-
Notifications
You must be signed in to change notification settings - Fork 5
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Addition of `FF019` and `FF020` flags - New flag rule set `pulldownFfpeRulesFragment.lst` including FF019 and FF020 made
- Loading branch information
Showing
42 changed files
with
1,758 additions
and
592 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,16 +1,17 @@ | ||
| --- | ||
| ______________________________________________________________________ | ||
|
|
||
| name: Issue/Bug/Question | ||
| about: Includes checks | ||
| title: '' | ||
| labels: '' | ||
| assignees: '' | ||
|
|
||
| --- | ||
| ______________________________________________________________________ | ||
|
|
||
| Please ensure that you have check the following before raising a new issue: | ||
|
|
||
| * [README](https://github.com/cancerit/cgpPindel/blob/dev/README.md) | ||
| * [Wiki](https://github.com/cancerit/cgpPindel/wiki) | ||
| * Existing issues (closed too) before raising a new item | ||
| - [README](https://github.com/cancerit/cgpPindel/blob/dev/README.md) | ||
| - [Wiki](https://github.com/cancerit/cgpPindel/wiki) | ||
| - Existing issues (closed too) before raising a new item | ||
|
|
||
| Please provide as much information as possible. |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,93 @@ | ||
| header: | ||
| license: | ||
| spdx-id: AGPL-3.0-or-later | ||
| copyright-owner: Genome Research Ltd | ||
| content: | | ||
| Copyright (c) 2014-2021 Genome Research Ltd | ||
| Author: CASM/Cancer IT <[email protected]> | ||
| This file is part of cgpPindel. | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU Affero General Public License as | ||
| published by the Free Software Foundation, either version 3 of the | ||
| License, or (at your option) any later version. | ||
| This program is distributed in the hope that it will be useful, | ||
| but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| GNU Affero General Public License for more details. | ||
| You should have received a copy of the GNU Affero General Public License | ||
| along with this program. If not, see <https://www.gnu.org/licenses/>. | ||
| 1. The usage of a range of years within a copyright statement contained within | ||
| this distribution should be interpreted as being equivalent to a list of years | ||
| including the first and last year specified and all consecutive years between | ||
| them. For example, a copyright statement that reads ‘Copyright (c) 2005, 2007- | ||
| 2009, 2011-2012’ should be interpreted as being identical to a statement that | ||
| reads ‘Copyright (c) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright | ||
| statement that reads ‘Copyright (c) 2005-2012’ should be interpreted as being | ||
| identical to a statement that reads ‘Copyright (c) 2005, 2006, 2007, 2008, | ||
| 2009, 2010, 2011, 2012’. | ||
| pattern: | | ||
| Copyright \(c\) [-0-9]+ .+ | ||
| Author: .+ | ||
| This file is part of .+ | ||
| This program is free software: you can redistribute it and/or modify | ||
| it under the terms of the GNU Affero General Public License as | ||
| published by the Free Software Foundation, either version 3 of the | ||
| License, or \(at your option\) any later version. | ||
| You should have received a copy of the GNU Affero General Public License | ||
| along with this program. If not, see <https://www.gnu.org/licenses/>. | ||
| 1. The usage of a range of years within a copyright statement contained within | ||
| this distribution should be interpreted as being equivalent to a list of years | ||
| including the first and last year specified and all consecutive years between | ||
| them. For example, a copyright statement that reads ‘Copyright \(c\) 2005, 2007- | ||
| 2009, 2011-2012’ should be interpreted as being identical to a statement that | ||
| reads ‘Copyright \(c\) 2005, 2007, 2008, 2009, 2011, 2012’ and a copyright | ||
| statement that reads ‘Copyright \(c\) 2005-2012’ should be interpreted as being | ||
| identical to a statement that reads ‘Copyright \(c\) 2005, 2006, 2007, 2008, | ||
| 2009, 2010, 2011, 2012’. | ||
| paths: | ||
| - '**' | ||
|
|
||
| paths-ignore: | ||
| - '.circleci' | ||
| - '.coveragerc' | ||
| - '.dockerignore' | ||
| - '.gitignore' | ||
| - '.pre-commit-config.yaml' | ||
| - 'CHANGES.md' | ||
| - 'Dockerfile' | ||
| - 'LICENSE' | ||
| - 'pyproject.toml' | ||
| - 'README.md' | ||
| - '**/*.yaml' | ||
| - 'tests/data/**/*' | ||
| - '**/*.egg-info/PKG-INFO' | ||
| - '.pytest_cache/' | ||
| - 'build/' | ||
| - 'MANIFEST.in' | ||
| - 'tests/htmlcov/' | ||
| - '.eggs/' | ||
| - 'c++/*.cpp' # not ours, distributed via agreement | ||
| - 'perl/t/' | ||
| - 'perl/rules/' | ||
| - 'perl/pm_to_blib' | ||
| - 'perl/blib/' | ||
| - 'perl/MANIFEST*' | ||
| - 'perl/MYMETA*' | ||
| - '.github/' | ||
| - 'INSTALL' | ||
| - 'Makefile' | ||
|
|
||
| comment: on-failure |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,27 @@ | ||
| repos: | ||
| - repo: https://github.com/pre-commit/pre-commit-hooks | ||
| rev: v4.0.1 | ||
| hooks: | ||
| - id: check-added-large-files | ||
| args: ['--maxkb=3000'] | ||
| - id: check-ast | ||
| - id: check-executables-have-shebangs | ||
| - id: check-shebang-scripts-are-executable | ||
| - id: check-merge-conflict | ||
| - id: check-toml | ||
| - id: check-yaml | ||
| - id: detect-aws-credentials | ||
| args: [--allow-missing-credentials] | ||
| - id: detect-private-key | ||
| - id: end-of-file-fixer | ||
| - id: name-tests-test | ||
| - id: requirements-txt-fixer | ||
| - id: trailing-whitespace | ||
| - repo: https://github.com/executablebooks/mdformat | ||
| rev: 0.7.6 | ||
| hooks: | ||
| - id: mdformat | ||
| - repo: https://github.com/hadolint/hadolint | ||
| rev: v2.4.1 | ||
| hooks: | ||
| - id: hadolint-docker |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.