diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json
deleted file mode 100644
index b290e09..0000000
--- a/.devcontainer/devcontainer.json
+++ /dev/null
@@ -1,20 +0,0 @@
-{
- "name": "nfcore",
- "image": "nfcore/gitpod:latest",
- "remoteUser": "gitpod",
- "runArgs": ["--privileged"],
-
- // Configure tool-specific properties.
- "customizations": {
- // Configure properties specific to VS Code.
- "vscode": {
- // Set *default* container specific settings.json values on container create.
- "settings": {
- "python.defaultInterpreterPath": "/opt/conda/bin/python"
- },
-
- // Add the IDs of extensions you want installed when the container is created.
- "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"]
- }
- }
-}
diff --git a/.editorconfig b/.editorconfig
deleted file mode 100644
index 72dda28..0000000
--- a/.editorconfig
+++ /dev/null
@@ -1,33 +0,0 @@
-root = true
-
-[*]
-charset = utf-8
-end_of_line = lf
-insert_final_newline = true
-trim_trailing_whitespace = true
-indent_size = 4
-indent_style = space
-
-[*.{md,yml,yaml,html,css,scss,js}]
-indent_size = 2
-
-# These files are edited and tested upstream in nf-core/modules
-[/modules/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-[/subworkflows/nf-core/**]
-charset = unset
-end_of_line = unset
-insert_final_newline = unset
-trim_trailing_whitespace = unset
-indent_style = unset
-
-[/assets/email*]
-indent_size = unset
-
-# ignore python and markdown
-[*.{py,md}]
-indent_style = unset
diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml
deleted file mode 100644
index 191fabd..0000000
--- a/.github/.dockstore.yml
+++ /dev/null
@@ -1,6 +0,0 @@
-# Dockstore config version, not pipeline version
-version: 1.2
-workflows:
- - subclass: nfl
- primaryDescriptorPath: /nextflow.config
- publish: True
diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md
index f270e63..9ee3f79 100644
--- a/.github/CONTRIBUTING.md
+++ b/.github/CONTRIBUTING.md
@@ -9,6 +9,9 @@ Please use the pre-filled template to save time.
However, don't be put off by this template - other more general issues and suggestions are welcome!
Contributions to the code are even more welcome ;)
+Since this repository is in construction, some of the points below might not apply yet (ex: tests, linter, naming conventions, versioning).
+Make sure to do the maximum possible. If you are not sure about current standards or need support, you can ask help on the [#bioinfo](https://cr-ste-justine.slack.com/archives/C074VMACUD9slack) slack channel.
+
## Contribution workflow
If you'd like to write some code for ferlab/postprocessing, the standard workflow is as follows:
@@ -17,7 +20,7 @@ If you'd like to write some code for ferlab/postprocessing, the standard workflo
2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [ferlab/postprocessing repository](https://github.com/ferlab/postprocessing) to your GitHub account
3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions)
4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10).
-5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged
+5. Submit a Pull Request against the main branch and wait for the code to be reviewed and merged
If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/).
@@ -48,13 +51,13 @@ Each `nf-core` pipeline should be set up with a minimal set of test-data.
If there are any failures then the automated tests fail.
These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code.
-## Patch
+## Hotfix
:warning: Only in the unlikely and regretful event of a release happening with a bug.
-- On your own fork, make a new branch `patch` based on `upstream/master`.
+- On your own fork, make a new branch `fix` based on `origin/main`.
- Fix the bug, and bump version (X.Y.Z+1).
-- A PR should be made on `master` from patch to directly this particular bug.
+- A PR should be made on `main` from fix to directly this particular bug.
## Pipeline contribution conventions
@@ -72,8 +75,7 @@ If you wish to contribute a new step, please use the following coding standards:
6. Add sanity checks and validation for all relevant parameters.
7. Perform local tests to validate that the new code works as expected.
8. If applicable, add a new test command in `.github/workflow/ci.yml`.
-9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module.
-10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`.
+9. Add a description of the output files if relevant to `docs/output.md`.
### Default values
@@ -102,17 +104,3 @@ If you are using a new feature from core Nextflow, you may bump the minimum requ
For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines).
-## GitHub Codespaces
-
-This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal.
-
-To get started:
-
-- Open the repo in [Codespaces](https://github.com/ferlab/postprocessing/codespaces)
-- Tools installed
- - nf-core
- - Nextflow
-
-Devcontainer specs:
-
-- [DevContainer config](.devcontainer/devcontainer.json)
diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md
index f0122c8..f96ab1f 100644
--- a/.github/PULL_REQUEST_TEMPLATE.md
+++ b/.github/PULL_REQUEST_TEMPLATE.md
@@ -4,10 +4,11 @@
Many thanks for contributing to ferlab/postprocessing!
Please fill in the appropriate checklist below (delete whatever is not relevant).
+Since this repository is in construction, some of the points below regarding tests and linter might not apply yet. Make sure
+to do the maximum possible. For now, the tests are performed manually. Add a description of your tests in your pull request.
+You can ask help on the [#bioinfo](https://cr-ste-justine.slack.com/archives/C074VMACUD9slack) channel.
These are the most common things requested on pull requests (PRs).
-Remember that PRs should be made against the dev branch, unless you're preparing a pipeline release.
-
Learn more about contributing: [CONTRIBUTING.md](https://github.com/ferlab/postprocessing/tree/master/.github/CONTRIBUTING.md)
-->
diff --git a/.github/workflows/clean-up.yml b/.github/workflows/clean-up.yml
deleted file mode 100644
index 0b6b1f2..0000000
--- a/.github/workflows/clean-up.yml
+++ /dev/null
@@ -1,24 +0,0 @@
-name: "Close user-tagged issues and PRs"
-on:
- schedule:
- - cron: "0 0 * * 0" # Once a week
-
-jobs:
- clean-up:
- runs-on: ubuntu-latest
- permissions:
- issues: write
- pull-requests: write
- steps:
- - uses: actions/stale@28ca1036281a5e5922ead5184a1bbf96e5fc984e # v9
- with:
- stale-issue-message: "This issue has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment otherwise this issue will be closed in 20 days."
- stale-pr-message: "This PR has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor. Remove stale label or add a comment if it is still useful."
- close-issue-message: "This issue was closed because it has been tagged as awaiting-changes or awaiting-feedback by an nf-core contributor and then staled 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: "${{ secrets.GITHUB_TOKEN }}"
diff --git a/.github/workflows/linting_comment.yml b/.github/workflows/linting_comment.yml
deleted file mode 100644
index 40acc23..0000000
--- a/.github/workflows/linting_comment.yml
+++ /dev/null
@@ -1,28 +0,0 @@
-name: nf-core linting comment
-# This workflow is triggered after the linting action is complete
-# It posts an automated comment to the PR, even if the PR is coming from a fork
-
-on:
- workflow_run:
- workflows: ["nf-core linting"]
-
-jobs:
- test:
- runs-on: ubuntu-latest
- steps:
- - name: Download lint results
- uses: dawidd6/action-download-artifact@09f2f74827fd3a8607589e5ad7f9398816f540fe # v3
- with:
- workflow: linting.yml
- workflow_conclusion: completed
-
- - name: Get PR number
- id: pr_number
- run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT
-
- - name: Post PR comment
- uses: marocchino/sticky-pull-request-comment@331f8f5b4215f0445d3c07b4967662a32a2d3e31 # v2
- with:
- GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
- number: ${{ steps.pr_number.outputs.pr_number }}
- path: linting-logs/lint_results.md
diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml
deleted file mode 100644
index 03ecfcf..0000000
--- a/.github/workflows/release-announcements.yml
+++ /dev/null
@@ -1,75 +0,0 @@
-name: release-announcements
-# Automatic release toot and tweet anouncements
-on:
- release:
- types: [published]
- workflow_dispatch:
-
-jobs:
- toot:
- runs-on: ubuntu-latest
- steps:
- - name: get topics and convert to hashtags
- id: get_topics
- run: |
- echo "topics=$(curl -s https://nf-co.re/pipelines.json | jq -r '.remote_workflows[] | select(.full_name == "${{ github.repository }}") | .topics[]' | awk '{print "#"$0}' | tr '\n' ' ')" >> $GITHUB_OUTPUT
-
- - uses: rzr/fediverse-action@master
- with:
- access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }}
- host: "mstdn.science" # custom host if not "mastodon.social" (default)
- # GitHub event payload
- # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release
- message: |
- Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
- Please see the changelog: ${{ github.event.release.html_url }}
-
- ${{ steps.get_topics.outputs.topics }} #nfcore #openscience #nextflow #bioinformatics
-
- send-tweet:
- runs-on: ubuntu-latest
-
- steps:
- - uses: actions/setup-python@82c7e631bb3cdc910f68e0081d67478d79c6982d # v5
- with:
- python-version: "3.10"
- - name: Install dependencies
- run: pip install tweepy==4.14.0
- - name: Send tweet
- shell: python
- run: |
- import os
- import tweepy
-
- client = tweepy.Client(
- access_token=os.getenv("TWITTER_ACCESS_TOKEN"),
- access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"),
- consumer_key=os.getenv("TWITTER_CONSUMER_KEY"),
- consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"),
- )
- tweet = os.getenv("TWEET")
- client.create_tweet(text=tweet)
- env:
- TWEET: |
- Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
- Please see the changelog: ${{ github.event.release.html_url }}
- TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }}
- TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }}
- TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }}
- TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }}
-
- bsky-post:
- runs-on: ubuntu-latest
- steps:
- - uses: zentered/bluesky-post-action@80dbe0a7697de18c15ad22f4619919ceb5ccf597 # v0.1.0
- with:
- post: |
- Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}!
-
- Please see the changelog: ${{ github.event.release.html_url }}
- env:
- BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }}
- BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }}
- #
diff --git a/.gitpod.yml b/.gitpod.yml
deleted file mode 100644
index 105a182..0000000
--- a/.gitpod.yml
+++ /dev/null
@@ -1,20 +0,0 @@
-image: nfcore/gitpod:latest
-tasks:
- - name: Update Nextflow and setup pre-commit
- command: |
- pre-commit install --install-hooks
- nextflow self-update
- - name: unset JAVA_TOOL_OPTIONS
- command: |
- unset JAVA_TOOL_OPTIONS
-
-vscode:
- extensions: # based on nf-core.nf-core-extensionpack
- - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code
- - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files
- - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar
- - mechatroner.rainbow-csv # Highlight columns in csv files in different colors
- # - nextflow.nextflow # Nextflow syntax highlighting
- - oderwat.indent-rainbow # Highlight indentation level
- - streetsidesoftware.code-spell-checker # Spelling checker for source code
- - charliermarsh.ruff # Code linter Ruff
diff --git a/.nf-core.yml b/.nf-core.yml
index 6bba344..257e8f2 100644
--- a/.nf-core.yml
+++ b/.nf-core.yml
@@ -7,12 +7,24 @@ lint:
- .github/ISSUE_TEMPLATE/config.yml
- .github/workflows/awstest.yml
- .github/workflows/awsfulltest.yml
+ - .github/workflows/linting_comment.yml
+ - .github/.dockstore.yml
+ - .editorconfig
+ - .prettierignore
+ - .prettierrc.yml
+ - LICENSE
+ - assets/email_template.html
+ - assets/email_template.txt
+ - assets/sendmail_template.txt
files_unchanged:
- CODE_OF_CONDUCT.md
- assets/nf-core-postprocessing_logo_light.png
- docs/images/nf-core-postprocessing_logo_light.png
- docs/images/nf-core-postprocessing_logo_dark.png
- .github/ISSUE_TEMPLATE/bug_report.yml
+ - .github/CONTRIBUTING.md
+ - .github/PULL_REQUEST_TEMPLATE.md
+ - .github/workflows/linting_comment.yml
multiqc_config:
- report_comment
nextflow_config:
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
deleted file mode 100644
index 4dc0f1d..0000000
--- a/.pre-commit-config.yaml
+++ /dev/null
@@ -1,13 +0,0 @@
-repos:
- - repo: https://github.com/pre-commit/mirrors-prettier
- rev: "v3.1.0"
- hooks:
- - id: prettier
- additional_dependencies:
- - prettier@3.2.5
-
- - repo: https://github.com/editorconfig-checker/editorconfig-checker.python
- rev: "2.7.3"
- hooks:
- - id: editorconfig-checker
- alias: ec
diff --git a/.prettierignore b/.prettierignore
deleted file mode 100644
index 437d763..0000000
--- a/.prettierignore
+++ /dev/null
@@ -1,12 +0,0 @@
-email_template.html
-adaptivecard.json
-slackreport.json
-.nextflow*
-work/
-data/
-results/
-.DS_Store
-testing/
-testing*
-*.pyc
-bin/
diff --git a/.prettierrc.yml b/.prettierrc.yml
deleted file mode 100644
index c81f9a7..0000000
--- a/.prettierrc.yml
+++ /dev/null
@@ -1 +0,0 @@
-printWidth: 120
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 48a82ea..81fb67f 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -21,4 +21,5 @@ Initial release of ferlab/postprocessing, created with the [nf-core](https://nf-
### `Removed`
[#1](https://github.com/FelixAntoineLeSieur/Post-processing-Pipeline/pull/1) Removed input_schema
[#2](https://github.com/FelixAntoineLeSieur/Post-processing-Pipeline/pull/2) Removed V1 format input. V2 is the only accepted format.
+[#5](https://github.com/Ferlab-Ste-Justine/Post-processing-Pipeline/pull/5) Removed many files related to workflows and email notifications
diff --git a/LICENSE b/LICENSE
deleted file mode 100644
index b90c546..0000000
--- a/LICENSE
+++ /dev/null
@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) Damien Geneste, David Morais, Felix-Antoine Le Sieur, Jeremy Costanza, Lysiane Bouchard
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
diff --git a/assets/email_template.html b/assets/email_template.html
deleted file mode 100644
index 7ec7cda..0000000
--- a/assets/email_template.html
+++ /dev/null
@@ -1,53 +0,0 @@
-
-
-
-
-
-
-
- ferlab/postprocessing Pipeline Report
-
-
-
-
-
-
-
ferlab/postprocessing ${version}
-
Run Name: $runName
-
-<% if (!success){
- out << """
-
-
ferlab/postprocessing execution completed unsuccessfully!
-
The exit status of the task that caused the workflow execution to fail was: $exitStatus.
-
The full error message was:
-
${errorReport}
-
- """
-} else {
- out << """
-
- ferlab/postprocessing execution completed successfully!
-
- """
-}
-%>
-
-
The workflow was completed at $dateComplete (duration: $duration)
-
The command used to launch the workflow was as follows:
-
$commandLine
-
-
Pipeline Configuration:
-
-
- <% out << summary.collect{ k,v -> "| $k | $v |
|---|
" }.join("\n") %>
-
-
-
-
ferlab/postprocessing
-
https://github.com/ferlab/postprocessing
-
-
Methods
- Data was processed using ferlab/postprocessing v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.
- The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:
- ${workflow.commandLine}
- ${tool_citations}
- References
-
- - Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. doi: 10.1038/nbt.3820
- - Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. doi: 10.1038/s41587-020-0439-x
- - Grüning, B., Dale, R., Sjödin, A., Chapman, B. A., Rowe, J., Tomkins-Tinch, C. H., Valieris, R., Köster, J., & Bioconda Team. (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature Methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7
- - da Veiga Leprevost, F., Grüning, B. A., Alves Aflitos, S., Röst, H. L., Uszkoreit, J., Barsnes, H., Vaudel, M., Moreno, P., Gatto, L., Weber, J., Bai, M., Jimenez, R. C., Sachsenberg, T., Pfeuffer, J., Vera Alvarez, R., Griss, J., Nesvizhskii, A. I., & Perez-Riverol, Y. (2017). BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics (Oxford, England), 33(16), 2580–2582. doi: 10.1093/bioinformatics/btx192
- ${tool_bibliography}
-
-
-
Notes:
-
- ${nodoi_text}
- - The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
- - You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
-
-