diff --git a/.devcontainer/devcontainer.json b/.devcontainer/devcontainer.json index ea27a58..4a9bc5c 100644 --- a/.devcontainer/devcontainer.json +++ b/.devcontainer/devcontainer.json @@ -2,6 +2,7 @@ "name": "nfcore", "image": "nfcore/gitpod:latest", "remoteUser": "gitpod", + "runArgs": ["--privileged"], // Configure tool-specific properties. "customizations": { @@ -17,11 +18,11 @@ "python.linting.flake8Path": "/opt/conda/bin/flake8", "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", - "python.linting.pylintPath": "/opt/conda/bin/pylint" + "python.linting.pylintPath": "/opt/conda/bin/pylint", }, // 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"] - } - } + "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"], + }, + }, } diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 048c967..8a17018 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -9,7 +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 ;) -> If you need help using or modifying nf-core/createpanelrefs then the best place to ask is on the nf-core Slack [#createpanelrefs](https://nfcore.slack.com/channels/createpanelrefs) channel ([join our Slack here](https://nf-co.re/join/slack)). +:::info +If you need help using or modifying nf-core/createpanelrefs then the best place to ask is on the nf-core Slack [#createpanelrefs](https://nfcore.slack.com/channels/createpanelrefs) channel ([join our Slack here](https://nf-co.re/join/slack)). +::: ## Contribution workflow @@ -25,6 +27,9 @@ If you're not used to this workflow with git, you can start with some [docs from ## Tests +You can optionally test your changes by running the pipeline locally. Then it is recommended to use the `debug` profile to +receive warnings about process selectors and other debug info. Example: `nextflow run . -profile debug,test,docker --outdir `. + When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 44f4971..7171a0f 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -19,6 +19,7 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/crea - [ ] If necessary, also make a PR on the nf-core/createpanelrefs _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). +- [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). - [ ] Usage Documentation in `docs/usage.md` is updated. - [ ] Output Documentation in `docs/output.md` is updated. - [ ] `CHANGELOG.md` is updated. diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index b4fad51..c0d9543 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -69,7 +69,7 @@ jobs: steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - uses: actions/cache@v3 with: diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index de2eba2..ecad004 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -13,7 +13,7 @@ jobs: runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 with: token: ${{ secrets.nf_core_bot_auth_token }} @@ -24,7 +24,7 @@ jobs: env: GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @prettier/plugin-php diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index 888cb4b..905c58e 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -14,9 +14,9 @@ jobs: EditorConfig: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install editorconfig-checker run: npm install -g editorconfig-checker @@ -27,9 +27,9 @@ jobs: Prettier: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - - uses: actions/setup-node@v3 + - uses: actions/setup-node@v4 - name: Install Prettier run: npm install -g prettier @@ -40,7 +40,7 @@ jobs: PythonBlack: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v3 + - uses: actions/checkout@v4 - name: Check code lints with Black uses: psf/black@stable @@ -71,14 +71,14 @@ jobs: runs-on: ubuntu-latest steps: - name: Check out pipeline code - uses: actions/checkout@v3 + uses: actions/checkout@v4 - name: Install Nextflow uses: nf-core/setup-nextflow@v1 - uses: actions/setup-python@v4 with: - python-version: "3.8" + python-version: "3.11" architecture: "x64" - name: Install dependencies diff --git a/.github/workflows/release-announcements.yml b/.github/workflows/release-announcements.yml new file mode 100644 index 0000000..6ad3392 --- /dev/null +++ b/.github/workflows/release-announcements.yml @@ -0,0 +1,68 @@ +name: release-announcements +# Automatic release toot and tweet anouncements +on: + release: + types: [published] + workflow_dispatch: + +jobs: + toot: + runs-on: ubuntu-latest + steps: + - 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 }} + + send-tweet: + runs-on: ubuntu-latest + + steps: + - uses: actions/setup-python@v4 + 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@v0.0.2 + 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 index 25488dc..acf7269 100644 --- a/.gitpod.yml +++ b/.gitpod.yml @@ -4,7 +4,9 @@ tasks: 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 - codezombiech.gitignore # Language support for .gitignore files diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index f4fd052..c089ec7 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,18 +1,20 @@ -# Code of Conduct at nf-core (v1.0) +# Code of Conduct at nf-core (v1.4) ## Our Pledge -In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: +In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: - Age +- Ability - Body size +- Caste - Familial status - Gender identity and expression - Geographical location - Level of experience - Nationality and national origins - Native language -- Physical and neurological ability +- Neurodiversity - Race or ethnicity - Religion - Sexual identity and orientation @@ -22,80 +24,133 @@ Please note that the list above is alphabetised and is therefore not ranked in a ## Preamble -> Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. +:::note +This Code of Conduct (CoC) has been drafted by Renuka Kudva, Cris Tuñí, and Michael Heuer, with input from the nf-core Core Team and Susanna Marquez from the nf-core community. "We", in this document, refers to the Safety Officers and members of the nf-core Core Team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will be amended periodically to keep it up-to-date. In case of any dispute, the most current version will apply. +::: -An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. +An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). + +Our Safety Officers are Saba Nafees, Cris Tuñí, and Michael Heuer. nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. -We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. +We have therefore adopted this CoC, which we require all members of our community and attendees of nf-core events to adhere to in all our workspaces at all times. Workspaces include, but are not limited to, Slack, meetings on Zoom, gather.town, YouTube live etc. -Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. +Our CoC will be strictly enforced and the nf-core team reserves the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. -We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. +We ask all members of our community to help maintain supportive and productive workspaces and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. -Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re +Questions, concerns, or ideas on what we can include? Contact members of the Safety Team on Slack or email safety [at] nf-co [dot] re. ## Our Responsibilities -The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. +Members of the Safety Team (the Safety Officers) are responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. -The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. +The Safety Team, in consultation with the nf-core core team, have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this CoC, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. -Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. +Members of the core team or the Safety Team who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and will be subject to the same actions as others in violation of the CoC. -## When are where does this Code of Conduct apply? +## When and where does this Code of Conduct apply? -Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: +Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events, such as hackathons, workshops, bytesize, and collaborative workspaces on gather.town. These guidelines include, but are not limited to, the following (listed alphabetically and therefore in no order of preference): - Communicating with an official project email address. - Communicating with community members within the nf-core Slack channel. - Participating in hackathons organised by nf-core (both online and in-person events). -- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. -- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. +- Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence, and on the nf-core gather.town workspace. +- Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, gather.town, Jitsi, YouTube live etc. - Representing nf-core on social media. This includes both official and personal accounts. ## nf-core cares 😊 -nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): +nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include, but are not limited to, the following (listed in alphabetical order): - Ask for consent before sharing another community member’s personal information (including photographs) on social media. - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. -- Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) +- Celebrate your accomplishments! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) - Focus on what is best for the team and the community. (When in doubt, ask) -- Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. +- Accept feedback, yet be unafraid to question, deliberate, and learn. - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) -- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) +- Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communication to be kind.**) - Take breaks when you feel like you need them. -- Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) +- Use welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack) ## nf-core frowns on 😕 -The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. +The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this CoC. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces: - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. - Spamming or trolling of individuals on social media. -- Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. -- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. +- Use of sexual or discriminatory imagery, comments, jokes, or unwelcome sexual attention. +- Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion, or work experience. ### Online Trolling -The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. +The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the risk of online trolling. This is unacceptable — reports of such behaviour will be taken very seriously and perpetrators will be excluded from activities immediately. -All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. +All community members are **required** to ask members of the group they are working with for explicit consent prior to taking screenshots of individuals during video calls. -## Procedures for Reporting CoC violations +## Procedures for reporting CoC violations If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). +You can reach out to members of the Safety Team (Saba Nafees, Cris Tuñí, and Michael Heuer) on Slack. Alternatively, contact a member of the nf-core core team [nf-core core team](https://nf-co.re/about), and they will forward your concerns to the Safety Team. + +Issues directly concerning members of the Core Team or the Safety Team will be dealt with by other members of the core team and the safety manager — possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson and details will be shared in due course. + +All reports will be handled with the utmost discretion and confidentiality. + +You can also report any CoC violations to safety [at] nf-co [dot] re. In your email report, please do your best to include: + +- Your contact information. +- Identifying information (e.g. names, nicknames, pseudonyms) of the participant who has violated the Code of Conduct. +- The behaviour that was in violation and the circumstances surrounding the incident. +- The approximate time of the behaviour (if different than the time the report was made). +- Other people involved in the incident, if applicable. +- If you believe the incident is ongoing. +- If there is a publicly available record (e.g. mailing list record, a screenshot). +- Any additional information. + +After you file a report, one or more members of our Safety Team will contact you to follow up on your report. + +## Who will read and handle reports + +All reports will be read and handled by the members of the Safety Team at nf-core. + +If members of the Safety Team are deemed to have a conflict of interest with a report, they will be required to recuse themselves as per our Code of Conduct and will not have access to any follow-ups. + +To keep this first report confidential from any of the Safety Team members, please submit your first report by direct messaging on Slack/direct email to any of the nf-core members you are comfortable disclosing the information to, and be explicit about which member(s) you do not consent to sharing the information with. + +## Reviewing reports + +After receiving the report, members of the Safety Team will review the incident report to determine whether immediate action is required, for example, whether there is immediate threat to participants’ safety. + +The Safety Team, in consultation with members of the nf-core core team, will assess the information to determine whether the report constitutes a Code of Conduct violation, for them to decide on a course of action. + +In the case of insufficient information, one or more members of the Safety Team may contact the reporter, the reportee, or any other attendees to obtain more information. -Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. +Once additional information is gathered, the Safety Team will collectively review and decide on the best course of action to take, if any. The Safety Team reserves the right to not act on a report. -All reports will be handled with utmost discretion and confidentially. +## Confidentiality + +All reports, and any additional information included, are only shared with the team of safety officers (and possibly members of the core team, in case the safety officer is in violation of the CoC). We will respect confidentiality requests for the purpose of protecting victims of abuse. + +We will not name harassment victims, beyond discussions between the safety officer and members of the nf-core team, without the explicit consent of the individuals involved. + +## Enforcement + +Actions taken by the nf-core’s Safety Team may include, but are not limited to: + +- Asking anyone to stop a behaviour. +- Asking anyone to leave the event and online spaces either temporarily, for the remainder of the event, or permanently. +- Removing access to the gather.town and Slack, either temporarily or permanently. +- Communicating to all participants to reinforce our expectations for conduct and remind what is unacceptable behaviour; this may be public for practical reasons. +- Communicating to all participants that an incident has taken place and how we will act or have acted — this may be for the purpose of letting event participants know we are aware of and dealing with the incident. +- Banning anyone from participating in nf-core-managed spaces, future events, and activities, either temporarily or permanently. +- No action. ## Attribution and Acknowledgements @@ -106,6 +161,22 @@ All reports will be handled with utmost discretion and confidentially. ## Changelog -### v1.0 - March 12th, 2021 +### v1.4 - February 8th, 2022 + +- Included a new member of the Safety Team. Corrected a typographical error in the text. + +### v1.3 - December 10th, 2021 + +- Added a statement that the CoC applies to nf-core gather.town workspaces. Corrected typographical errors in the text. + +### v1.2 - November 12th, 2021 + +- Removed information specific to reporting CoC violations at the Hackathon in October 2021. + +### v1.1 - October 14th, 2021 + +- Updated with names of new Safety Officers and specific information for the hackathon in October 2021. + +### v1.0 - March 15th, 2021 - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/README.md b/README.md index 5e94056..d360984 100644 --- a/README.md +++ b/README.md @@ -25,10 +25,8 @@ ## Usage -> **Note** -> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how -> to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) -> with `-profile test` before running the workflow on actual data. +> [!NOTE] +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. First, prepare a samplesheet with your input data that looks as follows: @@ -60,9 +58,8 @@ nextflow run nf-core/createpanelrefs \ --outdir ``` -> **Warning:** -> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those -> provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; +> [!WARNING] +> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; > see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). For more details and further functionality, please refer to the [usage documentation](https://nf-co.re/createpanelrefs/usage) and the [parameter documentation](https://nf-co.re/createpanelrefs/parameters). @@ -93,7 +90,8 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - + + An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index c7acb61..70e2e65 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,7 +1,7 @@ report_comment: > - This report has been generated by the nf-core/createpanelrefs + This report has been generated by the nf-core/createpanelrefs analysis pipeline. For information about how to interpret these results, please see the - documentation. + documentation. report_section_order: "nf-core-createpanelrefs-methods-description": order: -1000 diff --git a/assets/slackreport.json b/assets/slackreport.json index 663bd09..7badb7d 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "nf-core/createpanelrefs v${version} - ${runName}", + "author_name": "nf-core/createpanelrefs ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/conf/modules/base.config b/conf/modules/base.config index b4a9878..512da6e 100644 --- a/conf/modules/base.config +++ b/conf/modules/base.config @@ -26,4 +26,13 @@ process { ] } + withName: 'MULTIQC' { + ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + publishDir = [ + path: { "${params.outdir}/multiqc" }, + mode: params.publish_dir_mode, + saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + ] + } + } diff --git a/docs/output.md b/docs/output.md index e2cf332..f4fc045 100644 --- a/docs/output.md +++ b/docs/output.md @@ -35,7 +35,9 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) -> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. +:::note +The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. +::: ### GATK germlinecnvcaller @@ -82,6 +84,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. + - Parameters used by the pipeline run: `params.json`. diff --git a/docs/usage.md b/docs/usage.md index 91ff464..c2ac6a6 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -28,7 +28,7 @@ The pipeline will auto-detect whether a sample is aligned in bam/cram format usi A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 3 samples, where one sample, `SAMPLE_1` is missing its index file. -```console +```csv title="samplesheet.csv" sample,bam,bai SAMPLE_1,sample1.bam, SAMPLE_2,sample2.bam,sample2.bam.bai @@ -62,7 +62,9 @@ If you wish to repeatedly use the same parameters for multiple runs, rather than Pipeline settings can be provided in a `yaml` or `json` file via `-params-file `. -> ⚠️ Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +:::warning +Do not use `-c ` to specify parameters as this will result in errors. Custom config files specified with `-c` must only be used for [tuning process resource specifications](https://nf-co.re/docs/usage/configuration#tuning-workflow-resources), other infrastructural tweaks (such as output directories), or module arguments (args). +::: The above pipeline run specified with a params file in yaml format: @@ -99,7 +101,9 @@ This version number will be logged in reports when you run the pipeline, so that To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. -> 💡 If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. +:::tip +If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. +::: ## Workflow specific arguments @@ -134,7 +138,9 @@ process { ## Core Nextflow arguments -> **NB:** These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). +:::note +These options are part of Nextflow and use a _single_ hyphen (pipeline parameters use a double-hyphen). +::: ### `-profile` @@ -142,7 +148,9 @@ Use this parameter to choose a configuration profile. Profiles can give configur Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, Apptainer, Conda) - see below. -> We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. +:::info +We highly recommend the use of Docker or Singularity containers for full pipeline reproducibility, however when this is not possible, Conda is also supported. +::: The pipeline also dynamically loads configurations from [https://github.com/nf-core/configs](https://github.com/nf-core/configs) when it runs, making multiple config profiles for various institutional clusters available at run time. For more information and to see if your system is available in these configs please see the [nf-core/configs documentation](https://github.com/nf-core/configs#documentation). diff --git a/lib/NfcoreTemplate.groovy b/lib/NfcoreTemplate.groovy index 408951a..e248e4c 100755 --- a/lib/NfcoreTemplate.groovy +++ b/lib/NfcoreTemplate.groovy @@ -3,6 +3,8 @@ // import org.yaml.snakeyaml.Yaml +import groovy.json.JsonOutput +import nextflow.extension.FilesEx class NfcoreTemplate { @@ -140,12 +142,14 @@ class NfcoreTemplate { try { if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } // Try to send HTML e-mail using sendmail + def sendmail_tf = new File(workflow.launchDir.toString(), ".sendmail_tmp.html") + sendmail_tf.withWriter { w -> w << sendmail_html } [ 'sendmail', '-t' ].execute() << sendmail_html log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" } catch (all) { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] - if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { + if ( mqc_report != null && mqc_report.size() <= max_multiqc_email_size.toBytes() ) { mail_cmd += [ '-A', mqc_report ] } mail_cmd.execute() << email_html @@ -154,14 +158,16 @@ class NfcoreTemplate { } // Write summary e-mail HTML to a file - def output_d = new File("${params.outdir}/pipeline_info/") - if (!output_d.exists()) { - output_d.mkdirs() - } - def output_hf = new File(output_d, "pipeline_report.html") + def output_hf = new File(workflow.launchDir.toString(), ".pipeline_report.html") output_hf.withWriter { w -> w << email_html } - def output_tf = new File(output_d, "pipeline_report.txt") + FilesEx.copyTo(output_hf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.html"); + output_hf.delete() + + // Write summary e-mail TXT to a file + def output_tf = new File(workflow.launchDir.toString(), ".pipeline_report.txt") output_tf.withWriter { w -> w << email_txt } + FilesEx.copyTo(output_tf.toPath(), "${params.outdir}/pipeline_info/pipeline_report.txt"); + output_tf.delete() } // @@ -222,6 +228,20 @@ class NfcoreTemplate { } } + // + // Dump pipeline parameters in a json file + // + public static void dump_parameters(workflow, params) { + def timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') + def filename = "params_${timestamp}.json" + def temp_pf = new File(workflow.launchDir.toString(), ".${filename}") + def jsonStr = JsonOutput.toJson(params) + temp_pf.text = JsonOutput.prettyPrint(jsonStr) + + FilesEx.copyTo(temp_pf.toPath(), "${params.outdir}/pipeline_info/params_${timestamp}.json") + temp_pf.delete() + } + // // Print pipeline summary on completion // diff --git a/lib/WorkflowCreatepanelrefs.groovy b/lib/WorkflowCreatepanelrefs.groovy index 037c416..a8e2236 100755 --- a/lib/WorkflowCreatepanelrefs.groovy +++ b/lib/WorkflowCreatepanelrefs.groovy @@ -53,7 +53,7 @@ class WorkflowCreatepanelrefs { public static String toolCitationText(params) { - // TODO Optionally add in-text citation tools to this list. + // TODO nf-core: Optionally add in-text citation tools to this list. // Can use ternary operators to dynamically construct based conditions, e.g. params["run_xyz"] ? "Tool (Foo et al. 2023)" : "", // Uncomment function in methodsDescriptionText to render in MultiQC report def citation_text = [ diff --git a/modules.json b/modules.json index f1e9b78..8abdadf 100644 --- a/modules.json +++ b/modules.json @@ -7,67 +7,67 @@ "nf-core": { "cnvkit/batch": { "branch": "master", - "git_sha": "016397249f05f5af7b97e3ea8d64458a07df2928", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "gatk4/annotateintervals": { "branch": "master", - "git_sha": "016397249f05f5af7b97e3ea8d64458a07df2928", + "git_sha": "42ae163c3c6eb23646189c30c07a889ad39c9b0e", "installed_by": ["modules"] }, "gatk4/collectreadcounts": { "branch": "master", - "git_sha": "d25bf48327e86a7f737047a57ec264b90e22ce3d", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/determinegermlinecontigploidy": { "branch": "master", - "git_sha": "8c4542e5d421c4690cf1fa6ec729e9304763fdaf", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/filterintervals": { "branch": "master", - "git_sha": "016397249f05f5af7b97e3ea8d64458a07df2928", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/germlinecnvcaller": { "branch": "master", - "git_sha": "16bda00336e449b83d9b62abaa614f3880664ffb", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/intervallisttools": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "gatk4/preprocessintervals": { "branch": "master", - "git_sha": "1226419498a14d17f98d12d6488d333b0dbd0418", + "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5", "installed_by": ["modules"] }, "multiqc": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "8ec825f465b9c17f9d83000022995b4f7de6fe93", "installed_by": ["modules"] }, "picard/createsequencedictionary": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "20b0918591d4ba20047d7e13e5094bcceba81447", "installed_by": ["modules"] }, "samtools/faidx": { "branch": "master", - "git_sha": "fd742419940e01ba1c5ecb172c3e32ec840662fe", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] }, "samtools/index": { "branch": "master", - "git_sha": "911696ea0b62df80e900ef244d7867d177971f73", + "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c", "installed_by": ["modules"] } } diff --git a/modules/nf-core/cnvkit/batch/environment.yml b/modules/nf-core/cnvkit/batch/environment.yml new file mode 100644 index 0000000..a73ba50 --- /dev/null +++ b/modules/nf-core/cnvkit/batch/environment.yml @@ -0,0 +1,8 @@ +name: cnvkit_batch +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::cnvkit=0.9.10 + - bioconda::samtools=1.18 diff --git a/modules/nf-core/cnvkit/batch/main.nf b/modules/nf-core/cnvkit/batch/main.nf index 795053a..33a1dfa 100644 --- a/modules/nf-core/cnvkit/batch/main.nf +++ b/modules/nf-core/cnvkit/batch/main.nf @@ -2,10 +2,10 @@ process CNVKIT_BATCH { tag "$meta.id" label 'process_low' - conda "bioconda::cnvkit=0.9.10 bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' : - 'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:c94363856059151a2974dc501fb07a0360cc60a3-0' }" + 'https://depot.galaxyproject.org/singularity/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:f0ad4c1f9b5c0749c12c7a93277ad6f4319b6b72-0' : + 'biocontainers/mulled-v2-780d630a9bb6a0ff2e7b6f730906fd703e40e98f:f0ad4c1f9b5c0749c12c7a93277ad6f4319b6b72-0' }" input: tuple val(meta), path(tumor), path(normal) diff --git a/modules/nf-core/cnvkit/batch/meta.yml b/modules/nf-core/cnvkit/batch/meta.yml index 1543304..4f88ba3 100644 --- a/modules/nf-core/cnvkit/batch/meta.yml +++ b/modules/nf-core/cnvkit/batch/meta.yml @@ -62,7 +62,6 @@ input: type: file description: | Input reference cnn-file (only for germline and tumor-only running) - output: - meta: type: map @@ -97,7 +96,6 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@adamrtalbot" - "@drpatelh" @@ -108,3 +106,13 @@ authors: - "@MaxUlysse" - "@priesgo" - "@SusiJo" +maintainers: + - "@adamrtalbot" + - "@drpatelh" + - "@fbdtemme" + - "@kaurravneet4123" + - "@KevinMenden" + - "@lassefolkersen" + - "@MaxUlysse" + - "@priesgo" + - "@SusiJo" diff --git a/modules/nf-core/custom/dumpsoftwareversions/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml new file mode 100644 index 0000000..9b3272b --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -0,0 +1,7 @@ +name: custom_dumpsoftwareversions +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf index ebc8727..f218761 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/main.nf +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -2,10 +2,10 @@ process CUSTOM_DUMPSOFTWAREVERSIONS { label 'process_single' // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path versions diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml index c32657d..5f15a5f 100644 --- a/modules/nf-core/custom/dumpsoftwareversions/meta.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -1,4 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json name: custom_dumpsoftwareversions description: Custom module used to dump software versions within the nf-core pipeline template keywords: @@ -16,7 +16,6 @@ input: type: file description: YML file containing software versions pattern: "*.yml" - output: - yml: type: file @@ -30,7 +29,9 @@ output: type: file description: File containing software versions pattern: "versions.yml" - authors: - "@drpatelh" - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 0000000..b1e1630 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 0000000..5f59a93 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Should run without failures": { + "content": [ + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] + ], + "timestamp": "2024-01-09T23:01:18.710682" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 0000000..405aa24 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/gatk4/annotateintervals/environment.yml b/modules/nf-core/gatk4/annotateintervals/environment.yml new file mode 100644 index 0000000..6e91596 --- /dev/null +++ b/modules/nf-core/gatk4/annotateintervals/environment.yml @@ -0,0 +1,7 @@ +name: gatk4_annotateintervals +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/annotateintervals/main.nf b/modules/nf-core/gatk4/annotateintervals/main.nf index 8c5f59b..da7acd0 100644 --- a/modules/nf-core/gatk4/annotateintervals/main.nf +++ b/modules/nf-core/gatk4/annotateintervals/main.nf @@ -2,7 +2,7 @@ process GATK4_ANNOTATEINTERVALS { tag "$meta.id" label 'process_single' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" @@ -40,7 +40,8 @@ process GATK4_ANNOTATEINTERVALS { } """ - gatk --java-options "-Xmx${avail_mem}M" AnnotateIntervals \\ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + AnnotateIntervals \\ ${inputs} \\ --reference ${fasta} \\ --output ${prefix}.tsv \\ diff --git a/modules/nf-core/gatk4/annotateintervals/meta.yml b/modules/nf-core/gatk4/annotateintervals/meta.yml index 6f33e87..1c8e77f 100644 --- a/modules/nf-core/gatk4/annotateintervals/meta.yml +++ b/modules/nf-core/gatk4/annotateintervals/meta.yml @@ -1,11 +1,11 @@ name: "gatk4_annotateintervals" description: Annotates intervals with GC content, mappability, and segmental-duplication content keywords: - - gatk - annotateintervals - - intervals - - bed - annotation + - bed + - gatk4 + - intervals tools: - gatk4: description: | @@ -16,7 +16,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -92,7 +91,6 @@ input: type: file description: Optional - The index of the gzipped segmental-duplication track pattern: "*.bed.gz.tbi" - output: - meta: type: map @@ -107,6 +105,7 @@ output: type: file description: The output TSV file with a SAM-style header containing the annotated intervals pattern: "*.tsv" - authors: - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test new file mode 100644 index 0000000..8d411c6 --- /dev/null +++ b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test @@ -0,0 +1,186 @@ +nextflow_process { + + name "Test Process GATK4_ANNOTATEINTERVALS" + script "../main.nf" + process "GATK4_ANNOTATEINTERVALS" + config "./nextflow.config" + + tag "modules" + tag "modules_nfcore" + tag "gatk4" + tag "gatk4/annotateintervals" + + test("homo_sapiens genome [bed]") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + input[1] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] // fasta + input[2] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)] // fasta_fai + input[3] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] // dict + input[4] = [[:],[]] + input[5] = [[:],[]] + input[6] = [[:],[]] + input[7] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens genome multi-interval [bed]") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + [ + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true), + file(params.test_data['homo_sapiens']['genome']['genome_multi_interval_bed'], checkIfExists: true) + ] + ] + input[1] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] // fasta + input[2] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)] // fasta_fai + input[3] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] // dict + input[4] = [[:],[]] + input[5] = [[:],[]] + input[6] = [[:],[]] + input[7] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens genome [interval_list]") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true) + ] + input[1] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] // fasta + input[2] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)] // fasta_fai + input[3] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] // dict + input[4] = [[:],[]] + input[5] = [[:],[]] + input[6] = [[:],[]] + input[7] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens genome [interval_list] mappable_regions") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true) + ] + input[1] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] // fasta + input[2] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)] // fasta_fai + input[3] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] // dict + input[4] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)] // mappable_regions + input[5] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)] // mappable_regions_tbi + input[6] = [[:],[]] + input[7] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens genome [interval_list] duplication_regions") { + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_interval_list'], checkIfExists: true) + ] + input[1] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] // fasta + input[2] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)] // fasta_fai + input[3] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] // dict + input[4] = [[:],[]] + input[5] = [[:],[]] + input[6] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_bed_gz'], checkIfExists: true)] // segmental_duplication_regions + input[7] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_bed_gz_tbi'], checkIfExists: true)] // segmental_duplication_regions_tbi + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("homo_sapiens genome [bed] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = [ + [ id:'test', single_end:false ], // meta map + file(params.test_data['homo_sapiens']['genome']['genome_bed'], checkIfExists: true) + ] + input[1] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta'], checkIfExists: true)] // fasta + input[2] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_fasta_fai'], checkIfExists: true)] // fasta_fai + input[3] = [[:], file(params.test_data['homo_sapiens']['genome']['genome_dict'], checkIfExists: true)] // dict + input[4] = [[:],[]] + input[5] = [[:],[]] + input[6] = [[:],[]] + input[7] = [[:],[]] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.annotated_intervals.collect { file(it[1]).getName() } + + process.out.versions).match() } + ) + } + } +} diff --git a/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap new file mode 100644 index 0000000..16f81c3 --- /dev/null +++ b/modules/nf-core/gatk4/annotateintervals/tests/main.nf.test.snap @@ -0,0 +1,166 @@ +{ + "homo_sapiens genome [bed]": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,abf7cef9157e2b3c4554f48475f1b7a1" + ] + ], + "1": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ], + "annotated_intervals": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,abf7cef9157e2b3c4554f48475f1b7a1" + ] + ], + "versions": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ] + } + ], + "timestamp": "2023-12-31T01:23:13.232383464" + }, + "homo_sapiens genome [interval_list]": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,abf7cef9157e2b3c4554f48475f1b7a1" + ] + ], + "1": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ], + "annotated_intervals": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,abf7cef9157e2b3c4554f48475f1b7a1" + ] + ], + "versions": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ] + } + ], + "timestamp": "2023-12-31T01:23:44.26211215" + }, + "homo_sapiens genome multi-interval [bed]": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,abf7cef9157e2b3c4554f48475f1b7a1" + ] + ], + "1": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ], + "annotated_intervals": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,abf7cef9157e2b3c4554f48475f1b7a1" + ] + ], + "versions": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ] + } + ], + "timestamp": "2023-12-31T01:23:28.481436232" + }, + "homo_sapiens genome [interval_list] mappable_regions": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,428d33a03f2887e267d1cb6f0351bf9d" + ] + ], + "1": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ], + "annotated_intervals": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,428d33a03f2887e267d1cb6f0351bf9d" + ] + ], + "versions": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ] + } + ], + "timestamp": "2023-12-31T01:24:00.492783484" + }, + "homo_sapiens genome [bed] - stub": { + "content": [ + [ + "test.tsv", + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ] + ], + "timestamp": "2023-12-31T01:24:29.485750561" + }, + "homo_sapiens genome [interval_list] duplication_regions": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,0c59e93cc6e35ca14d3d25ef885156f8" + ] + ], + "1": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ], + "annotated_intervals": [ + [ + { + "id": "test", + "single_end": false + }, + "test.tsv:md5,0c59e93cc6e35ca14d3d25ef885156f8" + ] + ], + "versions": [ + "versions.yml:md5,e8bc10e7a98c24f21dd84b52f6e09d79" + ] + } + ], + "timestamp": "2023-12-31T01:24:15.933897396" + } +} \ No newline at end of file diff --git a/modules/nf-core/gatk4/annotateintervals/tests/nextflow.config b/modules/nf-core/gatk4/annotateintervals/tests/nextflow.config new file mode 100644 index 0000000..d92c94a --- /dev/null +++ b/modules/nf-core/gatk4/annotateintervals/tests/nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: GATK4_ANNOTATEINTERVALS { + ext.args = "--interval-merging-rule OVERLAPPING_ONLY" + } + +} diff --git a/modules/nf-core/gatk4/annotateintervals/tests/tags.yml b/modules/nf-core/gatk4/annotateintervals/tests/tags.yml new file mode 100644 index 0000000..74cc19b --- /dev/null +++ b/modules/nf-core/gatk4/annotateintervals/tests/tags.yml @@ -0,0 +1,2 @@ +gatk4/annotateintervals: + - "modules/nf-core/gatk4/annotateintervals/**" diff --git a/modules/nf-core/gatk4/collectreadcounts/environment.yml b/modules/nf-core/gatk4/collectreadcounts/environment.yml new file mode 100644 index 0000000..ebc8380 --- /dev/null +++ b/modules/nf-core/gatk4/collectreadcounts/environment.yml @@ -0,0 +1,7 @@ +name: gatk4_collectreadcounts +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/collectreadcounts/main.nf b/modules/nf-core/gatk4/collectreadcounts/main.nf index ce1985b..1cc3694 100644 --- a/modules/nf-core/gatk4/collectreadcounts/main.nf +++ b/modules/nf-core/gatk4/collectreadcounts/main.nf @@ -2,7 +2,7 @@ process GATK4_COLLECTREADCOUNTS { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" @@ -37,7 +37,8 @@ process GATK4_COLLECTREADCOUNTS { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}M" CollectReadCounts \\ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + CollectReadCounts \\ --input $input \\ --intervals $intervals \\ --output ${prefix}.$extension \\ diff --git a/modules/nf-core/gatk4/collectreadcounts/meta.yml b/modules/nf-core/gatk4/collectreadcounts/meta.yml index 938011c..25fb8b8 100644 --- a/modules/nf-core/gatk4/collectreadcounts/meta.yml +++ b/modules/nf-core/gatk4/collectreadcounts/meta.yml @@ -1,23 +1,18 @@ name: "gatk4_collectreadcounts" description: Collects read counts at specified intervals. The count for each interval is calculated by counting the number of read starts that lie in the interval. keywords: + - collectreadcounts - bam - cram - - CollectReadCounts - - gatk - gatk4 tools: - gatk4: - description: - Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + description: Genome Analysis Toolkit (GATK4). Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360037593911-CombineGVCFs tool_dev_url: https://github.com/broadinstitute/gatk doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -63,7 +58,6 @@ input: type: file description: Optional - Sequence dictionary of the reference FASTA file pattern: "*.dict" - output: - meta: type: map @@ -82,6 +76,7 @@ output: type: file description: The read counts in TSV format pattern: "*.tsv" - authors: - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml new file mode 100644 index 0000000..c30de09 --- /dev/null +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/environment.yml @@ -0,0 +1,5 @@ +name: gatk4_determinegermlinecontigploidy +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf index 3c21e74..5af101f 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/main.nf @@ -39,7 +39,8 @@ process GATK4_DETERMINEGERMLINECONTIGPLOIDY { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}M" DetermineGermlineContigPloidy \\ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + DetermineGermlineContigPloidy \\ ${input_list} \\ --output ./ \\ --output-prefix ${prefix} \\ diff --git a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml index 667d622..56eb408 100644 --- a/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml +++ b/modules/nf-core/gatk4/determinegermlinecontigploidy/meta.yml @@ -1,10 +1,10 @@ name: "gatk4_determinegermlinecontigploidy" description: Determines the baseline contig ploidy for germline samples given counts data keywords: - - gatk4 - - determinegermlinecontigploidy - - counts - copy number + - counts + - determinegermlinecontigploidy + - gatk4 tools: - gatk4: description: | @@ -15,7 +15,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map @@ -49,7 +48,6 @@ input: Optional - A folder containing the ploidy model. When a model is supplied to tool will run in CASE mode. pattern: '*-model/' - output: - meta: type: map @@ -70,6 +68,7 @@ output: A folder containing the model from the input files. This will only be created in COHORT mode (when no model is supplied to the process). pattern: "*-model/" - authors: - "@nvnieuwk" +maintainers: + - "@nvnieuwk" diff --git a/modules/nf-core/gatk4/filterintervals/environment.yml b/modules/nf-core/gatk4/filterintervals/environment.yml new file mode 100644 index 0000000..a1d59f2 --- /dev/null +++ b/modules/nf-core/gatk4/filterintervals/environment.yml @@ -0,0 +1,7 @@ +name: gatk4_filterintervals +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/filterintervals/main.nf b/modules/nf-core/gatk4/filterintervals/main.nf index 5032fa3..a6d4702 100644 --- a/modules/nf-core/gatk4/filterintervals/main.nf +++ b/modules/nf-core/gatk4/filterintervals/main.nf @@ -2,7 +2,7 @@ process GATK4_FILTERINTERVALS { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" @@ -32,12 +32,13 @@ process GATK4_FILTERINTERVALS { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}M" FilterIntervals \\ - $annotated_command \\ - $read_counts_command \\ - --intervals $intervals \\ - --output ${prefix}.interval_list \\ - $args + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + FilterIntervals \\ + $annotated_command \\ + $read_counts_command \\ + --intervals $intervals \\ + --output ${prefix}.interval_list \\ + $args cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-core/gatk4/filterintervals/meta.yml b/modules/nf-core/gatk4/filterintervals/meta.yml index b253d78..425c001 100644 --- a/modules/nf-core/gatk4/filterintervals/meta.yml +++ b/modules/nf-core/gatk4/filterintervals/meta.yml @@ -1,20 +1,16 @@ name: "gatk4_filterintervals" description: Filters intervals based on annotations and/or count statistics. keywords: + - filterintervals - gatk4 - interval_list - - filterintervals tools: - "gatk4": - description: - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] - input: - meta: type: map @@ -43,7 +39,6 @@ input: type: file description: Annotated intervals TSV file (annotated_intervals.tsv). pattern: "*.tsv" - output: - meta: type: map @@ -58,7 +53,9 @@ output: type: file description: Filtered interval list file pattern: "*.interval_list" - authors: - "@ryanjameskennedy" - "@ViktorHy" +maintainers: + - "@ryanjameskennedy" + - "@ViktorHy" diff --git a/modules/nf-core/gatk4/germlinecnvcaller/environment.yml b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml new file mode 100644 index 0000000..02ce4dd --- /dev/null +++ b/modules/nf-core/gatk4/germlinecnvcaller/environment.yml @@ -0,0 +1,5 @@ +name: gatk4_germlinecnvcaller +channels: + - conda-forge + - bioconda + - defaults diff --git a/modules/nf-core/gatk4/germlinecnvcaller/main.nf b/modules/nf-core/gatk4/germlinecnvcaller/main.nf index fed285c..f42ceb6 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/main.nf +++ b/modules/nf-core/gatk4/germlinecnvcaller/main.nf @@ -37,7 +37,8 @@ process GATK4_GERMLINECNVCALLER { avail_mem = (task.memory.mega*0.8).intValue() } """ - gatk --java-options "-Xmx${avail_mem}g" GermlineCNVCaller \\ + gatk --java-options "-Xmx${avail_mem}g -XX:-UsePerfData" \\ + GermlineCNVCaller \\ $input_list \\ $ploidy_command \\ $output_command \\ diff --git a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml index 36cd527..d4715ff 100644 --- a/modules/nf-core/gatk4/germlinecnvcaller/meta.yml +++ b/modules/nf-core/gatk4/germlinecnvcaller/meta.yml @@ -2,19 +2,15 @@ name: "gatk4_germlinecnvcaller" description: Calls copy-number variants in germline samples given their counts and the output of DetermineGermlineContigPloidy. keywords: - gatk - - gatk4_germlinecnvcaller - germline contig ploidy + - germlinecnvcaller tools: - "gatk4": - description: - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] - input: - meta: type: map @@ -37,7 +33,6 @@ input: type: directory description: Directory containing ploidy calls produced by determinegermlinecontigploidy case or cohort mode pattern: "*-calls" - output: - meta: type: map @@ -60,7 +55,9 @@ output: type: directory description: Tar gzipped directory containing calls produced by germlinecnvcaller case mode pattern: "*-cnv-calls/*-calls" - authors: - "@ryanjameskennedy" - "@ViktorHy" +maintainers: + - "@ryanjameskennedy" + - "@ViktorHy" diff --git a/modules/nf-core/gatk4/intervallisttools/environment.yml b/modules/nf-core/gatk4/intervallisttools/environment.yml new file mode 100644 index 0000000..b70e5e1 --- /dev/null +++ b/modules/nf-core/gatk4/intervallisttools/environment.yml @@ -0,0 +1,7 @@ +name: gatk4_intervallisttools +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/intervallisttools/main.nf b/modules/nf-core/gatk4/intervallisttools/main.nf index 0054659..10baa75 100644 --- a/modules/nf-core/gatk4/intervallisttools/main.nf +++ b/modules/nf-core/gatk4/intervallisttools/main.nf @@ -2,7 +2,7 @@ process GATK4_INTERVALLISTTOOLS { tag "$meta.id" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" @@ -31,7 +31,8 @@ process GATK4_INTERVALLISTTOOLS { mkdir ${prefix}_split - gatk --java-options "-Xmx${avail_mem}M" IntervalListTools \\ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + IntervalListTools \\ --INPUT $intervals \\ --OUTPUT ${prefix}_split \\ --TMP_DIR . \\ diff --git a/modules/nf-core/gatk4/intervallisttools/meta.yml b/modules/nf-core/gatk4/intervallisttools/meta.yml index 804645f..748dccf 100644 --- a/modules/nf-core/gatk4/intervallisttools/meta.yml +++ b/modules/nf-core/gatk4/intervallisttools/meta.yml @@ -1,10 +1,10 @@ name: gatk4_intervallisttools - description: Splits the interval list file into unique, equally-sized interval files and place it under a directory keywords: - - sort - bed - - interval list + - gatk4 + - interval_list + - sort tools: - gatk4: description: | @@ -15,19 +15,16 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: 10.1158/1538-7445.AM2017-3590 licence: ["Apache-2.0"] - input: - meta: type: map description: | Groovy Map containing sample information e.g. [ id:'test', single_end:false ] - - interval_list: type: file description: Interval list file pattern: "*.interval_list" - output: - meta: type: map @@ -42,6 +39,7 @@ output: type: file description: Interval list files pattern: "*.interval_list" - authors: - "@praveenraj2018" +maintainers: + - "@praveenraj2018" diff --git a/modules/nf-core/gatk4/preprocessintervals/environment.yml b/modules/nf-core/gatk4/preprocessintervals/environment.yml new file mode 100644 index 0000000..542d9ef --- /dev/null +++ b/modules/nf-core/gatk4/preprocessintervals/environment.yml @@ -0,0 +1,7 @@ +name: gatk4_preprocessintervals +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::gatk4=4.4.0.0 diff --git a/modules/nf-core/gatk4/preprocessintervals/main.nf b/modules/nf-core/gatk4/preprocessintervals/main.nf index aff482f..61b281d 100644 --- a/modules/nf-core/gatk4/preprocessintervals/main.nf +++ b/modules/nf-core/gatk4/preprocessintervals/main.nf @@ -2,7 +2,7 @@ process GATK4_PREPROCESSINTERVALS { tag "$fasta" label 'process_medium' - conda "bioconda::gatk4=4.4.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://depot.galaxyproject.org/singularity/gatk4:4.4.0.0--py36hdfd78af_0': 'biocontainers/gatk4:4.4.0.0--py36hdfd78af_0' }" @@ -35,7 +35,8 @@ process GATK4_PREPROCESSINTERVALS { } """ - gatk --java-options "-Xmx${avail_mem}M" PreprocessIntervals \\ + gatk --java-options "-Xmx${avail_mem}M -XX:-UsePerfData" \\ + PreprocessIntervals \\ $include_command \\ $exclude_command \\ --reference $fasta \\ diff --git a/modules/nf-core/gatk4/preprocessintervals/meta.yml b/modules/nf-core/gatk4/preprocessintervals/meta.yml index 8b6ae9b..cf3f6ac 100644 --- a/modules/nf-core/gatk4/preprocessintervals/meta.yml +++ b/modules/nf-core/gatk4/preprocessintervals/meta.yml @@ -1,21 +1,17 @@ name: "gatk4_preprocessintervals" description: Prepares bins for coverage collection. keywords: + - bed - gatk4 - - preprocessintervals - interval - - bed + - preprocessintervals tools: - "gatk4": - description: - Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools - with a primary focus on variant discovery and genotyping. Its powerful processing engine - and high-performance computing features make it capable of taking on projects of any size. + description: Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. homepage: https://gatk.broadinstitute.org/hc/en-us documentation: https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s doi: "10.1158/1538-7445.AM2017-3590" licence: ["Apache-2.0"] - input: - meta: type: map @@ -62,7 +58,6 @@ input: type: file description: Interval file (bed or interval_list) with the genomic regions to be excluded from the analysis (optional) pattern: "*.{bed,interval_list}" - output: - meta: type: map @@ -77,8 +72,11 @@ output: type: file description: Processed interval list file pattern: "*.{bed,interval_list}" - authors: - "@ryanjameskennedy" - "@ViktorHy" - "@ramprasadn" +maintainers: + - "@ryanjameskennedy" + - "@ViktorHy" + - "@ramprasadn" diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml new file mode 100644 index 0000000..7625b75 --- /dev/null +++ b/modules/nf-core/multiqc/environment.yml @@ -0,0 +1,7 @@ +name: multiqc +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::multiqc=1.19 diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf index 1fc387b..1b9f7c4 100644 --- a/modules/nf-core/multiqc/main.nf +++ b/modules/nf-core/multiqc/main.nf @@ -1,10 +1,10 @@ process MULTIQC { label 'process_single' - conda "bioconda::multiqc=1.14" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.14--pyhdfd78af_0' : - 'biocontainers/multiqc:1.14--pyhdfd78af_0' }" + 'https://depot.galaxyproject.org/singularity/multiqc:1.19--pyhdfd78af_0' : + 'biocontainers/multiqc:1.19--pyhdfd78af_0' }" input: path multiqc_files, stageAs: "?/*" @@ -25,12 +25,14 @@ process MULTIQC { def args = task.ext.args ?: '' def config = multiqc_config ? "--config $multiqc_config" : '' def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' + def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' """ multiqc \\ --force \\ $args \\ $config \\ $extra_config \\ + $logo \\ . cat <<-END_VERSIONS > versions.yml @@ -41,7 +43,7 @@ process MULTIQC { stub: """ - touch multiqc_data + mkdir multiqc_data touch multiqc_plots touch multiqc_report.html diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml index f93b5ee..45a9bc3 100644 --- a/modules/nf-core/multiqc/meta.yml +++ b/modules/nf-core/multiqc/meta.yml @@ -1,5 +1,4 @@ -# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/yaml-schema.json -name: MultiQC +name: multiqc description: Aggregate results from bioinformatics analyses across many samples into a single report keywords: - QC @@ -13,7 +12,6 @@ tools: homepage: https://multiqc.info/ documentation: https://multiqc.info/docs/ licence: ["GPL-3.0-or-later"] - input: - multiqc_files: type: file @@ -31,7 +29,6 @@ input: type: file description: Optional logo file for MultiQC pattern: "*.{png}" - output: - report: type: file @@ -54,3 +51,8 @@ authors: - "@bunop" - "@drpatelh" - "@jfy133" +maintainers: + - "@abhi18av" + - "@bunop" + - "@drpatelh" + - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test new file mode 100644 index 0000000..d0438ed --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test @@ -0,0 +1,83 @@ +nextflow_process { + + name "Test Process MULTIQC" + script "../main.nf" + process "MULTIQC" + tag "modules" + tag "modules_nfcore" + tag "multiqc" + + test("sarscov2 single-end [fastqc]") { + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + + } + + test("sarscov2 single-end [fastqc] [config]") { + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, + { assert process.out.data[0] ==~ ".*/multiqc_data" }, + { assert snapshot(process.out.versions).match("versions") } + ) + } + } + + test("sarscov2 single-end [fastqc] - stub") { + + options "-stub" + + when { + process { + """ + input[0] = Channel.of([file(params.test_data['sarscov2']['illumina']['test_1_fastq_gz_fastqc_zip'], checkIfExists: true)]) + input[1] = [] + input[2] = [] + input[3] = [] + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out.report.collect { file(it).getName() } + + process.out.data.collect { file(it).getName() } + + process.out.plots.collect { file(it).getName() } + + process.out.versions ).match() } + ) + } + + } +} diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap new file mode 100644 index 0000000..d37e730 --- /dev/null +++ b/modules/nf-core/multiqc/tests/main.nf.test.snap @@ -0,0 +1,21 @@ +{ + "versions": { + "content": [ + [ + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:02:49.911994" + }, + "sarscov2 single-end [fastqc] - stub": { + "content": [ + [ + "multiqc_report.html", + "multiqc_data", + "multiqc_plots", + "versions.yml:md5,14e9a2661241abd828f4f06a7b5c222d" + ] + ], + "timestamp": "2024-01-09T23:03:14.524346" + } +} \ No newline at end of file diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml new file mode 100644 index 0000000..bea6c0d --- /dev/null +++ b/modules/nf-core/multiqc/tests/tags.yml @@ -0,0 +1,2 @@ +multiqc: + - modules/nf-core/multiqc/** diff --git a/modules/nf-core/picard/createsequencedictionary/environment.yml b/modules/nf-core/picard/createsequencedictionary/environment.yml new file mode 100644 index 0000000..f355462 --- /dev/null +++ b/modules/nf-core/picard/createsequencedictionary/environment.yml @@ -0,0 +1,7 @@ +name: picard_createsequencedictionary +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::picard=3.1.1 diff --git a/modules/nf-core/picard/createsequencedictionary/main.nf b/modules/nf-core/picard/createsequencedictionary/main.nf index d07cc67..a1eb8be 100644 --- a/modules/nf-core/picard/createsequencedictionary/main.nf +++ b/modules/nf-core/picard/createsequencedictionary/main.nf @@ -2,10 +2,10 @@ process PICARD_CREATESEQUENCEDICTIONARY { tag "$meta.id" label 'process_medium' - conda "bioconda::picard=3.0.0" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/picard:3.0.0--hdfd78af_1' : - 'biocontainers/picard:3.0.0--hdfd78af_1' }" + 'https://depot.galaxyproject.org/singularity/picard:3.1.1--hdfd78af_0' : + 'biocontainers/picard:3.1.1--hdfd78af_0' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/picard/createsequencedictionary/meta.yml b/modules/nf-core/picard/createsequencedictionary/meta.yml index 3e04159..0cb79cf 100644 --- a/modules/nf-core/picard/createsequencedictionary/meta.yml +++ b/modules/nf-core/picard/createsequencedictionary/meta.yml @@ -12,7 +12,6 @@ tools: documentation: https://gatk.broadinstitute.org/hc/en-us/articles/360036712531-CreateSequenceDictionary-Picard- tool_dev_url: https://github.com/broadinstitute/picard licence: ["MIT"] - input: - meta: type: map @@ -23,7 +22,6 @@ input: type: file description: The reference fasta file pattern: "*.fasta" - output: - meta: type: map @@ -34,12 +32,15 @@ output: type: file description: File containing software versions pattern: "versions.yml" - - dict: + - reference_dict: type: file description: picard dictionary file pattern: "*.{dict}" - authors: - "@sateeshperi" - "@mjcipriano" - "@hseabolt" +maintainers: + - "@sateeshperi" + - "@mjcipriano" + - "@hseabolt" diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml new file mode 100644 index 0000000..01ccbcc --- /dev/null +++ b/modules/nf-core/samtools/faidx/environment.yml @@ -0,0 +1,7 @@ +name: samtools_faidx +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf index 59ed308..d346162 100644 --- a/modules/nf-core/samtools/faidx/main.nf +++ b/modules/nf-core/samtools/faidx/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_FAIDX { tag "$fasta" label 'process_single' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(fasta) diff --git a/modules/nf-core/samtools/faidx/meta.yml b/modules/nf-core/samtools/faidx/meta.yml index 957b25e..e189af2 100644 --- a/modules/nf-core/samtools/faidx/meta.yml +++ b/modules/nf-core/samtools/faidx/meta.yml @@ -55,3 +55,7 @@ authors: - "@drpatelh" - "@ewels" - "@phue" +maintainers: + - "@drpatelh" + - "@ewels" + - "@phue" diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml new file mode 100644 index 0000000..296ed99 --- /dev/null +++ b/modules/nf-core/samtools/index/environment.yml @@ -0,0 +1,7 @@ +name: samtools_index +channels: + - conda-forge + - bioconda + - defaults +dependencies: + - bioconda::samtools=1.18 diff --git a/modules/nf-core/samtools/index/main.nf b/modules/nf-core/samtools/index/main.nf index 0b20aa4..8ad18fd 100644 --- a/modules/nf-core/samtools/index/main.nf +++ b/modules/nf-core/samtools/index/main.nf @@ -2,10 +2,10 @@ process SAMTOOLS_INDEX { tag "$meta.id" label 'process_low' - conda "bioconda::samtools=1.17" + conda "${moduleDir}/environment.yml" container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/samtools:1.17--h00cdaf9_0' : - 'biocontainers/samtools:1.17--h00cdaf9_0' }" + 'https://depot.galaxyproject.org/singularity/samtools:1.18--h50ea8bc_1' : + 'biocontainers/samtools:1.18--h50ea8bc_1' }" input: tuple val(meta), path(input) diff --git a/modules/nf-core/samtools/index/meta.yml b/modules/nf-core/samtools/index/meta.yml index 8bd2fa6..01a4ee0 100644 --- a/modules/nf-core/samtools/index/meta.yml +++ b/modules/nf-core/samtools/index/meta.yml @@ -51,3 +51,7 @@ authors: - "@drpatelh" - "@ewels" - "@maxulysse" +maintainers: + - "@drpatelh" + - "@ewels" + - "@maxulysse" diff --git a/modules/nf-core/samtools/index/tests/csi.nextflow.config b/modules/nf-core/samtools/index/tests/csi.nextflow.config new file mode 100644 index 0000000..0ed260e --- /dev/null +++ b/modules/nf-core/samtools/index/tests/csi.nextflow.config @@ -0,0 +1,7 @@ +process { + + withName: SAMTOOLS_INDEX { + ext.args = '-c' + } + +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test b/modules/nf-core/samtools/index/tests/main.nf.test new file mode 100644 index 0000000..c76a916 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test @@ -0,0 +1,87 @@ +nextflow_process { + + name "Test Process SAMTOOLS_INDEX" + script "../main.nf" + process "SAMTOOLS_INDEX" + tag "modules" + tag "modules_nfcore" + tag "samtools" + tag "samtools/index" + + test("sarscov2 [BAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.bai).match("bai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CRAI]") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['homo_sapiens']['illumina']['test_paired_end_recalibrated_sorted_cram'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert snapshot(process.out.crai).match("crai") }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } + + test("homo_sapiens [CSI]") { + + config "./csi.nextflow.config" + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = [ + [ id:'test' ], // meta map + file(params.test_data['sarscov2']['illumina']['test_paired_end_sorted_bam'], checkIfExists: true) + ] + """ + } + } + + then { + assertAll ( + { assert process.success }, + { assert path(process.out.csi.get(0).get(1)).exists() }, + { assert path(process.out.versions.get(0)).getText().contains("samtools") } + ) + } + } +} diff --git a/modules/nf-core/samtools/index/tests/main.nf.test.snap b/modules/nf-core/samtools/index/tests/main.nf.test.snap new file mode 100644 index 0000000..b3baee7 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/main.nf.test.snap @@ -0,0 +1,28 @@ +{ + "crai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.recalibrated.sorted.cram.crai:md5,14bc3bd5c89cacc8f4541f9062429029" + ] + ] + ], + "timestamp": "2023-11-15T15:17:37.30801" + }, + "bai": { + "content": [ + [ + [ + { + "id": "test" + }, + "test.paired_end.sorted.bam.bai:md5,704c10dd1326482448ca3073fdebc2f4" + ] + ] + ], + "timestamp": "2023-11-15T15:17:30.869234" + } +} \ No newline at end of file diff --git a/modules/nf-core/samtools/index/tests/tags.yml b/modules/nf-core/samtools/index/tests/tags.yml new file mode 100644 index 0000000..e0f58a7 --- /dev/null +++ b/modules/nf-core/samtools/index/tests/tags.yml @@ -0,0 +1,2 @@ +samtools/index: + - modules/nf-core/samtools/index/** diff --git a/nextflow.config b/nextflow.config index 75bd145..b5fe870 100644 --- a/nextflow.config +++ b/nextflow.config @@ -13,7 +13,7 @@ params { input = null // References genome = null - igenomes_base = 's3://ngi-igenomes/igenomes' + igenomes_base = 's3://ngi-igenomes/igenomes/' igenomes_ignore = false // Building Panel of Normals and models @@ -66,7 +66,7 @@ params { // Schema validation default options validationFailUnrecognisedParams = false validationLenientMode = false - validationSchemaIgnoreParams = 'genomes' + validationSchemaIgnoreParams = 'genomes,igenomes_base' validationShowHiddenParams = false validate_params = true @@ -94,6 +94,7 @@ profiles { dumpHashes = true process.beforeScript = 'echo $HOSTNAME' cleanup = false + nextflow.enable.configProcessNamesValidation = true } conda { conda.enabled = true @@ -116,16 +117,16 @@ profiles { } docker { docker.enabled = true - docker.userEmulation = true conda.enabled = false singularity.enabled = false podman.enabled = false shifter.enabled = false charliecloud.enabled = false apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' } arm { - docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' + docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { singularity.enabled = true @@ -166,6 +167,7 @@ profiles { } apptainer { apptainer.enabled = true + apptainer.autoMounts = true conda.enabled = false docker.enabled = false singularity.enabled = false @@ -175,8 +177,8 @@ profiles { } gitpod { executor.name = 'local' - executor.cpus = 16 - executor.memory = 60.GB + executor.cpus = 4 + executor.memory = 8.GB } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } @@ -192,7 +194,7 @@ singularity.registry = 'quay.io' // Nextflow plugins plugins { - id 'nf-validation' // Validation of pipeline parameters and creation of an input channel from a sample sheet + id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } // Load igenomes.config if required @@ -215,6 +217,9 @@ env { // Capture exit codes from upstream processes when piping process.shell = ['/bin/bash', '-euo', 'pipefail'] +// Disable process selector warnings by default. Use debug profile to enable warnings. +nextflow.enable.configProcessNamesValidation = false + def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') timeline { enabled = true diff --git a/nextflow_schema.json b/nextflow_schema.json index dafa1b2..5a0a915 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -161,14 +161,6 @@ "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", "fa_icon": "far fa-file-code" }, - "igenomes_base": { - "type": "string", - "format": "directory-path", - "description": "Directory / URL base for iGenomes references.", - "default": "s3://ngi-igenomes/igenomes", - "fa_icon": "fas fa-cloud-download-alt", - "hidden": true - }, "igenomes_ignore": { "type": "boolean", "description": "Do not load the iGenomes reference config.", diff --git a/tests/pipeline/cnvkit.nf.test.snap b/tests/pipeline/cnvkit.nf.test.snap index 7807a75..97975fc 100644 --- a/tests/pipeline/cnvkit.nf.test.snap +++ b/tests/pipeline/cnvkit.nf.test.snap @@ -1,9 +1,9 @@ { "software_versions": { "content": [ - "{CNVKIT_BATCH={cnvkit=0.9.10}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, Workflow={nf-core/createpanelrefs=1.0dev}}" + "{CNVKIT_BATCH={cnvkit=0.9.10}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, Workflow={nf-core/createpanelrefs=1.0dev}}" ], - "timestamp": "2023-07-08T16:51:32+0000" + "timestamp": "2024-01-17T10:32:05.468312" }, "cnvkit": { "content": [ @@ -15,4 +15,4 @@ ], "timestamp": "2023-07-08T16:51:32+0000" } -} +} \ No newline at end of file diff --git a/tests/pipeline/default.nf.test.snap b/tests/pipeline/default.nf.test.snap index 807ac4d..4eb14f5 100644 --- a/tests/pipeline/default.nf.test.snap +++ b/tests/pipeline/default.nf.test.snap @@ -1,9 +1,9 @@ { "software_versions": { "content": [ - "{CNVKIT_BATCH={cnvkit=0.9.10}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.0, yaml=6.0}, Workflow={nf-core/createpanelrefs=1.0dev}}" + "{CNVKIT_BATCH={cnvkit=0.9.10}, CUSTOM_DUMPSOFTWAREVERSIONS={python=3.11.7, yaml=5.4.1}, Workflow={nf-core/createpanelrefs=1.0dev}}" ], - "timestamp": "2023-07-08T16:47:57+0000" + "timestamp": "2024-01-17T10:30:57.668525" }, "cnvkit": { "content": [ @@ -15,4 +15,4 @@ ], "timestamp": "2023-07-08T16:47:57+0000" } -} +} \ No newline at end of file diff --git a/workflows/createpanelrefs.nf b/workflows/createpanelrefs.nf index 5105db9..6e768c8 100644 --- a/workflows/createpanelrefs.nf +++ b/workflows/createpanelrefs.nf @@ -169,6 +169,7 @@ workflow.onComplete { if (params.email || params.email_on_fail) { NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) } + NfcoreTemplate.dump_parameters(workflow, params) NfcoreTemplate.summary(workflow, params, log) if (params.hook_url) { NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log)
Process Name \\", + " \\ Software Version
CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
yaml5.4.1
TOOL1tool10.11.9
TOOL2tool21.9
WorkflowNextflow