill: #7ae998 } +.terminal-3477423502-r19 { fill: #0a180e;font-weight: bold } +.terminal-3477423502-r20 { fill: #008139 } +.terminal-3477423502-r21 { fill: #fea62b;font-weight: bold } +.terminal-3477423502-r22 { fill: #a7a9ab } +.terminal-3477423502-r23 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use a GitHub Create a GitHub  Show help  -▁▁▁▁▁▁▁▁        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add Github CI testsThe pipeline will  Show help  -▁▁▁▁▁▁▁▁include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI)  -testing▄▄ - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use reference genomesThe pipeline will be  Hide help  -▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most  -common reference  -genome files from  -iGenomes - - -Nf-core pipelines are configured to use a copy of the most common reference  -genome files. - -By selecting this option, your pipeline will include a configuration file  -specifying the paths to these files. - -The required code to use these files will also be included in the template.  -When the pipeline user provides an appropriate genome key, the pipeline will -automatically download the required reference files. -▅▅ -For more information about reference genomes in nf-core pipelines, see the  - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add Github badgesThe README.md file of  Show help  -▁▁▁▁▁▁▁▁the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▔▔▔▔▔▔▔▔ +        Toggle all features +▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use a GitHub Create a GitHub  Show help  +▁▁▁▁▁▁▁▁        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add Github CI testsThe pipeline will  Show help  +▁▁▁▁▁▁▁▁include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI)  +testing + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use reference genomesThe pipeline will be  Hide help  +▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + + +Nf-core pipelines are configured to use a copy of the most common reference  +genome files. + +By selecting this option, your pipeline will include a configuration file  +specifying the paths to these files. + +The required code to use these files will also be included in the template.  +When the pipeline user provides an appropriate genome key, the pipeline will +automatically download the required reference files. +▅▅ +For more information about reference genomes in nf-core pipelines, see the  + + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add Github badgesThe README.md file of  Show help  +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg index c8537c6d17..cff0309159 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_custom.svg @@ -19,255 +19,256 @@ font-weight: 700; } - .terminal-3873418736-matrix { + .terminal-829842075-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3873418736-title { + .terminal-829842075-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3873418736-r1 { fill: #c5c8c6 } -.terminal-3873418736-r2 { fill: #e3e3e3 } -.terminal-3873418736-r3 { fill: #989898 } -.terminal-3873418736-r4 { fill: #e1e1e1 } -.terminal-3873418736-r5 { fill: #4ebf71;font-weight: bold } -.terminal-3873418736-r6 { fill: #1e1e1e } -.terminal-3873418736-r7 { fill: #507bb3 } -.terminal-3873418736-r8 { fill: #e2e2e2 } -.terminal-3873418736-r9 { fill: #808080 } -.terminal-3873418736-r10 { fill: #dde6ed;font-weight: bold } -.terminal-3873418736-r11 { fill: #001541 } -.terminal-3873418736-r12 { fill: #14191f } -.terminal-3873418736-r13 { fill: #454a50 } -.terminal-3873418736-r14 { fill: #7ae998 } -.terminal-3873418736-r15 { fill: #e2e3e3;font-weight: bold } -.terminal-3873418736-r16 { fill: #0a180e;font-weight: bold } -.terminal-3873418736-r17 { fill: #000000 } -.terminal-3873418736-r18 { fill: #008139 } -.terminal-3873418736-r19 { fill: #fea62b;font-weight: bold } -.terminal-3873418736-r20 { fill: #a7a9ab } -.terminal-3873418736-r21 { fill: #e2e3e3 } + .terminal-829842075-r1 { fill: #c5c8c6 } +.terminal-829842075-r2 { fill: #e3e3e3 } +.terminal-829842075-r3 { fill: #989898 } +.terminal-829842075-r4 { fill: #e1e1e1 } +.terminal-829842075-r5 { fill: #4ebf71;font-weight: bold } +.terminal-829842075-r6 { fill: #1e1e1e } +.terminal-829842075-r7 { fill: #0178d4 } +.terminal-829842075-r8 { fill: #e2e2e2 } +.terminal-829842075-r9 { fill: #507bb3 } +.terminal-829842075-r10 { fill: #808080 } +.terminal-829842075-r11 { fill: #dde6ed;font-weight: bold } +.terminal-829842075-r12 { fill: #001541 } +.terminal-829842075-r13 { fill: #14191f } +.terminal-829842075-r14 { fill: #454a50 } +.terminal-829842075-r15 { fill: #7ae998 } +.terminal-829842075-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-829842075-r17 { fill: #0a180e;font-weight: bold } +.terminal-829842075-r18 { fill: #000000 } +.terminal-829842075-r19 { fill: #008139 } +.terminal-829842075-r20 { fill: #fea62b;font-weight: bold } +.terminal-829842075-r21 { fill: #a7a9ab } +.terminal-829842075-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Template features - - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use a GitHub Create a GitHub  Show help  -▁▁▁▁▁▁▁▁        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add Github CI testsThe pipeline will  Show help  -▁▁▁▁▁▁▁▁include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -actions for Continuous -Integration (CI)  -testing -▃▃ -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use reference genomesThe pipeline will be  Show help  -▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -copy of the most  -common reference  -genome files from  -iGenomes - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add Github badgesThe README.md file of  Show help  -▁▁▁▁▁▁▁▁the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -include GitHub badges - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Add configuration The pipeline will  Show help  -▁▁▁▁▁▁▁▁        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -profiles containing  -custom parameters  -requried to run  -nf-core pipelines at  -different institutions - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -        Use code lintersThe pipeline will  Show help  -▁▁▁▁▁▁▁▁include code linters ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -and CI tests to lint  -your code: pre-commit, -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Continue  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - d Toggle dark mode  q Quit  a Toggle all  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Template features + + +▔▔▔▔▔▔▔▔ +        Toggle all features +▁▁▁▁▁▁▁▁ +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use a GitHub Create a GitHub  Show help  +▁▁▁▁▁▁▁▁        repository.repository for the ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add Github CI testsThe pipeline will  Show help  +▁▁▁▁▁▁▁▁include several GitHub▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +actions for Continuous +Integration (CI) ▁▁ +testing + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use reference genomesThe pipeline will be  Show help  +▁▁▁▁▁▁▁▁configured to use a ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +copy of the most  +common reference  +genome files from  +iGenomes + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add Github badgesThe README.md file of  Show help  +▁▁▁▁▁▁▁▁the pipeline will ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +include GitHub badges + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Add configuration The pipeline will  Show help  +▁▁▁▁▁▁▁▁        filesinclude configuration ▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +profiles containing  +custom parameters  +requried to run  +nf-core pipelines at  +different institutions + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +        Use code lintersThe pipeline will  Show help  +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Continue  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + d Toggle dark mode  q Quit  a Toggle all  diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index fd6f2532c8..f99e463b3c 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,255 +19,256 @@ font-weight: 700; } - .terminal-3655041559-matrix { + .terminal-3014688925-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3655041559-title { + .terminal-3014688925-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3655041559-r1 { fill: #c5c8c6 } -.terminal-3655041559-r2 { fill: #e3e3e3 } -.terminal-3655041559-r3 { fill: #989898 } -.terminal-3655041559-r4 { fill: #e1e1e1 } -.terminal-3655041559-r5 { fill: #4ebf71;font-weight: bold } -.terminal-3655041559-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-3655041559-r7 { fill: #1e1e1e } -.terminal-3655041559-r8 { fill: #0f4e2a } -.terminal-3655041559-r9 { fill: #7b3042 } -.terminal-3655041559-r10 { fill: #a7a7a7 } -.terminal-3655041559-r11 { fill: #787878 } -.terminal-3655041559-r12 { fill: #e2e2e2 } -.terminal-3655041559-r13 { fill: #b93c5b } -.terminal-3655041559-r14 { fill: #454a50 } -.terminal-3655041559-r15 { fill: #7ae998 } -.terminal-3655041559-r16 { fill: #e2e3e3;font-weight: bold } -.terminal-3655041559-r17 { fill: #000000 } -.terminal-3655041559-r18 { fill: #008139 } -.terminal-3655041559-r19 { fill: #fea62b;font-weight: bold } -.terminal-3655041559-r20 { fill: #a7a9ab } -.terminal-3655041559-r21 { fill: #e2e3e3 } + .terminal-3014688925-r1 { fill: #c5c8c6 } +.terminal-3014688925-r2 { fill: #e3e3e3 } +.terminal-3014688925-r3 { fill: #989898 } +.terminal-3014688925-r4 { fill: #e1e1e1 } +.terminal-3014688925-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3014688925-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-3014688925-r7 { fill: #1e1e1e } +.terminal-3014688925-r8 { fill: #0f4e2a } +.terminal-3014688925-r9 { fill: #7b3042 } +.terminal-3014688925-r10 { fill: #a7a7a7 } +.terminal-3014688925-r11 { fill: #787878 } +.terminal-3014688925-r12 { fill: #e2e2e2 } +.terminal-3014688925-r13 { fill: #b93c5b } +.terminal-3014688925-r14 { fill: #454a50 } +.terminal-3014688925-r15 { fill: #166d39 } +.terminal-3014688925-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-3014688925-r17 { fill: #3c8b54;font-weight: bold } +.terminal-3014688925-r18 { fill: #000000 } +.terminal-3014688925-r19 { fill: #5aa86f } +.terminal-3014688925-r20 { fill: #fea62b;font-weight: bold } +.terminal-3014688925-r21 { fill: #a7a9ab } +.terminal-3014688925-r22 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Basic details - - - - -GitHub organisationWorkflow name - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -nf-core                                   Pipeline Name -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Must be lowercase without  -punctuation. - - - -A short description of your pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Description -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Author(s) -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +nf-core                                   Pipeline Name +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Must be lowercase without  +punctuation. + + + +A short description of your pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Description +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Author(s) +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  From 8379afd14ea4d66565a14f8873303fbfdc57d59c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Matthias=20H=C3=B6rtenhuber?= Date: Tue, 15 Oct 2024 15:35:23 +0000 Subject: [PATCH 27/30] update snapshots --- .../test_type_nfcore_validation.svg | 255 +++++++++--------- 1 file changed, 127 insertions(+), 128 deletions(-) diff --git a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg index f99e463b3c..fd6f2532c8 100644 --- a/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg +++ b/tests/pipelines/__snapshots__/test_create_app/test_type_nfcore_validation.svg @@ -19,256 +19,255 @@ font-weight: 700; } - .terminal-3014688925-matrix { + .terminal-3655041559-matrix { font-family: Fira Code, monospace; font-size: 20px; line-height: 24.4px; font-variant-east-asian: full-width; } - .terminal-3014688925-title { + .terminal-3655041559-title { font-size: 18px; font-weight: bold; font-family: arial; } - .terminal-3014688925-r1 { fill: #c5c8c6 } -.terminal-3014688925-r2 { fill: #e3e3e3 } -.terminal-3014688925-r3 { fill: #989898 } -.terminal-3014688925-r4 { fill: #e1e1e1 } -.terminal-3014688925-r5 { fill: #4ebf71;font-weight: bold } -.terminal-3014688925-r6 { fill: #a5a5a5;font-style: italic; } -.terminal-3014688925-r7 { fill: #1e1e1e } -.terminal-3014688925-r8 { fill: #0f4e2a } -.terminal-3014688925-r9 { fill: #7b3042 } -.terminal-3014688925-r10 { fill: #a7a7a7 } -.terminal-3014688925-r11 { fill: #787878 } -.terminal-3014688925-r12 { fill: #e2e2e2 } -.terminal-3014688925-r13 { fill: #b93c5b } -.terminal-3014688925-r14 { fill: #454a50 } -.terminal-3014688925-r15 { fill: #166d39 } -.terminal-3014688925-r16 { fill: #e2e3e3;font-weight: bold } -.terminal-3014688925-r17 { fill: #3c8b54;font-weight: bold } -.terminal-3014688925-r18 { fill: #000000 } -.terminal-3014688925-r19 { fill: #5aa86f } -.terminal-3014688925-r20 { fill: #fea62b;font-weight: bold } -.terminal-3014688925-r21 { fill: #a7a9ab } -.terminal-3014688925-r22 { fill: #e2e3e3 } + .terminal-3655041559-r1 { fill: #c5c8c6 } +.terminal-3655041559-r2 { fill: #e3e3e3 } +.terminal-3655041559-r3 { fill: #989898 } +.terminal-3655041559-r4 { fill: #e1e1e1 } +.terminal-3655041559-r5 { fill: #4ebf71;font-weight: bold } +.terminal-3655041559-r6 { fill: #a5a5a5;font-style: italic; } +.terminal-3655041559-r7 { fill: #1e1e1e } +.terminal-3655041559-r8 { fill: #0f4e2a } +.terminal-3655041559-r9 { fill: #7b3042 } +.terminal-3655041559-r10 { fill: #a7a7a7 } +.terminal-3655041559-r11 { fill: #787878 } +.terminal-3655041559-r12 { fill: #e2e2e2 } +.terminal-3655041559-r13 { fill: #b93c5b } +.terminal-3655041559-r14 { fill: #454a50 } +.terminal-3655041559-r15 { fill: #7ae998 } +.terminal-3655041559-r16 { fill: #e2e3e3;font-weight: bold } +.terminal-3655041559-r17 { fill: #000000 } +.terminal-3655041559-r18 { fill: #008139 } +.terminal-3655041559-r19 { fill: #fea62b;font-weight: bold } +.terminal-3655041559-r20 { fill: #a7a9ab } +.terminal-3655041559-r21 { fill: #e2e3e3 } - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - + - nf-core pipelines create + nf-core pipelines create - - - - nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… - - -Basic details - - - - -GitHub organisationWorkflow name - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -nf-core                                   Pipeline Name -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Must be lowercase without  -punctuation. - - - -A short description of your pipeline. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Description -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Cannot be left empty. - - - -Name of the main author / authors - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ -Author(s) -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ -Value error, Cannot be left empty. - -▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ - Back  Next  -▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ - - - - - - - - - - - - - d Toggle dark mode  q Quit  a Toggle all  + + + + nf-core pipelines create — Create a new pipeline with the nf-core pipeline templa… + + +Basic details + + + + +GitHub organisationWorkflow name + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +nf-core                                   Pipeline Name +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Must be lowercase without  +punctuation. + + + +A short description of your pipeline. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Description +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Cannot be left empty. + + + +Name of the main author / authors + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ +Author(s) +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ +Value error, Cannot be left empty. + +▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔▔ + Back  Next  +▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁▁ + + + + + + + + + + + + + d Toggle dark mode  q Quit  a Toggle all  From ff32ff114895e5858c1d825c30840b392db76518 Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 18 Oct 2024 07:31:41 +0000 Subject: [PATCH 28/30] chore(deps): update dependency prompt_toolkit to <=3.0.48 --- requirements.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/requirements.txt b/requirements.txt index f167a55804..b7f1c39cab 100644 --- a/requirements.txt +++ b/requirements.txt @@ -9,7 +9,7 @@ packaging pillow pdiff pre-commit -prompt_toolkit<=3.0.36 +prompt_toolkit<=3.0.48 pydantic>=2.2.1 pyyaml questionary>=2.0.1 From 5d56b43976a145b5a24f2a3a2572c3f638872e8c Mon Sep 17 00:00:00 2001 From: "renovate[bot]" <29139614+renovate[bot]@users.noreply.github.com> Date: Fri, 18 Oct 2024 07:31:47 +0000 Subject: [PATCH 29/30] chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 --- .pre-commit-config.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 67aa3204c4..f8b13439ea 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,6 +1,6 @@ repos: - repo: https://github.com/astral-sh/ruff-pre-commit - rev: v0.6.9 + rev: v0.7.0 hooks: - id: ruff # linter args: [--fix, --exit-non-zero-on-fix] # sort imports and fix From 09a47327466533f4cd87dce25116e0a82cd14927 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Fri, 18 Oct 2024 07:32:43 +0000 Subject: [PATCH 30/30] [automated] Update CHANGELOG.md --- CHANGELOG.md | 1 + 1 file changed, 1 insertion(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 364a079a70..3683b8f500 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -20,6 +20,7 @@ - Include .nf-core.yml in `nf-core pipelines bump-version` ([#3220](https://github.com/nf-core/tools/pull/3220)) - create: add shortcut to toggle all switches ([#3226](https://github.com/nf-core/tools/pull/3226)) +- chore(deps): update pre-commit hook astral-sh/ruff-pre-commit to v0.7.0 ([#3229](https://github.com/nf-core/tools/pull/3229)) ## [v3.0.2 - Titanium Tapir Patch](https://github.com/nf-core/tools/releases/tag/3.0.2) - [2024-10-11]