From 11253e759ca54841957eb05ec35ecdf8e39f954a Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 16 Feb 2023 14:27:41 +0100 Subject: [PATCH 1/5] add stale GHA in tools --- .github/workflows/stale.yml | 24 ++++++++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 .github/workflows/stale.yml diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml new file mode 100644 index 0000000000..8e121b39fa --- /dev/null +++ b/.github/workflows/stale.yml @@ -0,0 +1,24 @@ +name: "Close stale issues and stale PRs" +on: + schedule: + - cron: "30 1 * * 7" # Once a week + +jobs: + stale: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue is stale because it has been inactive for more than 30 days. More information is required. Remove stale label or comment or this will be closed in 20 days." + stale-pr-message: "This PR is stale because it has been open more than 45 days with no activity. Remove stale label or comment if it is still useful. In any case a PR will be automatically closed." + close-issue-message: "This issue was closed because it has been stalled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: ${{ secrets.GITHUB_TOKEN }} From 8cd4990f6f80fd93fe46836cb5edb384ac329008 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 16 Feb 2023 14:30:24 +0100 Subject: [PATCH 2/5] add stale action to pipeline template, not mandatory --- .../.github/workflows/stale.yml | 24 +++++++++++++++++++ 1 file changed, 24 insertions(+) create mode 100644 nf_core/pipeline-template/.github/workflows/stale.yml diff --git a/nf_core/pipeline-template/.github/workflows/stale.yml b/nf_core/pipeline-template/.github/workflows/stale.yml new file mode 100644 index 0000000000..8e121b39fa --- /dev/null +++ b/nf_core/pipeline-template/.github/workflows/stale.yml @@ -0,0 +1,24 @@ +name: "Close stale issues and stale PRs" +on: + schedule: + - cron: "30 1 * * 7" # Once a week + +jobs: + stale: + runs-on: ubuntu-latest + permissions: + issues: write + pull-requests: write + steps: + - uses: actions/stale@v7 + with: + stale-issue-message: "This issue is stale because it has been inactive for more than 30 days. More information is required. Remove stale label or comment or this will be closed in 20 days." + stale-pr-message: "This PR is stale because it has been open more than 45 days with no activity. Remove stale label or comment if it is still useful. In any case a PR will be automatically closed." + close-issue-message: "This issue was closed because it has been stalled for 20 days with no activity." + days-before-stale: 30 + days-before-close: 20 + days-before-pr-close: -1 + any-of-labels: "awaiting-changes,awaiting-feedback" + exempt-issue-labels: "WIP" + exempt-pr-labels: "WIP" + repo-token: ${{ secrets.GITHUB_TOKEN }} From 501931231f8c0c6e419d26593262daa273d4773e Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Thu, 16 Feb 2023 14:35:58 +0100 Subject: [PATCH 3/5] update changelog --- CHANGELOG.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/CHANGELOG.md b/CHANGELOG.md index 67e6ada896..f36e6b84ad 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -7,6 +7,7 @@ - Turn on automatic clean up of intermediate files in `work/` on successful pipeline completion in full-test config ([#2163](https://github.com/nf-core/tools/pull/2163)) [Contributed by @jfy133] - Add documentation to `usage.md` on how to use `params.yml` files, based on nf-core/ampliseq text ([#2173](https://github.com/nf-core/tools/pull/2173/)) [Contributed by @jfy133, @d4straub] - Make jobs automatically resubmit for a much wider range of exit codes (now `104` and `130..145`) ([#2170](https://github.com/nf-core/tools/pull/2170)) +- Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183)) ### Linting @@ -22,6 +23,7 @@ ### General - `nf-core modules/subworkflows info` now prints the include statement for the module/subworkflow ([#2182](https://github.com/nf-core/tools/pull/2182)). +- Add a stale GHA wich stale + close issues and stale PRs with specific labels ([#2183](https://github.com/nf-core/tools/pull/2183)) ## [v2.7.2 - Mercury Eagle Patch](https://github.com/nf-core/tools/releases/tag/2.7.2) - [2022-12-19] From a1645dacd369c04857051116aa4fc43a5b795319 Mon Sep 17 00:00:00 2001 From: mirpedrol Date: Fri, 17 Feb 2023 13:13:37 +0100 Subject: [PATCH 4/5] try fixing pytest GHA --- .github/workflows/pytest-frozen-ubuntu-20.04.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/.github/workflows/pytest-frozen-ubuntu-20.04.yml b/.github/workflows/pytest-frozen-ubuntu-20.04.yml index 6d49145ed7..b015376633 100644 --- a/.github/workflows/pytest-frozen-ubuntu-20.04.yml +++ b/.github/workflows/pytest-frozen-ubuntu-20.04.yml @@ -33,6 +33,7 @@ jobs: - name: Downgrade git to the Ubuntu official repository's version run: | + sudo apt update sudo apt remove git git-man sudo add-apt-repository --remove ppa:git-core/ppa sudo apt install git From 958a889265049625f1a0fd18c9e22a279bc90b26 Mon Sep 17 00:00:00 2001 From: nf-core-bot Date: Thu, 30 Mar 2023 07:46:00 +0000 Subject: [PATCH 5/5] [automated] Fix code linting --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 63bf235bc7..2fe09e80d2 100644 --- a/README.md +++ b/README.md @@ -612,7 +612,7 @@ The graphical interface is oganzised in groups and within the groups the single Now you can start to change the parameter itself. The `ID` of a new parameter should be defined in small letters without whitespaces. The description is a short free text explanation about the parameter, that appears if you run your pipeline with the `--help` flag. By clicking on the dictionary icon you can add a longer explanation for the parameter page of your pipeline. Usually, they contain a small paragraph about the parameter settings or a used datasource, like databases or references. If you want to specify some conditions for your parameter, like the file extension, you can use the nut icon to open the settings. This menu depends on the `type` you assigned to your parameter. For integers you can define a min and max value, and for strings the file extension can be specified. -The `type` field is one of the most important points in your pipeline schema, since it defines the datatype of your input and how it will be interpreted. This allows extensive testing prior to starting the pipeline. +The `type` field is one of the most important points in your pipeline schema, since it defines the datatype of your input and how it will be interpreted. This allows extensive testing prior to starting the pipeline. The basic datatypes for a pipeline schema are: @@ -621,7 +621,7 @@ The basic datatypes for a pipeline schema are: - `integer` - `boolean` -For the `string` type you have three different options in the settings (nut icon): `enumerated values`, `pattern` and `format`. The first option, `enumerated values`, allows you to specify a list of specific input values. The list has to be separated with a pipe. The `pattern` and `format` settings can depend on each other. The `format` has to be either a directory or a file path. Depending on the `format` setting selected, specifying the `pattern` setting can be the most efficient and time saving option, especially for `file paths`. The `number` and `integer` types share the same settings. Similarly to `string`, there is an `enumerated values` option with the possibility of specifying a `min` and `max` value. For the `boolean` there is no further settings and the default value is usually `false`. The `boolean` value can be switched to `true` by adding the flag to the command. This parameter type is often used to skip specific sections of a pipeline. +For the `string` type you have three different options in the settings (nut icon): `enumerated values`, `pattern` and `format`. The first option, `enumerated values`, allows you to specify a list of specific input values. The list has to be separated with a pipe. The `pattern` and `format` settings can depend on each other. The `format` has to be either a directory or a file path. Depending on the `format` setting selected, specifying the `pattern` setting can be the most efficient and time saving option, especially for `file paths`. The `number` and `integer` types share the same settings. Similarly to `string`, there is an `enumerated values` option with the possibility of specifying a `min` and `max` value. For the `boolean` there is no further settings and the default value is usually `false`. The `boolean` value can be switched to `true` by adding the flag to the command. This parameter type is often used to skip specific sections of a pipeline. After filling the schema, click on the `Finished` button in the top right corner, this will automatically update your `nextflow_schema.json`. If this is not working, the schema can be copied from the graphical interface and pasted in your `nextflow_schema.json` file.