diff --git a/.github/.dockstore.yml b/.github/.dockstore.yml index 030138a0..191fabd2 100644 --- a/.github/.dockstore.yml +++ b/.github/.dockstore.yml @@ -3,3 +3,4 @@ version: 1.2 workflows: - subclass: nfl primaryDescriptorPath: /nextflow.config + publish: True diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 570aa1de..540ee958 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -69,7 +69,7 @@ If you wish to contribute a new step, please use the following coding standards: 2. Write the process block (see below). 3. Define the output channel if needed (see below). 4. Add any new flags/options to `nextflow.config` with a default (see below). -5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`) +5. Add any new flags/options to `nextflow_schema.json` with help text (with `nf-core schema build .`). 6. Add any new flags/options to the help message (for integer/text parameters, print to help the corresponding `nextflow.config` parameter). 7. Add sanity checks for all relevant parameters. 8. Add any new software to the `scrape_software_versions.py` script in `bin/` and the version command to the `scrape_software_versions` process in `main.nf`. @@ -87,7 +87,7 @@ Once there, use `nf-core schema build .` to add to `nextflow_schema.json`. ### Default processes resource requirements -Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/%7B%7Bcookiecutter.name_noslash%7D%7D/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. +Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. diff --git a/.github/ISSUE_TEMPLATE/bug_report.md b/.github/ISSUE_TEMPLATE/bug_report.md index 550bc402..45a66fda 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.md +++ b/.github/ISSUE_TEMPLATE/bug_report.md @@ -55,7 +55,7 @@ Have you provided the following extra information/files: ## Container engine -- Engine: +- Engine: - version: - Image tag: diff --git a/.github/ISSUE_TEMPLATE/feature_request.md b/.github/ISSUE_TEMPLATE/feature_request.md index 3340f8f1..570b1b96 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.md +++ b/.github/ISSUE_TEMPLATE/feature_request.md @@ -1,6 +1,6 @@ --- name: Feature request -about: Suggest an idea for the nf-core website +about: Suggest an idea for the nf-core/pgdb pipeline labels: enhancement --- diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 6f6c41ca..8e375aad 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -15,9 +15,9 @@ Learn more about contributing: [CONTRIBUTING.md](https://github.com/nf-core/pgdb - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! - - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py` - - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pgdb/tree/master/.github/CONTRIBUTING.md) - - [ ] If necessary, also make a PR on the nf-core/pgdb _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. + - [ ] If you've added a new tool - add to the software_versions process and a regex to `scrape_software_versions.py` + - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/pgdb/tree/master/.github/CONTRIBUTING.md) + - [ ] If necessary, also make a PR on the nf-core/pgdb _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`). - [ ] Usage Documentation in `docs/usage.md` is updated. diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 7a9e38f3..2954f521 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -9,6 +9,16 @@ on: types: [completed] workflow_dispatch: + +env: + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} + AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} + AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} + AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} + + jobs: run-awstest: name: Run AWS full tests @@ -23,21 +33,13 @@ jobs: - name: Install awscli run: conda install -c conda-forge awscli - name: Start AWS batch job - # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters # Then specify `-profile test_full` instead of `-profile test` on the AWS batch command - env: - AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} - AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} - TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} - AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} - AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} - AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} run: | aws batch submit-job \ --region eu-west-1 \ --job-name nf-core-pgdb \ --job-queue $AWS_JOB_QUEUE \ --job-definition $AWS_JOB_DEFINITION \ - --container-overrides '{"command": ["nf-core/pgdb", "-r '"${GITHUB_SHA}"' -profile test --outdir s3://'"${AWS_S3_BUCKET}"'/pgdb/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/pgdb/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' + --container-overrides '{"command": ["nf-core/pgdb", "-r '"${GITHUB_SHA}"' -profile test_full --outdir s3://'"${AWS_S3_BUCKET}"'/pgdb/results-'"${GITHUB_SHA}"' -w s3://'"${AWS_S3_BUCKET}"'/pgdb/work-'"${GITHUB_SHA}"' -with-tower"], "environment": [{"name": "TOWER_ACCESS_TOKEN", "value": "'"$TOWER_ACCESS_TOKEN"'"}]}' diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index 7ec9f445..aed85cd1 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -6,6 +6,16 @@ name: nf-core AWS test on: workflow_dispatch: + +env: + AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} + AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} + TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} + AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} + AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} + AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} + + jobs: run-awstest: name: Run AWS tests @@ -20,16 +30,8 @@ jobs: - name: Install awscli run: conda install -c conda-forge awscli - name: Start AWS batch job - # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix - env: - AWS_ACCESS_KEY_ID: ${{ secrets.AWS_ACCESS_KEY_ID }} - AWS_SECRET_ACCESS_KEY: ${{ secrets.AWS_SECRET_ACCESS_KEY }} - TOWER_ACCESS_TOKEN: ${{ secrets.AWS_TOWER_TOKEN }} - AWS_JOB_DEFINITION: ${{ secrets.AWS_JOB_DEFINITION }} - AWS_JOB_QUEUE: ${{ secrets.AWS_JOB_QUEUE }} - AWS_S3_BUCKET: ${{ secrets.AWS_S3_BUCKET }} run: | aws batch submit-job \ --region eu-west-1 \ diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index e10c3dfe..0f1a83f6 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -13,7 +13,7 @@ jobs: - name: Check PRs if: github.repository == 'nf-core/pgdb' run: | - { [[ ${{github.event.pull_request.head.repo.full_name}} == nf-core/pgdb ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/pgdb ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure @@ -23,13 +23,22 @@ jobs: uses: mshick/add-pr-comment@v1 with: message: | + ## This PR is against the `master` branch :x: + + * Do not close this PR + * Click _Edit_ and change the `base` to `dev` + * This CI test will remain failed until you push a new commit + + --- + Hi @${{ github.event.pull_request.user.login }}, - It looks like this pull-request is has been made against the ${{github.event.pull_request.head.repo.full_name}} `master` branch. + It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. The `master` branch on nf-core repositories should always contain code from the latest release. - Because of this, PRs to `master` are only allowed if they come from the ${{github.event.pull_request.head.repo.full_name}} `dev` branch. + Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. + Note that even after this, the test will continue to show as failing until you push a new commit. Thanks again for your contribution! repo-token: ${{ secrets.GITHUB_TOKEN }} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 086e4a7a..35199e2e 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -17,41 +17,35 @@ jobs: env: NXF_VER: ${{ matrix.nxf_ver }} NXF_ANSI_LOG: false + strategy: matrix: # Nextflow versions: check pipeline minimum and current latest - nxf_ver: ['20.04.0', ''] + nxf_ver: ['20.04.0', '21.03.0-edge'] steps: - name: Check out pipeline code uses: actions/checkout@v2 - - name: Check if Dockerfile or Conda environment changed uses: technote-space/get-diff-action@v4 with: FILES: | Dockerfile environment.yml - - name: Build new docker image if: env.MATCHED_FILES - run: docker build --no-cache . -t nfcore/pgdb:dev - + run: docker build --no-cache . -t nfcore/pgdb:1.0.0 - name: Pull docker image if: ${{ !env.MATCHED_FILES }} run: | docker pull nfcore/pgdb:dev - docker tag nfcore/pgdb:dev nfcore/pgdb:dev - + docker tag nfcore/pgdb:dev nfcore/pgdb:1.0.0 - name: Install Nextflow env: CAPSULE_LOG: none run: | wget -qO- get.nextflow.io | bash sudo mv nextflow /usr/local/bin/ - - name: Run pipeline with test data - # TODO nf-core: You can customise CI pipeline run tests as required # For example: adding multiple test runs with different parameters # Remember that you can parallelise this by using strategy.matrix - run: | - nextflow run ${GITHUB_WORKSPACE} -profile test,docker + run: nextflow run ${GITHUB_WORKSPACE} -profile test,docker diff --git a/.github/workflows/linting.yml b/.github/workflows/linting.yml index bef81e61..fcde400c 100644 --- a/.github/workflows/linting.yml +++ b/.github/workflows/linting.yml @@ -19,6 +19,34 @@ jobs: run: npm install -g markdownlint-cli - name: Run Markdownlint run: markdownlint ${GITHUB_WORKSPACE} -c ${GITHUB_WORKSPACE}/.github/markdownlint.yml + + # If the above check failed, post a comment on the PR explaining the failure + - name: Post PR comment + if: failure() + uses: mshick/add-pr-comment@v1 + with: + message: | + ## Markdown linting is failing + + To keep the code consistent with lots of contributors, we run automated code consistency checks. + To fix this CI test, please run: + + * Install `markdownlint-cli` + * On Mac: `brew install markdownlint-cli` + * Everything else: [Install `npm`](https://www.npmjs.com/get-npm) then [install `markdownlint-cli`](https://www.npmjs.com/package/markdownlint-cli) (`npm install -g markdownlint-cli`) + * Fix the markdown errors + * Automatically: `markdownlint . --config .github/markdownlint.yml --fix` + * Manually resolve anything left from `markdownlint . --config .github/markdownlint.yml` + + Once you push these changes the test should pass, and you can hide this comment :+1: + + We highly recommend setting up markdownlint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + + Thanks again for your contribution! + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false + + YAML: runs-on: ubuntu-latest steps: @@ -29,7 +57,34 @@ jobs: - name: Install yaml-lint run: npm install -g yaml-lint - name: Run yaml-lint - run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml") + run: yamllint $(find ${GITHUB_WORKSPACE} -type f -name "*.yml" -o -name "*.yaml") + + # If the above check failed, post a comment on the PR explaining the failure + - name: Post PR comment + if: failure() + uses: mshick/add-pr-comment@v1 + with: + message: | + ## YAML linting is failing + + To keep the code consistent with lots of contributors, we run automated code consistency checks. + To fix this CI test, please run: + + * Install `yaml-lint` + * [Install `npm`](https://www.npmjs.com/get-npm) then [install `yaml-lint`](https://www.npmjs.com/package/yaml-lint) (`npm install -g yaml-lint`) + * Fix the markdown errors + * Run the test locally: `yamllint $(find . -type f -name "*.yml" -o -name "*.yaml")` + * Fix any reported errors in your YAML files + + Once you push these changes the test should pass, and you can hide this comment :+1: + + We highly recommend setting up yaml-lint in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! + + Thanks again for your contribution! + repo-token: ${{ secrets.GITHUB_TOKEN }} + allow-repeats: false + + nf-core: runs-on: ubuntu-latest steps: @@ -69,7 +124,7 @@ jobs: if: ${{ always() }} uses: actions/upload-artifact@v2 with: - name: linting-log-file + name: linting-logs path: | lint_log.txt lint_results.md diff --git a/.gitignore b/.gitignore index aa4bb5b3..dfe5cf11 100644 --- a/.gitignore +++ b/.gitignore @@ -7,3 +7,5 @@ tests/ testing/ testing* *.pyc + +.idea/ diff --git a/.nf-core-lint.yml b/.nf-core-lint.yml new file mode 100644 index 00000000..be600998 --- /dev/null +++ b/.nf-core-lint.yml @@ -0,0 +1,5 @@ +## NOTE - after nf-core/tools release 1.14 delete this line and +## uncomment the ones below. See https://github.com/nf-core/tools/pull/1019 +nextflow_config: False +# nextflow_config: +# - params.input diff --git a/CHANGELOG.md b/CHANGELOG.md index 1eb7aefc..84070553 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,12 +3,23 @@ The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). -## v1.0dev - [date] +## 1.0.0 Initial release of nf-core/pgdb, created with the [nf-core](https://nf-co.re/) template. ### `Added` +The initial version of the pipeline features the following steps: + +- (optional) ENSEMBL Reference proteomes included in final proteome +- Convert a Variant genome database like COSMIC or CBioPortal to proteomes +- Convert provided VCF to proteome database +- (optional) Generate the decoy database and attach it to the final proteome + +### `Known issues` + +If you experience nextflow running forever after a failed step, try settings errorStrategy = terminate. See the corresponding [nextflow issue](https://github.com/nextflow-io/nextflow/issues/1457). + ### `Fixed` ### `Dependencies` diff --git a/CITATIONS.md b/CITATIONS.md new file mode 100644 index 00000000..72f9f6e5 --- /dev/null +++ b/CITATIONS.md @@ -0,0 +1,34 @@ +# nf-core/pgdb: Citations + +## Pipeline tools + +* [Nextflow](https://www.ncbi.nlm.nih.gov/pubmed/28398311/) + > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. + +* [pypgatk](https://zenodo.org/record/4651319) + > Yasset Perez-Riverol, & Husen M. Umer. (2021, March 31). py-pgatk: Pre-release v0.0.19 (Version v0.0.19). Zenodo. + +## Data sources + +* [ENSEMBL](https://pubmed.ncbi.nlm.nih.gov/31691826/) + > Yates, A. D., Achuthan, P., Akanni, W., Allen, J., Allen, J., Alvarez-Jarreta, J., ... & Flicek, P. (2020). Ensembl 2020. Nucleic acids research, 48(D1), D682-D688. + +* [COSMIC](https://pubmed.ncbi.nlm.nih.gov/15188009/) + > Bamford, S., Dawson, E., Forbes, S., Clements, J., Pettett, R., Dogan, A., ... & Wooster, R. (2004). The COSMIC (Catalogue of Somatic Mutations in Cancer) database and website. British journal of cancer, 91(2), 355-358. + +* [cBioPortal](https://pubmed.ncbi.nlm.nih.gov/23550210/) + > Gao, J., Aksoy, B. A., Dogrusoz, U., Dresdner, G., Gross, B., Sumer, S. O., ... & Schultz, N. (2013). Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Science signaling, 6(269), pl1-pl1. + +## Software packaging/containerisation tools + +* [BioContainers](https://www.ncbi.nlm.nih.gov/pubmed/28379341/) + > da Veiga Leprevost F, Grüning BA, Alves Aflitos S, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Vera Alvarez R, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341. + +* [Singularity](https://www.ncbi.nlm.nih.gov/pubmed/28494014/) + > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. + +* [Conda](https://www.ncbi.nlm.nih.gov/pubmed/29967506/) + > Grüning B., Dale R., Sjödin A., Chapman BA., Rowe J., Tomkins-Tinch CH., Valieris R., Köster J., Bioconda Team (2018). Bioconda: sustainable and comprehensive software distribution for the life sciences. Nature methods, 15(7), 475–476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. + +* [Docker](https://www.docker.com/) + > Merkel D. (2014). Docker: lightweight Linux containers for consistent development and deployment. Linux journal, 2014(239), 2. diff --git a/CODE_OF_CONDUCT.md b/CODE_OF_CONDUCT.md index 405fb1bf..f4fd052f 100644 --- a/CODE_OF_CONDUCT.md +++ b/CODE_OF_CONDUCT.md @@ -1,46 +1,111 @@ -# Contributor Covenant Code of Conduct +# Code of Conduct at nf-core (v1.0) ## Our Pledge -In the interest of fostering an open and welcoming environment, we as contributors and maintainers pledge to making participation in our project and our community a harassment-free experience for everyone, regardless of age, body size, disability, ethnicity, gender identity and expression, level of experience, nationality, personal appearance, race, religion, or sexual identity and orientation. +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: -## Our Standards +- Age +- Body size +- Familial status +- Gender identity and expression +- Geographical location +- Level of experience +- Nationality and national origins +- Native language +- Physical and neurological ability +- Race or ethnicity +- Religion +- Sexual identity and orientation +- Socioeconomic status -Examples of behavior that contributes to creating a positive environment include: +Please note that the list above is alphabetised and is therefore not ranked in any order of preference or importance. -* Using welcoming and inclusive language -* Being respectful of differing viewpoints and experiences -* Gracefully accepting constructive criticism -* Focusing on what is best for the community -* Showing empathy towards other community members +## Preamble -Examples of unacceptable behavior by participants include: +> 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. -* The use of sexualized language or imagery and unwelcome sexual attention or advances -* Trolling, insulting/derogatory comments, and personal or political attacks -* Public or private harassment -* Publishing others' private information, such as a physical or electronic address, without explicit permission -* Other conduct which could reasonably be considered inappropriate in a professional setting +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. + +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. + +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. + +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. + +Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re ## Our Responsibilities -Project maintainers 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 behavior. +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. + +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. + +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. + +## When are 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: + +- 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. +- 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): + +- 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 🎉 🥳 💯 🙌 !) +- 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. +- 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.**) +- 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.) + +## 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. + +- 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. + +### 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. + +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. + +## Procedures for Reporting CoC violations -Project maintainers 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. +If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. -## Scope +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). -This Code of Conduct applies both within project spaces and in public spaces when an individual is representing the project or its community. Examples of representing a project or community include using an official project e-mail address, posting via an official social media account, or acting as an appointed representative at an online or offline event. Representation of a project may be further defined and clarified by project maintainers. +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. -## Enforcement +All reports will be handled with utmost discretion and confidentially. -Instances of abusive, harassing, or otherwise unacceptable behavior may be reported by contacting the project team on [Slack](https://nf-co.re/join/slack). The project team will review and investigate all complaints, and will respond in a way that it deems appropriate to the circumstances. The project team is obligated to maintain confidentiality with regard to the reporter of an incident. Further details of specific enforcement policies may be posted separately. +## Attribution and Acknowledgements -Project maintainers who do not follow or enforce the Code of Conduct in good faith may face temporary or permanent repercussions as determined by other members of the project's leadership. +- The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4) +- The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition) +- The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/) +- The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla) -## Attribution +## Changelog -This Code of Conduct is adapted from the [Contributor Covenant][homepage], version 1.4, available at [https://www.contributor-covenant.org/version/1/4/code-of-conduct/][version] +### v1.0 - March 12th, 2021 -[homepage]: https://contributor-covenant.org -[version]: https://www.contributor-covenant.org/version/1/4/code-of-conduct/ +- Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. diff --git a/Dockerfile b/Dockerfile index 26138738..a138f1ea 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,4 +1,4 @@ -FROM nfcore/base:1.12.1 +FROM nfcore/base:1.13.3 LABEL authors="Husen M. Umer & Yasset Perez-Riverol" \ description="Docker image containing all software requirements for the nf-core/pgdb pipeline" @@ -7,11 +7,7 @@ COPY environment.yml / RUN conda env create --quiet -f /environment.yml && conda clean -a # Add conda installation dir to PATH (instead of doing 'conda activate') -ENV PATH /opt/conda/envs/nf-core-pgdb-1.0dev/bin:$PATH +ENV PATH /opt/conda/envs/nf-core-pgdb-1.0.0/bin:$PATH # Dump the details of the installed packages to a file for posterity -RUN conda env export --name nf-core-pgdb-1.0dev > nf-core-pgdb-1.0dev.yml - -# Instruct R processes to use these empty files instead of clashing with a local version -RUN touch .Rprofile -RUN touch .Renviron +RUN conda env export --name nf-core-pgdb-1.0.0 > nf-core-pgdb-1.0.0.yml diff --git a/README.md b/README.md index 57cbdd16..8823e3d4 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@ # ![nf-core/pgdb](docs/images/nf-core-pgdb_logo.png) -**The ProteoGenomics database generation workflow (pgdb) use the pypgatk and nextflow to create different protein databases for ProteoGenomics data analysis.**. +The ProteoGenomics database generation workflow (**pgdb**) use the [pypgatk](https://github.com/bigbio/py-pgatk) and [nextflow](https://www.nextflow.io/) to create different protein databases for ProteoGenomics data analysis. [![GitHub Actions CI Status](https://github.com/nf-core/pgdb/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/pgdb/actions) [![GitHub Actions Linting Status](https://github.com/nf-core/pgdb/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/pgdb/actions) @@ -12,8 +12,13 @@ ## Introduction - -**nf-core/pgdb** is a bioinformatics best-practise analysis pipeline for +**nf-core/pgdb** is a bioinformatics pipeline to generate proteogenomics databases. pgdb allows users to create proteogenomics databases using EMSEMBL as the reference proteome database. Three different major databases can be attached to the final proteogenomics database: + +* The reference proteome (ENSEMBL Reference proteome) +* Non canonical proteins: pseudo-genes, sORFs, lncRNA. +* Variants: COSMIC, cBioPortal, GENOMAD variants + +The pipeline allows to estimate decoy proteins with different methods and attach them to the final proteogenomics database. The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It comes with docker containers making installation trivial and results highly reproducible. @@ -21,49 +26,44 @@ The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool 1. Install [`nextflow`](https://nf-co.re/usage/installation) -2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) or [`Podman`](https://podman.io/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ +2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(please only use [`Conda`](https://conda.io/miniconda.html) as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_ -3. Download the pipeline and test it on a minimal dataset with a single command: +3. Download the pipeline and test it on a minimal dataset with a single command (This run will download the canonical ENSEMBL reference proteome and create proteomics database with it): ```bash - nextflow run nf-core/pgdb -profile test, + nextflow run nf-core/pgdb -profile test, ``` > Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. 4. Start running your own analysis! - - ```bash - nextflow run nf-core/pgdb -profile --input '*_R{1,2}.fastq.gz' --genome GRCh37 + nextflow run nf-core/pgdb -profile --ncrna true --pseudogenes true --altorfs true ``` + > This will create a proteogenomics database with the ENSEMBL reference proteome and non canonical proteins like pseudo genes, non coding rnas or alternative open reading frames. + See [usage docs](https://nf-co.re/pgdb/usage) for all of the available options when running the pipeline. ## Pipeline Summary By default, the pipeline currently performs the following: - +![ProteoGenomics Database](/docs/images/pgdb-databases.png) -* Sequencing quality control (`FastQC`) -* Overall pipeline run summaries (`MultiQC`) +* Download protein databases from ENSEMBL +* Translate from Genomics Variant databases into ProteoGenomics Databases (`COSMIC`, `GNOMAD`) +* Add to a Reference proteomics database, non-coding RNAs + pseudogenes. +* Compute Decoy for a proteogenomics databases ## Documentation The nf-core/pgdb pipeline comes with documentation about the pipeline: [usage](https://nf-co.re/pgdb/usage) and [output](https://nf-co.re/pgdb/output). - - ## Credits -nf-core/pgdb was originally written by Husen M. Umer & Yasset Perez-Riverol. - -We thank the following people for their extensive assistance in the development -of this pipeline: - - +nf-core/pgdb was originally written by Husen M. Umer (EMBL-EBI) & Yasset Perez-Riverol (Karolinska Institute) ## Contributions and Support @@ -83,8 +83,5 @@ You can cite the `nf-core` publication as follows: > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). -> ReadCube: [Full Access Link](https://rdcu.be/b1GjZ) - -In addition, references of tools and data used in this pipeline are as follows: - +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/email_template.html b/assets/email_template.html index 25eac41b..1c6536c1 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -1,11 +1,10 @@ - - + nf-core/pgdb Pipeline Report diff --git a/bin/scrape_software_versions.py b/bin/scrape_software_versions.py index 0bde138a..391d8916 100755 --- a/bin/scrape_software_versions.py +++ b/bin/scrape_software_versions.py @@ -3,18 +3,15 @@ from collections import OrderedDict import re -# TODO nf-core: Add additional regexes for new tools in process get_software_versions regexes = { "nf-core/pgdb": ["v_pipeline.txt", r"(\S+)"], "Nextflow": ["v_nextflow.txt", r"(\S+)"], - "FastQC": ["v_fastqc.txt", r"FastQC v(\S+)"], - "MultiQC": ["v_multiqc.txt", r"multiqc, version (\S+)"], + "pypgatk": ["v_pypgatk.txt", r"(\S+)"], } results = OrderedDict() results["nf-core/pgdb"] = 'N/A' results["Nextflow"] = 'N/A' -results["FastQC"] = 'N/A' -results["MultiQC"] = 'N/A' +results["pypgatk"] = 'N/A' # Search each file using its regex for k, v in regexes.items(): diff --git a/conf/assemblies_conf.json b/conf/assemblies_conf.json new file mode 100644 index 00000000..09c801fc --- /dev/null +++ b/conf/assemblies_conf.json @@ -0,0 +1,49114 @@ +[ + { + "assembly_name": "KH", + "assembly_level": "chromosome", + 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"assembly_ucsc": null + }, + { + "assembly_name": "LAFA0", + "assembly_level": "chromosome", + "assembly_accession": "GCA_900074735.1", + "assembly_id": 53507, + "base_count": 11336659, + "assembly_ucsc": null + }, + { + "assembly_name": "LADA0", + "assembly_level": "chromosome", + "assembly_accession": "GCA_900074725.1", + "assembly_id": 53508, + "base_count": 10701617, + "assembly_ucsc": null + }, + { + "assembly_name": "Msy_ATCC_42132_Feb2016", + "assembly_level": "chromosome", + "assembly_accession": "GCA_900149145.1", + "assembly_id": 53511, + "base_count": 7786082, + "assembly_ucsc": null + }, + { + "assembly_name": "ASM207223v1", + "assembly_level": "chromosome", + "assembly_accession": "GCA_002072235.1", + "assembly_id": 53522, + "base_count": 33213390, + "assembly_ucsc": null + }, + { + "assembly_name": "ASM207226v1", + "assembly_level": "chromosome", + "assembly_accession": "GCA_002072265.1", + "assembly_id": 53523, + "base_count": 32404688, + "assembly_ucsc": null + }, + { + "assembly_name": "ASM207225v1", + "assembly_level": "chromosome", + "assembly_accession": "GCA_002072255.1", + "assembly_id": 53524, + "base_count": 31061096, + "assembly_ucsc": null + }, + { + "assembly_name": "ASM185786v1", + "assembly_level": "chromosome", + "assembly_accession": "GCA_001857865.1", + "assembly_id": 53538, + "base_count": 38906597, + "assembly_ucsc": null + }, + { + "assembly_name": "UBRO_v3", + "assembly_level": "chromosome", + "assembly_accession": "GCA_900080155.1", + "assembly_id": 53543, + "base_count": 20625025, + "assembly_ucsc": null + }, + { + "assembly_name": "ASM198439v2", + "assembly_level": "chromosome", + "assembly_accession": "GCA_001984395.2", + "assembly_id": 53544, + "base_count": 20864403, + "assembly_ucsc": null + } +] \ No newline at end of file diff --git a/conf/base.config b/conf/base.config index 6fed5aff..59c36447 100644 --- a/conf/base.config +++ b/conf/base.config @@ -3,7 +3,7 @@ * nf-core/pgdb Nextflow base config file * ------------------------------------------------- * A 'blank slate' config file, appropriate for general - * use on most high performace compute environments. + * use on most high performance compute environments. * Assumes that all software is installed and available * on the PATH. Runs in `local` mode - all jobs will be * run on the logged in environment. @@ -11,7 +11,6 @@ process { - // TODO nf-core: Check the defaults for all processes cpus = { check_max( 1 * task.attempt, 'cpus' ) } memory = { check_max( 7.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } @@ -24,21 +23,20 @@ process { // NOTE - Only one of the labels below are used in the fastqc process in the main script. // If possible, it would be nice to keep the same label naming convention when // adding in your processes. - // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_low { cpus = { check_max( 2 * task.attempt, 'cpus' ) } - memory = { check_max( 14.GB * task.attempt, 'memory' ) } + memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 6.h * task.attempt, 'time' ) } } withLabel:process_medium { cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 42.GB * task.attempt, 'memory' ) } + memory = { check_max( 12.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } withLabel:process_high { cpus = { check_max( 12 * task.attempt, 'cpus' ) } - memory = { check_max( 84.GB * task.attempt, 'memory' ) } + memory = { check_max( 32.GB * task.attempt, 'memory' ) } time = { check_max( 10.h * task.attempt, 'time' ) } } withLabel:process_long { @@ -47,5 +45,5 @@ process { withName:get_software_versions { cache = false } - + } diff --git a/conf/cbioportal_config.yaml b/conf/cbioportal_config.yaml new file mode 100644 index 00000000..5e582809 --- /dev/null +++ b/conf/cbioportal_config.yaml @@ -0,0 +1,21 @@ +cbioportal_data_downloader: + output_directory: database_cbioportal + list_studies: False + cbioportal_api: + base_url: https://www.cbioportal.org/webservice.do + cancer_studies: cmd=getCancerStudies + cbioportal_download_url: https://cbioportal-datahub.s3.amazonaws.com + logger: + formatters: + DEBUG: "%(asctime)s [%(levelname)7s][%(name)48s][%(module)32s, %(lineno)4s] %(message)s" + INFO: "%(asctime)s [%(levelname)7s][%(name)48s] %(message)s" + loglevel: DEBUG + multithreading: True +proteindb: + filter_info: + filter_column: 'CANCER_TYPE' + accepted_values: 'all' + split_by_filter_column: False + clinical_sample_file: '' + + diff --git a/conf/cosmic_config.yaml b/conf/cosmic_config.yaml new file mode 100644 index 00000000..445b1c81 --- /dev/null +++ b/conf/cosmic_config.yaml @@ -0,0 +1,24 @@ +cosmic_data: + output_directory: database_cosmic + cosmic_server: + cosmic_ftp: https://cancer.sanger.ac.uk + mutations_url: cosmic/file_download/GRCh38/cosmic/v88 + all_cds_genes_file: All_COSMIC_Genes.fasta.gz + mutations_file: CosmicMutantExport.tsv.gz + mutations_cellline_url: cosmic/file_download/GRCh38/cell_lines/v92 + mutations_cellline_file: CosmicCLP_MutantExport.tsv.gz + all_celllines_genes_file: All_CellLines_Genes.fasta.gz + cosmic_user: '' + cosmic_password: '' + logger: + formatters: + DEBUG: "%(asctime)s [%(levelname)7s][%(name)48s][%(module)32s, %(lineno)4s] %(message)s" + INFO: "%(asctime)s [%(levelname)7s][%(name)48s] %(message)s" + loglevel: DEBUG +proteindb: + filter_info: + filter_column: 'Histology subtype 1' + accepted_values: 'all' + split_by_filter_column: False + clinical_sample_file: '' + diff --git a/conf/ensembl_config.yaml b/conf/ensembl_config.yaml new file mode 100644 index 00000000..fab2bdd7 --- /dev/null +++ b/conf/ensembl_config.yaml @@ -0,0 +1,29 @@ +ensembl_translation: + translation_table: 1 + proteindb_output_file: 'peptide-database.fa' + ensembl_translation: + mito_translation_table: 2 + var_prefix: "var" + report_ref_seq: False + annotation_field_name: 'CSQ' + af_field: '' + af_threshold: 0.01 + transcript_index: 3 + consequence_index: 1 + exclude_biotypes: '' + exclude_consequences: 'downstream_gene_variant, upstream_gene_variant, intergenic_variant, intron_variant, synonymous_variant, regulatory_region_variant' + skip_including_all_cds: False + include_biotypes: 'protein_coding,polymorphic_pseudogene,non_stop_decay,nonsense_mediated_decay,IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,TR_C_gene,TR_D_gene,TR_J_gene,TR_V_gene,TEC' + include_consequences: 'all' + biotype_str: 'transcript_biotype' + num_orfs: 3 + num_orfs_complement: 0 + expression_str: "" + expression_thresh: 5.0 + ignore_filters: False + accepted_filters: '' + logger: + formatters: + DEBUG: "%(asctime)s [%(levelname)7s][%(name)48s][%(module)32s, %(lineno)4s] %(message)s" + INFO: "%(asctime)s [%(levelname)7s][%(name)48s] %(message)s" + loglevel: DEBUG diff --git a/conf/ensembl_downloader_config.yaml b/conf/ensembl_downloader_config.yaml new file mode 100644 index 00000000..dac81407 --- /dev/null +++ b/conf/ensembl_downloader_config.yaml @@ -0,0 +1,35 @@ +ensembl_data_downloader: + output_directory: database_ensembl + list_taxonomies: False + skip_gtf: False + skip_protein: False + skip_cds: False + skip_cdna: False + skip_ncrna: False + skip_dna: False + skip_vcf: False + ensembl_ftp: + base_url: ftp://ftp.ensembl.org/pub + rewrite_local_path_ensembl_repo: 'False' + ensembl_file_names: + protein_sequence_file: + file_type: pep + file_suffixes: + - all + - abinitio + file_extension: fa + gtf_file: + file_suffixes: + - '' + - abinitio. + - chr. + - chr_patch_hapl_scaff. + file_extension: gtf + ensembl_api: + server: http://rest.ensembl.org + species: /info/species + logger: + formatters: + DEBUG: "%(asctime)s [%(levelname)7s][%(name)48s][%(module)32s, %(lineno)4s] %(message)s" + INFO: "%(asctime)s [%(levelname)7s][%(name)48s] %(message)s" + loglevel: DEBUG diff --git a/conf/ensembl_species.txt b/conf/ensembl_species.txt new file mode 100644 index 00000000..aa2eb60c --- /dev/null +++ b/conf/ensembl_species.txt @@ -0,0 +1,216 @@ +Aardvark,Orycteropus afer afer,1230840 +Abingdon island giant tortoise,Chelonoidis abingdonii,106734 +Agassiz's desert tortoise,Gopherus agassizii,38772 +Algerian mouse,Mus spretus,10096 +Alpaca,Vicugna pacos,30538 +Alpine marmot,Marmota marmota marmota,9994 +Amazon molly,Poecilia formosa,48698 +American beaver,Castor canadensis,51338 +American bison,Bison bison bison,43346 +American black bear,Ursus americanus,9643 +American mink,Neovison vison,452646 +Angola colobus,Colobus angolensis palliatus,336983 +Anole lizard,Anolis carolinensis,28377 +Arctic ground squirrel,Urocitellus parryii,9999 +Argentine black and white tegu,Salvator merianae,96440 +Armadillo,Dasypus novemcinctus,9361 +Asian bonytongue,Scleropages formosus,113540 +Australian saltwater crocodile,Crocodylus porosus,8502 +Ballan wrasse,Labrus bergylta,56723 +Barramundi perch,Lates calcarifer,8187 +Bengalese finch,Lonchura striata domestica,299123 +Bicolor damselfish,Stegastes partitus,144197 +Black snub-nosed monkey,Rhinopithecus bieti,61621 +Blue tit,Cyanistes caeruleus,156563 +Blue-crowned manakin,Lepidothrix coronata,321398 +Bolivian squirrel monkey,Saimiri boliviensis boliviensis,39432 +Bonobo,Pan paniscus,9597 +Brazilian guinea pig,Cavia aperea,37548 +Budgerigar,Melopsittacus undulatus,13146 +Burton's mouthbrooder,Haplochromis burtoni,8153 +Bushbaby,Otolemur garnettii,30611 +C.intestinalis,Ciona intestinalis,7719 +C.savignyi,Ciona savignyi,51511 +C. elegans,Caenorhabditis elegans,6239 +Capuchin,Cebus capucinus imitator,1737458 +Cat,Felis catus,9685 +Central bearded dragon,Pogona vitticeps,103695 +Channel catfish,Ictalurus punctatus,7998 +Chicken,Gallus gallus,9031 +Chilean tinamou,Nothoprocta perdicaria,30464 +Chimpanzee,Pan troglodytes,9598 +Chinese hamster CHOK1GS,Cricetulus griseus,10029 +Chinese hamster CriGri,Cricetulus griseus,10029 +Chinese hamster PICR,Cricetulus griseus,10029 +Chinese softshell turtle,Pelodiscus sinensis,13735 +Climbing perch,Anabas testudineus,64144 +Clown anemonefish,Amphiprion ocellaris,80972 +Cod,Gadus morhua,8049 +Coelacanth,Latimeria chalumnae,7897 +Common canary,Serinus canaria,9135 +Common wombat,Vombatus ursinus,29139 +Coquerel's sifaka,Propithecus coquereli,379532 +Cow,Bos taurus,9913 +Crab-eating macaque,Macaca fascicularis,9541 +Damara mole rat,Fukomys damarensis,885580 +Dark-eyed junco,Junco hyemalis,40217 +Daurian ground squirrel,Spermophilus dauricus,99837 +Degu,Octodon degus,10160 +Dingo,Canis lupus dingo,286419 +Dog,Canis lupus familiaris,9615 +Dolphin,Tursiops truncatus,9739 +Dolphin,Tursiops truncatus,9739 +Donkey,Equus asinus asinus,83772 +Drill,Mandrillus leucophaeus,9568 +D. melanogaster,Drosophila melanogaster,7227 +Duck,Anas platyrhynchos platyrhynchos,8840 +Eastern happy,Astatotilapia calliptera,8154 +Electric eel,Electrophorus electricus,8005 +Elephant,Loxodonta africana,9785 +Elephant shark,Callorhinchus milii,7868 +Emu,Dromaius novaehollandiae,8790 +Ferret,Mustela putorius furo,9669 +Flycatcher,Ficedula albicollis,59894 +Fugu,Takifugu rubripes,31033 +Gelada,Theropithecus gelada,9565 +Gibbon,Nomascus leucogenys,61853 +Goat,Capra hircus,9925 +Golden Hamster,Mesocricetus auratus,10036 +Golden snub-nosed monkey,Rhinopithecus roxellana,61622 +Golden-collared manakin,Manacus vitellinus,328815 +Gorilla,Gorilla gorilla gorilla,9595 +Great Tit,Parus major,9157 +Great spotted kiwi,Apteryx haastii,8823 +Greater amberjack,Seriola dumerili,41447 +Greater bamboo lemur,Prolemur simus,1328070 +Guinea Pig,Cavia porcellus,10141 +Guppy,Poecilia reticulata,8081 +Hagfish,Eptatretus burgeri,7764 +Hamadryas Baboon,Papio hamadryas,9557 +Hedgehog,Erinaceus europaeus,9365 +Hedgehog,Erinaceus europaeus,9365 +Helmeted guineafowl,Numida meleagris,8996 +Horse,Equus caballus,9796 +Huchen,Hucho hucho,62062 +Human,Homo sapiens,9606 +Hybrid - Bos Indicus,Bos indicus x Bos taurus,30522 +Hybrid - Bos Taurus,Bos indicus x Bos taurus,30522 +Hyrax,Procavia capensis,9813 +Indian medaka,Oryzias melastigma,30732 +Japanese medaka HNI,Oryzias latipes,8090 +Japanese medaka HSOK,Oryzias latipes,8090 +Japanese medaka HdrR,Oryzias latipes,8090 +Japanese quail,Coturnix japonica,93934 +Kangaroo rat,Dipodomys ordii,10020 +Koala,Phascolarctos cinereus,38626 +Lamprey,Petromyzon marinus,7757 +Leopard,Panthera pardus,9691 +Lesser Egyptian jerboa,Jaculus jaculus,51337 +Lesser hedgehog tenrec,Echinops telfairi,9371 +Little spotted kiwi,Apteryx owenii,8824 +Long-tailed chinchilla,Chinchilla lanigera,34839 +Lyretail cichlid,Neolamprologus brichardi,32507 +Ma's night monkey,Aotus nancymaae,37293 +Macaque,Macaca mulatta,9544 +Mainland tiger snake,Notechis scutatus,8663 +Makobe Island cichlid,Pundamilia nyererei,303518 +Mangrove rivulus,Kryptolebias marmoratus,37003 +Marmoset,Callithrix jacchus,9483 +Megabat,Pteropus vampyrus,132908 +Mexican tetra,Astyanax mexicanus,7994 +Microbat,Myotis lucifugus,59463 +Midas cichlid,Amphilophus citrinellus,61819 +Mongolian gerbil,Meriones unguiculatus,10047 +Monterrey platyfish,Xiphophorus couchianus,32473 +Mouse,Mus musculus,10090 +Mouse 129S1/SvImJ,Mus musculus,10090 +Mouse A/J,Mus musculus,10090 +Mouse AKR/J,Mus musculus,10090 +Mouse BALB/cJ,Mus musculus,10090 +Mouse C3H/HeJ,Mus musculus,10090 +Mouse C57BL/6NJ,Mus musculus,10090 +Mouse CAST/EiJ,Mus musculus castaneus,10091 +Mouse CBA/J,Mus musculus,10090 +Mouse DBA/2J,Mus musculus,10090 +Mouse FVB/NJ,Mus musculus,10090 +Mouse LP/J,Mus musculus,10090 +Mouse Lemur,Microcebus murinus,30608 +Mouse NOD/ShiLtJ,Mus musculus,10090 +Mouse NZO/HlLtJ,Mus musculus,10090 +Mouse PWK/PhJ,Mus musculus musculus,39442 +Mouse WSB/EiJ,Mus musculus domesticus,10092 +Mummichog,Fundulus heteroclitus,8078 +Naked mole-rat female,Heterocephalus glaber,10181 +Naked mole-rat male,Heterocephalus glaber,10181 +Northern American deer mouse,Peromyscus maniculatus bairdii,230844 +Northern pike,Esox lucius,8010 +Ocean sunfish,Mola mola,94237 +Okarito brown kiwi,Apteryx rowi,308060 +Olive baboon,Papio anubis,9555 +Opossum,Monodelphis domestica,13616 +Orange clownfish,Amphiprion percula,161767 +Orangutan,Pongo abelii,9601 +Painted turtle,Chrysemys picta bellii,8478 +Panda,Ailuropoda melanoleuca,9646 +P. kingsleyae,Paramormyrops kingsleyae,1676925 +P. magnuspinnatus,Periophthalmus magnuspinnatus,409849 +Pig,Sus scrofa,9823 +Pig FPC map,Sus scrofa map, +Pig USMARC,Sus scrofa,9823 +Pig-tailed macaque,Macaca nemestrina,9545 +Pika,Ochotona princeps,9978 +Pika,Ochotona princeps,9978 +Pink-footed goose,Anser brachyrhynchus,132585 +Platyfish,Xiphophorus maculatus,8083 +Platypus,Ornithorhynchus anatinus,9258 +Polar bear,Ursus maritimus,29073 +Prairie vole,Microtus ochrogaster,79684 +Rabbit,Oryctolagus cuniculus,9986 +Rat,Rattus norvegicus,10116 +Red fox,Vulpes vulpes,9627 +Red-bellied piranha,Pygocentrus nattereri,42514 +Rhinoceros,Ceratotherium simum simum,73337 +Ruff,Calidris pugnax,198806 +Ryukyu mouse,Mus caroli,10089 +S. cerevisiae,Saccharomyces cerevisiae,4932 +Sailfin molly,Poecilia latipinna,48699 +Sheep,Ovis aries,9940 +Sheepshead minnow,Cyprinodon variegatus,28743 +Shortfin molly,Poecilia mexicana,48701 +Shrew,Sorex araneus,42254 +Shrew,Sorex araneus,42254 +Shrew mouse,Mus pahari,10093 +Sloth,Choloepus hoffmanni,9358 +Sooty mangabey,Cercocebus atys,9531 +Sperm whale,Physter macrocephalus,9755 +Spiny chromis,Acanthochromis polyacanthus,80966 +Spoon-billed sandpiper,Calidris pygmaea,425635 +Spotted gar,Lepisosteus oculatus,7918 +Squirrel,Ictidomys tridecemlineatus,43179 +Steppe mouse,Mus spicilegus,10103 +Stickleback,Gasterosteus aculeatus,69293 +Swamp eel,Monopterus albus,43700 +Tarsier,Carlito syrichta,1868482 +Tasmanian devil,Sarcophilus harrisii,9305 +Tetraodon,Tetraodon nigroviridis,99883 +Tiger,Panthera tigris altaica,74533 +Tiger tail seahorse,Hippocampus comes,109280 +Tilapia,Oreochromis niloticus,8128 +Tongue sole,Cynoglossus semilaevis,244447 +Tree Shrew,Tupaia belangeri,37347 +Tuatara,Sphenodon punctatus,8508 +Turbot,Scophthalmus maximus,52904 +Turkey,Meleagris gallopavo,9103 +Ugandan red Colobus,Piliocolobus tephrosceles,591936 +Upper Galilee mountains blind mole rat,Nannospalax galili,1026970 +Vervet-AGM,Chlorocebus sabaeus,60711 +Wallaby,Notamacropus eugenii,9315 +Western mosquitofish,Gambusia affinis,33528 +White-throated sparrow,Zonotrichia albicollis,44394 +Wild yak,Bos mutus,72004 +Xenopus,Xenopus tropicalis,8364 +Yellowtail amberjack,Seriola lalandi dorsalis,1841481 +Zebra Finch,Taeniopygia guttata,59729 +Zebra mbuna,Maylandia zebra,106582 +Zebrafish,Danio rerio,7955 +Zig-zag eel,Mastacembelus armatus,205130 diff --git a/conf/protein_decoy.yaml b/conf/protein_decoy.yaml new file mode 100644 index 00000000..c6c691d7 --- /dev/null +++ b/conf/protein_decoy.yaml @@ -0,0 +1,23 @@ +proteindb_decoy: + output: protein-decoy.fa + cleavage_sites: KR + cleavage_position: c + max_missed_cleavages: 2 + anti_cleavage_sites: '' + min_peptide_length: 5 + max_iterations: 100 + keep_target_hits: true + enzyme: trypsin + method: decoypyrat + max_peptide_length: 100 + do_not_shuffle: False + do_not_switch: False + decoy_prefix: DECOY_ + temp_file: tmp.fa + no_isobaric: False + memory_save: False + logger: + formatters: + DEBUG: "%(asctime)s [%(levelname)7s][%(name)48s][%(module)32s, %(lineno)4s] %(message)s" + INFO: "%(asctime)s [%(levelname)7s][%(name)48s] %(message)s" + loglevel: DEBUG diff --git a/conf/test.config b/conf/test.config index 5c8c6433..e4f566b0 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,17 +10,18 @@ params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' + // Limit resources so that this can run on GitHub Actions max_cpus = 2 max_memory = 6.GB max_time = 48.h - // Input data - // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets - // TODO nf-core: Give any required params for the test so that command line flags are not needed - single_end = false - input_paths = [ - ['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']], - ['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']] - ] + ensembl_name = 'meleagris_gallopavo' + ensembl = false + gnomad = false + cosmic = false + cosmic_celllines = false + cbioportal = false + decoy = true + clean_database = true } diff --git a/conf/test_full.config b/conf/test_full.config index fae3976b..96e2f8dd 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -9,14 +9,14 @@ params { config_profile_name = 'Full test profile' - config_profile_description = 'Full test dataset to check pipeline function' + config_profile_description = 'Full test COSMIC generation' // Input data for full size test - // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) - // TODO nf-core: Give any required params for the test so that command line flags are not needed - single_end = false - input_paths = [ - ['Testdata', ['https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R1.tiny.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/exoseq/testdata/Testdata_R2.tiny.fastq.gz']], - ['SRR389222', ['https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub1.fastq.gz', 'https://github.com/nf-core/test-datasets/raw/methylseq/testdata/SRR389222_sub2.fastq.gz']] - ] + ensembl_name = 'homo_sapiens' + ensembl = false + gnomad = false + cosmic = false + cosmic_celllines = false + cbioportal = true + decoy = true } diff --git a/docs/images/pgdb-databases.png b/docs/images/pgdb-databases.png new file mode 100644 index 00000000..14910b43 Binary files /dev/null and b/docs/images/pgdb-databases.png differ diff --git a/docs/output.md b/docs/output.md index aa44a34f..819380b5 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,63 +1,53 @@ # nf-core/pgdb: Output -## :warning: Please read this documentation on the nf-core website: [https://nf-co.re/pgdb/output](https://nf-co.re/pgdb/output) - -> _Documentation of pipeline parameters is generated automatically from the pipeline schema and can no longer be found in markdown files._ - ## Introduction -This document describes the output produced by the pipeline. Most of the plots are taken from the MultiQC report, which summarises results at the end of the pipeline. +This document describes the output produced by the pipeline. The main output of the pgdb pipeline is the protein sequence database. Protein databases are use for peptide and protein [identification algorithms](https://pubmed.ncbi.nlm.nih.gov/27975215/). In most of the proteomics experiments, researchers tried to quantified the peptides and proteins using canonical protein databases such as ENSEMBL or UNIPROT. -The directories listed below will be created in the results directory after the pipeline has finished. All paths are relative to the top-level results directory. +[Proteogenomics](https://www.nature.com/articles/nmeth.3144) is the field of research at the interface of proteomics and genomics. In this approach, "customized" protein sequence databases generated using genomic and transcriptomic information are used to help identify "novel" peptides (not present in reference/canonical protein sequence databases) from mass spectrometry–based proteomic data; in turn, the proteomic data can be used to provide protein-level evidence of gene expression and to help refine gene models. In recent years, owing to the emergence of new sequencing technologies such as RNA-seq and dramatic improvements in the depth and throughput of mass spectrometry–based proteomics, the pace of proteogenomic research has greatly accelerated. - +pgdb allows researchers to create custom proteogenomic databses using different sources such as COSMIC, cBioPortal, ENSEMBL variants of gNOMAD. ## Pipeline overview -The pipeline is built using [Nextflow](https://www.nextflow.io/) -and processes data using the following steps: +The pipeline is built using [Nextflow](https://www.nextflow.io/) and aim to create a final protein database by adding different protein sequences depending of the options provided by the user/researcher. The pipeline will handle the download from the different sources and perform the operations in the data like translation from genome and transcript sequences into protein sequences, etc. -* [FastQC](#fastqc) - Read quality control -* [MultiQC](#multiqc) - Aggregate report describing results from the whole pipeline -* [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +The main source of canonical protein sequence in pgdb is ENSEMBL. The user can then attach to the proteogenomic database protein vairants from COSMIC or cBioPortal. In addition, the pseudogenes, lncRNAs and other novel translation events can be configure to get novel protein sequences. The main sources of sequences are: -## FastQC +* [Ensembl](#ensembl) - Download the Ensembl databases proteins and add canonical proteins. +* [Ensemblnoncanonical](#ensemblnoncanonical) - ENSEMBL non canonical proteins +* [Variants](#variants) - Add the COSMIC and cPortal variant databases. +* [Decoy](#decoys) - Add decoy proteins to the final database. +* [Output](#output) - Output results including clean databases and decoy generation -[FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/) gives general quality metrics about your sequenced reads. It provides information about the quality score distribution across your reads, per base sequence content (%A/T/G/C), adapter contamination and overrepresented sequences. +## Pipeline modes -For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). +### Ensembl -**Output files:** +The pipeline will download the the ENSEMBL protein reference proteome, this will be added to the final protein database. The protein database is downloaded from [ENSEMBL FTP](http://www.ensembl.org/info/data/ftp/index.html). -* `fastqc/` - * `*_fastqc.html`: FastQC report containing quality metrics for your untrimmed raw fastq files. -* `fastqc/zips/` - * `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. +### Ensembl non canonical -> **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. +The Ensembl non canonical includes the pseudogenes, lncRNAs, etc. The accessions of each type of kind of novel protein is predefined by the [pypgatk tool](https://github.com/bigbio/py-pgatk). -## MultiQC +* `ncRNA_ENST00000456688` - non coding RNA transcript. +* `altorf_ENST00000310473` - alternative open reading frame +* `pseudo_ENST00000436135` - pseudo gene translation -[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarizing all samples in your project. Most of the pipeline QC results are visualised in the report and further statistics are available in the report data directory. +### Variants -The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. +The COSMIC or cBioPortal variants are downloaded automatically from these resources. The accessions of those proteins are: -For more information about how to use MultiQC reports, see [https://multiqc.info](https://multiqc.info). +* `COSMIC:ANXA3_ENST00000503570:p.A67T:Substitution-Missense` - Accession of the protein includes the position of the amino acid variant. -**Output files:** +### Decoy -* `multiqc/` - * `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. - * `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. - * `multiqc_plots/`: directory containing static images from the report in various formats. +Decoy can be added to the final database. Decoys accessions are prefix with `DECOY_` by default, but they can be configured by the users. -## Pipeline information +## Output files -[Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. +The nf-core/pgdb pipeline produces one single output file: `/final_proteinDB.fa` _(or whatever `params.final_database_protein` is set to)_. -**Output files:** +This FASTA database includes all of the protein sequences including the reference proteomes, variants, pseudo-genes, etc. -* `pipeline_info/` - * 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.csv`. - * Documentation for interpretation of results in HTML format: `results_description.html`. +A directory called `pipeline_info` is also created with logs and reports from the pipeline execution. diff --git a/docs/usage.md b/docs/usage.md index a1b0e42d..0663b6b0 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,14 +6,20 @@ ## Introduction - +General usage: -## Running the pipeline +```bash +nextflow run nf-core/pgdb -profile --taxonomy 9606 --decoy +``` + +This command will download the ENSEMBL human proteome and attach the decoy database to it. -The typical command for running the pipeline is as follows: +## Adding non canonical proteins + +Te main purpose of the pgdb pipeline to add non-canonical proteins to the database including varriants, ncRNAs, altORFs: ```bash -nextflow run nf-core/pgdb --input '*_R{1,2}.fastq.gz' -profile docker +nextflow run nf-core/pgdb --taxonomy 9606 --altorfs --decoy -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -27,6 +33,10 @@ results # Finished results (configurable, see below) # Other nextflow hidden files, eg. history of pipeline runs and old logs. ``` +## Pipeline full documentation and examples + +The full documentation of the pipeline can be found [here](https://pgatk.readthedocs.io/) including examples to generate databases from COSMIC or cBioportal. + ### Updating the pipeline When you run the above command, Nextflow automatically pulls the pipeline code from GitHub and stores it as a cached version. When running the pipeline after this, it will always use the cached version if available - even if the pipeline has been updated since. To make sure that you're running the latest version of the pipeline, make sure that you regularly update the cached version of the pipeline: @@ -51,7 +61,7 @@ This version number will be logged in reports when you run the pipeline, so that Use this parameter to choose a configuration profile. Profiles can give configuration presets for different compute environments. -Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Conda) - see below. +Several generic profiles are bundled with the pipeline which instruct the pipeline to use software packaged using different methods (Docker, Singularity, Podman, Shifter, Charliecloud, 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. @@ -71,8 +81,14 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof * `podman` * A generic configuration profile to be used with [Podman](https://podman.io/) * Pulls software from Docker Hub: [`nfcore/pgdb`](https://hub.docker.com/r/nfcore/pgdb/) +* `shifter` + * A generic configuration profile to be used with [Shifter](https://nersc.gitlab.io/development/shifter/how-to-use/) + * Pulls software from Docker Hub: [`nfcore/pgdb`](https://hub.docker.com/r/nfcore/pgdb/) +* `charliecloud` + * A generic configuration profile to be used with [Charliecloud](https://hpc.github.io/charliecloud/) + * Pulls software from Docker Hub: [`nfcore/pgdb`](https://hub.docker.com/r/nfcore/pgdb/) * `conda` - * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity or Podman. + * Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter or Charliecloud. * A generic configuration profile to be used with [Conda](https://conda.io/docs/) * Pulls most software from [Bioconda](https://bioconda.github.io/) * `test` @@ -103,6 +119,8 @@ process { } ``` +To find the exact name of a process you wish to modify the compute resources, check the live-status of a nextflow run displayed on your terminal or check the nextflow error for a line like so: `Error executing process > 'bwa'`. In this case the name to specify in the custom config file is `bwa`. + See the main [Nextflow documentation](https://www.nextflow.io/docs/latest/config.html) for more information. If you are likely to be running `nf-core` pipelines regularly it may be a good idea to request that your custom config file is uploaded to the `nf-core/configs` git repository. Before you do this please can you test that the config file works with your pipeline of choice using the `-c` parameter (see definition above). You can then create a pull request to the `nf-core/configs` repository with the addition of your config file, associated documentation file (see examples in [`nf-core/configs/docs`](https://github.com/nf-core/configs/tree/master/docs)), and amending [`nfcore_custom.config`](https://github.com/nf-core/configs/blob/master/nfcore_custom.config) to include your custom profile. diff --git a/environment.yml b/environment.yml index c521ea94..dd229dad 100644 --- a/environment.yml +++ b/environment.yml @@ -1,15 +1,18 @@ # You can use this file to create a conda environment for this pipeline: # conda env create -f environment.yml -name: nf-core-pgdb-1.0dev +name: nf-core-pgdb-1.0.0 channels: - conda-forge - bioconda - defaults dependencies: - - conda-forge::python=3.7.3 - - conda-forge::markdown=3.1.1 - - conda-forge::pymdown-extensions=6.0 - - conda-forge::pygments=2.5.2 - # TODO nf-core: Add required software dependencies here - - bioconda::fastqc=0.11.8 - - bioconda::multiqc=1.7 + - conda-forge::python=3.9.2 + - conda-forge::markdown=3.3.4 + - conda-forge::pymdown-extensions=8.1.1 + - conda-forge::pygments=2.8.1 + # All the dependencies of the pipeline. + - conda-forge::coreutils=8.31 + - conda-forge::git-lfs=2.13.3 + - conda-forge::git=2.30.2 + - bioconda::gffread=0.12.1 + - bioconda::pypgatk=0.0.19 diff --git a/lib/Headers.groovy b/lib/Headers.groovy new file mode 100644 index 00000000..15d1d388 --- /dev/null +++ b/lib/Headers.groovy @@ -0,0 +1,43 @@ +/* + * This file holds several functions used to render the nf-core ANSI header. + */ + +class Headers { + + private static Map log_colours(Boolean monochrome_logs) { + Map colorcodes = [:] + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['yellow_bold'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + colorcodes['red'] = monochrome_logs ? '' : "\033[1;91m" + return colorcodes + } + + static String dashed_line(monochrome_logs) { + Map colors = log_colours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" + } + + static String nf_core(workflow, monochrome_logs) { + Map colors = log_colours(monochrome_logs) + String.format( + """\n + ${dashed_line(monochrome_logs)} + ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} + ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} + ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} + ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} + ${colors.green}`._,._,\'${colors.reset} + ${colors.purple} ${workflow.manifest.name} v${workflow.manifest.version}${colors.reset} + ${dashed_line(monochrome_logs)} + """.stripIndent() + ) + } +} diff --git a/lib/NfcoreSchema.groovy b/lib/NfcoreSchema.groovy new file mode 100644 index 00000000..54935ec8 --- /dev/null +++ b/lib/NfcoreSchema.groovy @@ -0,0 +1,571 @@ +/* + * This file holds several functions used to perform JSON parameter validation, help and summary rendering for the nf-core pipeline template. + */ + +import org.everit.json.schema.Schema +import org.everit.json.schema.loader.SchemaLoader +import org.everit.json.schema.ValidationException +import org.json.JSONObject +import org.json.JSONTokener +import org.json.JSONArray +import groovy.json.JsonSlurper +import groovy.json.JsonBuilder + +class NfcoreSchema { + + /* + * Function to loop over all parameters defined in schema and check + * whether the given paremeters adhere to the specificiations + */ + /* groovylint-disable-next-line UnusedPrivateMethodParameter */ + private static void validateParameters(params, jsonSchema, log) { + def has_error = false + //=====================================================================// + // Check for nextflow core params and unexpected params + def json = new File(jsonSchema).text + def Map schemaParams = (Map) new JsonSlurper().parseText(json).get('definitions') + def nf_params = [ + // Options for base `nextflow` command + 'bg', + 'c', + 'C', + 'config', + 'd', + 'D', + 'dockerize', + 'h', + 'log', + 'q', + 'quiet', + 'syslog', + 'v', + 'version', + + // Options for `nextflow run` command + 'ansi', + 'ansi-log', + 'bg', + 'bucket-dir', + 'c', + 'cache', + 'config', + 'dsl2', + 'dump-channels', + 'dump-hashes', + 'E', + 'entry', + 'latest', + 'lib', + 'main-script', + 'N', + 'name', + 'offline', + 'params-file', + 'pi', + 'plugins', + 'poll-interval', + 'pool-size', + 'profile', + 'ps', + 'qs', + 'queue-size', + 'r', + 'resume', + 'revision', + 'stdin', + 'stub', + 'stub-run', + 'test', + 'w', + 'with-charliecloud', + 'with-conda', + 'with-dag', + 'with-docker', + 'with-mpi', + 'with-notification', + 'with-podman', + 'with-report', + 'with-singularity', + 'with-timeline', + 'with-tower', + 'with-trace', + 'with-weblog', + 'without-docker', + 'without-podman', + 'work-dir' + ] + def unexpectedParams = [] + + // Collect expected parameters from the schema + def expectedParams = [] + for (group in schemaParams) { + for (p in group.value['properties']) { + expectedParams.push(p.key) + } + } + + for (specifiedParam in params.keySet()) { + // nextflow params + if (nf_params.contains(specifiedParam)) { + log.error "ERROR: You used a core Nextflow option with two hyphens: '--${specifiedParam}'. Please resubmit with '-${specifiedParam}'" + has_error = true + } + // unexpected params + def params_ignore = params.schema_ignore_params.split(',') + 'schema_ignore_params' + if (!expectedParams.contains(specifiedParam) && !params_ignore.contains(specifiedParam)) { + unexpectedParams.push(specifiedParam) + } + } + + //=====================================================================// + // Validate parameters against the schema + InputStream inputStream = new File(jsonSchema).newInputStream() + JSONObject rawSchema = new JSONObject(new JSONTokener(inputStream)) + + // Remove anything that's in params.schema_ignore_params + rawSchema = removeIgnoredParams(rawSchema, params) + + Schema schema = SchemaLoader.load(rawSchema) + + // Clean the parameters + def cleanedParams = cleanParameters(params) + + // Convert to JSONObject + def jsonParams = new JsonBuilder(cleanedParams) + JSONObject paramsJSON = new JSONObject(jsonParams.toString()) + + // Validate + try { + schema.validate(paramsJSON) + } catch (ValidationException e) { + println '' + log.error 'ERROR: Validation of pipeline parameters failed!' + JSONObject exceptionJSON = e.toJSON() + printExceptions(exceptionJSON, paramsJSON, log) + println '' + has_error = true + } + + // Check for unexpected parameters + if (unexpectedParams.size() > 0) { + Map colors = log_colours(params.monochrome_logs) + println '' + def warn_msg = 'Found unexpected parameters:' + for (unexpectedParam in unexpectedParams) { + warn_msg = warn_msg + "\n* --${unexpectedParam}: ${params[unexpectedParam].toString()}" + } + log.warn warn_msg + log.info "- ${colors.dim}Ignore this warning: params.schema_ignore_params = \"${unexpectedParams.join(',')}\" ${colors.reset}" + println '' + } + + if (has_error) { + System.exit(1) + } + } + + // Loop over nested exceptions and print the causingException + private static void printExceptions(exJSON, paramsJSON, log) { + def causingExceptions = exJSON['causingExceptions'] + if (causingExceptions.length() == 0) { + def m = exJSON['message'] =~ /required key \[([^\]]+)\] not found/ + // Missing required param + if (m.matches()) { + log.error "* Missing required parameter: --${m[0][1]}" + } + // Other base-level error + else if (exJSON['pointerToViolation'] == '#') { + log.error "* ${exJSON['message']}" + } + // Error with specific param + else { + def param = exJSON['pointerToViolation'] - ~/^#\// + def param_val = paramsJSON[param].toString() + log.error "* --${param}: ${exJSON['message']} (${param_val})" + } + } + for (ex in causingExceptions) { + printExceptions(ex, paramsJSON, log) + } + } + + // Remove an element from a JSONArray + private static JSONArray removeElement(jsonArray, element){ + def list = [] + int len = jsonArray.length() + for (int i=0;i + if(rawSchema.keySet().contains('definitions')){ + rawSchema.definitions.each { definition -> + for (key in definition.keySet()){ + if (definition[key].get("properties").keySet().contains(ignore_param)){ + // Remove the param to ignore + definition[key].get("properties").remove(ignore_param) + // If the param was required, change this + if (definition[key].has("required")) { + def cleaned_required = removeElement(definition[key].required, ignore_param) + definition[key].put("required", cleaned_required) + } + } + } + } + } + if(rawSchema.keySet().contains('properties') && rawSchema.get('properties').keySet().contains(ignore_param)) { + rawSchema.get("properties").remove(ignore_param) + } + if(rawSchema.keySet().contains('required') && rawSchema.required.contains(ignore_param)) { + def cleaned_required = removeElement(rawSchema.required, ignore_param) + rawSchema.put("required", cleaned_required) + } + } + return rawSchema + } + + private static Map cleanParameters(params) { + def new_params = params.getClass().newInstance(params) + for (p in params) { + // remove anything evaluating to false + if (!p['value']) { + new_params.remove(p.key) + } + // Cast MemoryUnit to String + if (p['value'].getClass() == nextflow.util.MemoryUnit) { + new_params.replace(p.key, p['value'].toString()) + } + // Cast Duration to String + if (p['value'].getClass() == nextflow.util.Duration) { + new_params.replace(p.key, p['value'].toString()) + } + // Cast LinkedHashMap to String + if (p['value'].getClass() == LinkedHashMap) { + new_params.replace(p.key, p['value'].toString()) + } + } + return new_params + } + + /* + * This method tries to read a JSON params file + */ + private static LinkedHashMap params_load(String json_schema) { + def params_map = new LinkedHashMap() + try { + params_map = params_read(json_schema) + } catch (Exception e) { + println "Could not read parameters settings from JSON. $e" + params_map = new LinkedHashMap() + } + return params_map + } + + private static Map log_colours(Boolean monochrome_logs) { + Map colorcodes = [:] + + // Reset / Meta + colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" + colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" + colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" + colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" + colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" + colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" + colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" + + // Regular Colors + colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" + colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" + colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" + colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" + colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" + colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" + colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" + colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" + + // Bold + colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" + colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" + colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" + colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" + colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" + colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" + colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" + colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" + + // Underline + colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" + colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" + colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" + colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" + colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" + colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" + colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" + colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" + + // High Intensity + colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" + colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" + colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" + colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" + colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" + colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" + colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" + colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" + + // Bold High Intensity + colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" + colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" + colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" + colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" + colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" + colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" + colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" + colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" + + return colorcodes + } + + static String dashed_line(monochrome_logs) { + Map colors = log_colours(monochrome_logs) + return "-${colors.dim}----------------------------------------------------${colors.reset}-" + } + + /* + Method to actually read in JSON file using Groovy. + Group (as Key), values are all parameters + - Parameter1 as Key, Description as Value + - Parameter2 as Key, Description as Value + .... + Group + - + */ + private static LinkedHashMap params_read(String json_schema) throws Exception { + def json = new File(json_schema).text + def Map schema_definitions = (Map) new JsonSlurper().parseText(json).get('definitions') + def Map schema_properties = (Map) new JsonSlurper().parseText(json).get('properties') + /* Tree looks like this in nf-core schema + * definitions <- this is what the first get('definitions') gets us + group 1 + title + description + properties + parameter 1 + type + description + parameter 2 + type + description + group 2 + title + description + properties + parameter 1 + type + description + * properties <- parameters can also be ungrouped, outside of definitions + parameter 1 + type + description + */ + + // Grouped params + def params_map = new LinkedHashMap() + schema_definitions.each { key, val -> + def Map group = schema_definitions."$key".properties // Gets the property object of the group + def title = schema_definitions."$key".title + def sub_params = new LinkedHashMap() + group.each { innerkey, value -> + sub_params.put(innerkey, value) + } + params_map.put(title, sub_params) + } + + // Ungrouped params + def ungrouped_params = new LinkedHashMap() + schema_properties.each { innerkey, value -> + ungrouped_params.put(innerkey, value) + } + params_map.put("Other parameters", ungrouped_params) + + return params_map + } + + /* + * Get maximum number of characters across all parameter names + */ + private static Integer params_max_chars(params_map) { + Integer max_chars = 0 + for (group in params_map.keySet()) { + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + if (param.size() > max_chars) { + max_chars = param.size() + } + } + } + return max_chars + } + + /* + * Beautify parameters for --help + */ + private static String params_help(workflow, params, json_schema, command) { + Map colors = log_colours(params.monochrome_logs) + Integer num_hidden = 0 + String output = '' + output += 'Typical pipeline command:\n\n' + output += " ${colors.cyan}${command}${colors.reset}\n\n" + Map params_map = params_load(json_schema) + Integer max_chars = params_max_chars(params_map) + 1 + Integer desc_indent = max_chars + 14 + Integer dec_linewidth = 160 - desc_indent + for (group in params_map.keySet()) { + Integer num_params = 0 + String group_output = colors.underlined + colors.bold + group + colors.reset + '\n' + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + if (group_params.get(param).hidden && !params.show_hidden_params) { + num_hidden += 1 + continue; + } + def type = '[' + group_params.get(param).type + ']' + def description = group_params.get(param).description + def defaultValue = group_params.get(param).default ? " [default: " + group_params.get(param).default.toString() + "]" : '' + def description_default = description + colors.dim + defaultValue + colors.reset + // Wrap long description texts + // Loosely based on https://dzone.com/articles/groovy-plain-text-word-wrap + if (description_default.length() > dec_linewidth){ + List olines = [] + String oline = "" // " " * indent + description_default.split(" ").each() { wrd -> + if ((oline.size() + wrd.size()) <= dec_linewidth) { + oline += wrd + " " + } else { + olines += oline + oline = wrd + " " + } + } + olines += oline + description_default = olines.join("\n" + " " * desc_indent) + } + group_output += " --" + param.padRight(max_chars) + colors.dim + type.padRight(10) + colors.reset + description_default + '\n' + num_params += 1 + } + group_output += '\n' + if (num_params > 0){ + output += group_output + } + } + output += dashed_line(params.monochrome_logs) + if (num_hidden > 0){ + output += colors.dim + "\n Hiding $num_hidden params, use --show_hidden_params to show.\n" + colors.reset + output += dashed_line(params.monochrome_logs) + } + return output + } + + /* + * Groovy Map summarising parameters/workflow options used by the pipeline + */ + private static LinkedHashMap params_summary_map(workflow, params, json_schema) { + // Get a selection of core Nextflow workflow options + def Map workflow_summary = [:] + if (workflow.revision) { + workflow_summary['revision'] = workflow.revision + } + workflow_summary['runName'] = workflow.runName + if (workflow.containerEngine) { + workflow_summary['containerEngine'] = "$workflow.containerEngine" + } + if (workflow.container) { + workflow_summary['container'] = "$workflow.container" + } + workflow_summary['launchDir'] = workflow.launchDir + workflow_summary['workDir'] = workflow.workDir + workflow_summary['projectDir'] = workflow.projectDir + workflow_summary['userName'] = workflow.userName + workflow_summary['profile'] = workflow.profile + workflow_summary['configFiles'] = workflow.configFiles.join(', ') + + // Get pipeline parameters defined in JSON Schema + def Map params_summary = [:] + def blacklist = ['hostnames'] + def params_map = params_load(json_schema) + for (group in params_map.keySet()) { + def sub_params = new LinkedHashMap() + def group_params = params_map.get(group) // This gets the parameters of that particular group + for (param in group_params.keySet()) { + if (params.containsKey(param) && !blacklist.contains(param)) { + def params_value = params.get(param) + def schema_value = group_params.get(param).default + def param_type = group_params.get(param).type + if (schema_value == null) { + if (param_type == 'boolean') { + schema_value = false + } + if (param_type == 'string') { + schema_value = '' + } + if (param_type == 'integer') { + schema_value = 0 + } + } else { + if (param_type == 'string') { + if (schema_value.contains('$projectDir') || schema_value.contains('${projectDir}')) { + def sub_string = schema_value.replace('\$projectDir', '') + sub_string = sub_string.replace('\${projectDir}', '') + if (params_value.contains(sub_string)) { + schema_value = params_value + } + } + if (schema_value.contains('$params.outdir') || schema_value.contains('${params.outdir}')) { + def sub_string = schema_value.replace('\$params.outdir', '') + sub_string = sub_string.replace('\${params.outdir}', '') + if ("${params.outdir}${sub_string}" == params_value) { + schema_value = params_value + } + } + } + } + + if (params_value != schema_value) { + sub_params.put("$param", params_value) + } + } + } + params_summary.put(group, sub_params) + } + return [ 'Core Nextflow options' : workflow_summary ] << params_summary + } + + /* + * Beautify parameters for summary and return as string + */ + private static String params_summary_log(workflow, params, json_schema) { + String output = '' + def params_map = params_summary_map(workflow, params, json_schema) + def max_chars = params_max_chars(params_map) + for (group in params_map.keySet()) { + def group_params = params_map.get(group) // This gets the parameters of that particular group + if (group_params) { + output += group + '\n' + for (param in group_params.keySet()) { + output += " \u001B[1m" + param.padRight(max_chars) + ": \u001B[1m" + group_params.get(param) + '\n' + } + output += '\n' + } + } + output += "[Only displaying parameters that differ from pipeline default]\n" + output += dashed_line(params.monochrome_logs) + output += '\n\n' + dashed_line(params.monochrome_logs) + return output + } + +} diff --git a/lib/nfcore_external_java_deps.jar b/lib/nfcore_external_java_deps.jar new file mode 100644 index 00000000..805c8bb5 Binary files /dev/null and b/lib/nfcore_external_java_deps.jar differ diff --git a/main.nf b/main.nf index 2d41f0fd..0311b725 100644 --- a/main.nf +++ b/main.nf @@ -1,135 +1,84 @@ #!/usr/bin/env nextflow + /* ======================================================================================== nf-core/pgdb ======================================================================================== - nf-core/pgdb Analysis Pipeline. + nf-core/pgdb Proteogenomics database generation #### Homepage / Documentation https://github.com/nf-core/pgdb ---------------------------------------------------------------------------------------- */ -def helpMessage() { - // TODO nf-core: Add to this help message with new command line parameters - log.info nfcoreHeader() - log.info""" - - Usage: - - The typical command for running the pipeline is as follows: - - nextflow run nf-core/pgdb --input '*_R{1,2}.fastq.gz' -profile docker - - Mandatory arguments: - --input [file] Path to input data (must be surrounded with quotes) - -profile [str] Configuration profile to use. Can use multiple (comma separated) - Available: conda, docker, singularity, test, awsbatch, and more - - Options: - --genome [str] Name of iGenomes reference - --single_end [bool] Specifies that the input is single-end reads +log.info Headers.nf_core(workflow, params.monochrome_logs) - References If not specified in the configuration file or you wish to overwrite any of the references - --fasta [file] Path to fasta reference - - Other options: - --outdir [file] The output directory where the results will be saved - --publish_dir_mode [str] Mode for publishing results in the output directory. Available: symlink, rellink, link, copy, copyNoFollow, move (Default: copy) - --email [email] Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits - --email_on_fail [email] Same as --email, except only send mail if the workflow is not successful - --max_multiqc_email_size [str] Threshold size for MultiQC report to be attached in notification email. If file generated by pipeline exceeds the threshold, it will not be attached (Default: 25MB) - -name [str] Name for the pipeline run. If not specified, Nextflow will automatically generate a random mnemonic - - AWSBatch options: - --awsqueue [str] The AWSBatch JobQueue that needs to be set when running on AWSBatch - --awsregion [str] The AWS Region for your AWS Batch job to run on - --awscli [str] Path to the AWS CLI tool - """.stripIndent() -} - -// Show help message +//////////////////////////////////////////////////// +/* -- PRINT HELP -- */ +////////////////////////////////////////////////////+ +def json_schema = "$projectDir/nextflow_schema.json" if (params.help) { - helpMessage() + def command = "nextflow run nf-core/pgdb -profile docker --ensembl_name homo_sapiens" + log.info NfcoreSchema.params_help(workflow, params, json_schema, command) exit 0 } -/* - * SET UP CONFIGURATION VARIABLES - */ +//////////////////////////////////////////////////// +/* -- VALIDATE PARAMETERS -- */ +////////////////////////////////////////////////////+ -// Check if genome exists in the config file -if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { - exit 1, "The provided genome '${params.genome}' is not available in the iGenomes file. Currently the available genomes are ${params.genomes.keySet().join(", ")}" +if (params.validate_params) { + NfcoreSchema.validateParameters(params, json_schema, log) } -// TODO nf-core: Add any reference files that are needed -// Configurable reference genomes -// -// NOTE - THIS IS NOT USED IN THIS PIPELINE, EXAMPLE ONLY -// If you want to use the channel below in a process, define the following: -// input: -// file fasta from ch_fasta -// -params.fasta = params.genome ? params.genomes[ params.genome ].fasta ?: false : false -if (params.fasta) { ch_fasta = file(params.fasta, checkIfExists: true) } - -// Has the run name been specified by the user? -// this has the bonus effect of catching both -name and --name -custom_runName = params.name -if (!(workflow.runName ==~ /[a-z]+_[a-z]+/)) { - custom_runName = workflow.runName -} +/* + * SET UP CONFIGURATION VARIABLES + */ // Check AWS batch settings if (workflow.profile.contains('awsbatch')) { // AWSBatch sanity checking - if (!params.awsqueue || !params.awsregion) exit 1, "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" + if (!params.awsqueue || !params.awsregion) exit 1, 'Specify correct --awsqueue and --awsregion parameters on AWSBatch!' // Check outdir paths to be S3 buckets if running on AWSBatch // related: https://github.com/nextflow-io/nextflow/issues/813 - if (!params.outdir.startsWith('s3:')) exit 1, "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" + if (!params.outdir.startsWith('s3:')) exit 1, 'Outdir not on S3 - specify S3 Bucket to run on AWSBatch!' // Prevent trace files to be stored on S3 since S3 does not support rolling files. - if (params.tracedir.startsWith('s3:')) exit 1, "Specify a local tracedir or run without trace! S3 cannot be used for tracefiles." + if (params.tracedir.startsWith('s3:')) exit 1, 'Specify a local tracedir or run without trace! S3 cannot be used for tracefiles.' } // Stage config files -ch_multiqc_config = file("$projectDir/assets/multiqc_config.yaml", checkIfExists: true) -ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath(params.multiqc_config, checkIfExists: true) : Channel.empty() ch_output_docs = file("$projectDir/docs/output.md", checkIfExists: true) ch_output_docs_images = file("$projectDir/docs/images/", checkIfExists: true) +ensembl_downloader_config = file(params.ensembl_downloader_config, checkIfExists: true) +ensembl_config = file(params.ensembl_config) +cosmic_config = file(params.cosmic_config) +cbioportal_config = file(params.cbioportal_config) +protein_decoy_config = file(params.protein_decoy_config) + +af_field = params.af_field +ensembl_af_field = params.af_field +if (params.ensembl_name == "homo_sapiens"){ + ensembl_af_field = "MAF" +} -/* - * Create a channel for input read files - */ -if (params.input_paths) { - if (params.single_end) { - Channel - .from(params.input_paths) - .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true) ] ] } - .ifEmpty { exit 1, "params.input_paths was empty - no input files supplied" } - .into { ch_read_files_fastqc; ch_read_files_trimming } - } else { - Channel - .from(params.input_paths) - .map { row -> [ row[0], [ file(row[1][0], checkIfExists: true), file(row[1][1], checkIfExists: true) ] ] } - .ifEmpty { exit 1, "params.input_paths was empty - no input files supplied" } - .into { ch_read_files_fastqc; ch_read_files_trimming } - } -} else { - Channel - .fromFilePairs(params.input, size: params.single_end ? 1 : 2) - .ifEmpty { exit 1, "Cannot find any reads matching: ${params.input}\nNB: Path needs to be enclosed in quotes!\nIf this is single-end data, please specify --single_end on the command line." } - .into { ch_read_files_fastqc; ch_read_files_trimming } +// Pipeline checks +if ((params.cosmic || params.cosmic_celllines) && (!params.cosmic_user_name || !params.cosmic_password)){ + exit 1, "User name and password has to be provided. In order to be able to download COSMIC data. Please first register in COSMIC database (https://cancer.sanger.ac.uk/cosmic/register)." } + +//--------------------------------------------------------------- // +//---------------------- Nextflow specifics --------------------- // +//--------------------------------------------------------------- // + +//////////////////////////////////////////////////// +/* -- PRINT PARAMETER SUMMARY -- */ +//////////////////////////////////////////////////// +log.info NfcoreSchema.params_summary_log(workflow, params, json_schema) + // Header log info -log.info nfcoreHeader() def summary = [:] if (workflow.revision) summary['Pipeline Release'] = workflow.revision -summary['Run Name'] = custom_runName ?: workflow.runName -// TODO nf-core: Report custom parameters here -summary['Input'] = params.input -summary['Fasta Ref'] = params.fasta -summary['Data Type'] = params.single_end ? 'Single-End' : 'Paired-End' +summary['Run Name'] = workflow.runName summary['Max Resources'] = "$params.max_memory memory, $params.max_cpus cpus, $params.max_time time per job" if (workflow.containerEngine) summary['Container'] = "$workflow.containerEngine - $workflow.container" summary['Output dir'] = params.outdir @@ -150,10 +99,7 @@ summary['Config Files'] = workflow.configFiles.join(', ') if (params.email || params.email_on_fail) { summary['E-mail Address'] = params.email summary['E-mail on failure'] = params.email_on_fail - summary['MultiQC maxsize'] = params.max_multiqc_email_size } -log.info summary.collect { k,v -> "${k.padRight(18)}: $v" }.join("\n") -log.info "-\033[2m--------------------------------------------------\033[0m-" // Check the hostnames against configured profiles checkHostname() @@ -180,81 +126,705 @@ Channel.from(summary.collect{ [it.key, it.value] }) process get_software_versions { publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode, saveAs: { filename -> - if (filename.indexOf(".csv") > 0) filename + if (filename.indexOf('.csv') > 0) filename else null - } + } output: file 'software_versions_mqc.yaml' into ch_software_versions_yaml - file "software_versions.csv" + file 'software_versions.csv' script: - // TODO nf-core: Get all tools to print their version number here """ echo $workflow.manifest.version > v_pipeline.txt echo $workflow.nextflow.version > v_nextflow.txt - fastqc --version > v_fastqc.txt - multiqc --version > v_multiqc.txt scrape_software_versions.py &> software_versions_mqc.yaml """ } -/* - * STEP 1 - FastQC +/** + * Download data from ensembl for the particular species. + */ +process ensembl_fasta_download { + + when: + params.add_reference || params.ensembl || params.altorfs || params.ncrna || params.pseudogenes || params.vcf + + input: + file ensembl_downloader_config + + output: + file 'database_ensembl/*.pep.all.fa' into ensembl_protein_database_sub + file 'database_ensembl/*cdna.all.fa' into ensembl_cdna_database, ensembl_cdna_database_sub + file 'database_ensembl/*ncrna.fa' into ensembl_ncrna_database, ensembl_ncrna_database_sub + file 'database_ensembl/*.dna*.fa' into genome_fasta + file 'database_ensembl/*.gtf' into gtf + + script: + """ + pypgatk_cli.py ensembl-downloader \\ + --config_file $ensembl_downloader_config \\ + --ensembl_name $params.ensembl_name \\ + -sv -sc + """ +} + +process add_reference_proteome { + + when: + params.add_reference + + input: + file reference_proteome from ensembl_protein_database_sub + + output: + file 'reference_proteome.fa' into ensembl_protein_database + + script: + """ + cat $reference_proteome >> reference_proteome.fa + """ + +} + +/** + * Concatenate cDNA and ncRNA databases + **/ +process merge_cdnas { + + input: + file a from ensembl_cdna_database_sub.collect() + file b from ensembl_ncrna_database_sub.collect() + + output: + file 'total_cdnas.fa' into total_cdnas + + script: + """ + cat $a >> total_cdnas.fa + cat $b >> total_cdnas.fa + """ +} + +/** + * Creates the ncRNA protein database + */ +process add_ncrna { + + when: + params.ncrna + + input: + file x from total_cdnas + file ensembl_config + + output: + file 'ncRNAs_proteinDB.fa' into optional_ncrna + + script: + """ + pypgatk_cli.py dnaseq-to-proteindb \\ + --config_file "$ensembl_config" \\ + --input_fasta $x \\ + --output_proteindb ncRNAs_proteinDB.fa \\ + --include_biotypes "${params.biotypes['ncRNA']}" \\ + --skip_including_all_cds --var_prefix ncRNA_ + """ +} + +merged_databases = ensembl_protein_database.mix(optional_ncrna) + +/** + * Creates the pseudogenes protein database + */ +process add_pseudogenes { + + when: + params.pseudogenes + + input: + file x from total_cdnas + file ensembl_config + + output: + file 'pseudogenes_proteinDB.fa' into optional_pseudogenes + + script: + """ + pypgatk_cli.py dnaseq-to-proteindb \\ + --config_file "$ensembl_config" \\ + --input_fasta "$x" \\ + --output_proteindb pseudogenes_proteinDB.fa \\ + --include_biotypes "${params.biotypes['pseudogene']}" \\ + --skip_including_all_cds \\ + --var_prefix pseudo_ + """ +} + +merged_databases = merged_databases.mix(optional_pseudogenes) + +/** + * Creates the altORFs protein database + */ +process add_altorfs { + + when: + params.altorfs + + input: + file x from ensembl_cdna_database + file ensembl_config + + output: + file('altorfs_proteinDB.fa') into optional_altorfs + + script: + """ + pypgatk_cli.py dnaseq-to-proteindb \\ + --config_file "$ensembl_config" {{ + --input_fasta "$x" \\ + --output_proteindb altorfs_proteinDB.fa \\ + --include_biotypes "${params.biotypes['protein_coding']}'" \\ + --skip_including_all_cds \\ + --var_prefix altorf_ + """ +} + +merged_databases = merged_databases.mix(optional_altorfs) + +/* Mutations to proteinDB */ + +/** + * Download COSMIC Mutations + */ +process cosmic_download { + + when: + params.cosmic || params.cosmic_celllines + + input: + file cosmic_config + + output: + file "database_cosmic/All_COSMIC_Genes.fasta" into cosmic_genes + file "database_cosmic/CosmicMutantExport.tsv" into cosmic_mutations + file "database_cosmic/All_CellLines_Genes.fasta" into cosmic_celllines_genes + file "database_cosmic/CosmicCLP_MutantExport.tsv" into cosmic_celllines_mutations + + script: + """ + pypgatk_cli.py cosmic-downloader \\ + --config_file "$cosmic_config" \\ + --username $params.cosmic_user_name \\ + --password $params.cosmic_password + """ +} + +/** + * Generate proteindb from cosmic mutations +*/ +process cosmic_proteindb { + + when: + params.cosmic + + input: + file g from cosmic_genes + file m from cosmic_mutations + file cosmic_config + + output: + file 'cosmic_proteinDB*.fa' into cosmic_proteindbs + + script: + """ + pypgatk_cli.py cosmic-to-proteindb \\ + --config_file "$cosmic_config" \\ + --input_mutation $m --input_genes $g \\ + --filter_column 'Histology subtype 1' \\ + --accepted_values $params.cosmic_cancer_type \\ + --output_db cosmic_proteinDB.fa + """ +} + +merged_databases = merged_databases.mix(cosmic_proteindbs) + +/** + * Generate proteindb from cosmic cell lines mutations +*/ +process cosmic_celllines_proteindb { + + when: + params.cosmic_celllines + + input: + file g from cosmic_celllines_genes + file m from cosmic_celllines_mutations + file cosmic_config + + output: + file 'cosmic_celllines_proteinDB*.fa' into cosmic_celllines_proteindbs + + script: + """ + pypgatk_cli.py cosmic-to-proteindb \\ + --config_file "$cosmic_config" \\ + --input_mutation $m \\ + --input_genes $g \\ + --filter_column 'Sample name' \\ + --accepted_values $params.cosmic_cellline_name \\ + --output_db cosmic_celllines_proteinDB.fa + """ +} + +merged_databases = merged_databases.mix(cosmic_celllines_proteindbs) + +/** + * Download VCF files from ensembl for the particular species. + */ +process ensembl_vcf_download { + + when: + params.ensembl + + input: + file ensembl_downloader_config + + output: + file "database_ensembl/*.vcf" into ensembl_vcf_files + + script: + """ + pypgatk_cli.py ensembl-downloader \\ + --config_file $ensembl_downloader_config \\ + --ensembl_name $params.ensembl_name \\ + -sg -sp -sc -sd -sn + """ +} + +process check_ensembl_vcf { + + label 'process_medium' + label 'process_single_thread' + + when: + params.ensembl + + input: + file vcf_file from ensembl_vcf_files + + output: + file "checked_*.vcf" into ensembl_vcf_files_checked + + script: + """ + awk 'BEGIN{FS=OFS="\t"}{if(\$1~"#" || (\$5!="" && \$4!="")) print}' $vcf_file > checked_$vcf_file + """ +} + +/** + * Generate protein database(s) from ENSEMBL vcf file(s) */ -process fastqc { - tag "$name" +process ensembl_vcf_proteinDB { + label 'process_medium' - publishDir "${params.outdir}/fastqc", mode: params.publish_dir_mode, + label 'process_single_thread' + + when: + params.ensembl + + input: + file v from ensembl_vcf_files_checked + file f from total_cdnas + file g from gtf + file e from ensembl_config + + output: + file "${v}_proteinDB.fa" into proteinDB_vcf + + script: + """ + pypgatk_cli.py vcf-to-proteindb \\ + --config_file $e \\ + --af_field "$ensembl_af_field" \\ + --input_fasta $f \\ + --gene_annotations_gtf $g \\ + --vcf $v \\ + --output_proteindb "${v}_proteinDB.fa" \\ + --var_prefix ensvar \\ + --annotation_field_name 'CSQ' + """ +} + +//concatenate all ensembl proteindbs into one +proteinDB_vcf.collectFile(name: 'ensembl_proteindb.fa', newLine: false, storeDir: "${projectDir}/result") + .set {proteinDB_vcf_final} + +merged_databases = merged_databases.mix(proteinDB_vcf_final) + +/****** Custom VCF *****/ +/** + * Generate protein databse for a given VCF + */ +process gtf_to_fasta { + + when: + params.vcf + + input: + file g from gtf + file f from genome_fasta + + output: + file "transcripts.fa" into gtf_transcripts_fasta + + script: + """ + gffread -w transcripts.fa -g $f $g + """ +} + +vcf_file = params.vcf_file ? Channel.fromPath(params.vcf_file, checkIfExists: true) : Channel.empty() + +process vcf_proteinDB { + + when: + params.vcf + + input: + file v from vcf_file + file f from gtf_transcripts_fasta + file g from gtf + file e from ensembl_config + + output: + file "*_proteinDB.fa" into proteinDB_custom_vcf + + script: + """ + awk 'BEGIN{FS=OFS="\t"}{if(\$1=="chrM") \$1="MT"; gsub("chr","",\$1); print}' \\ + $v > ${v.baseName}_changedChrNames.vcf + + pypgatk_cli.py vcf-to-proteindb \\ + --config_file $e \\ + --af_field "$af_field" \\ + --input_fasta $f \\ + --gene_annotations_gtf $g \\ + --vcf ${v.baseName}_changedChrNames.vcf \\ + --output_proteindb ${v.baseName}_proteinDB.fa \\ + --annotation_field_name '' + """ +} + +merged_databases = merged_databases.mix(proteinDB_custom_vcf) + + +/****** gnomAD variatns *****/ + +/** + * Download gencode files (fasta and gtf) + */ +process gencode_download { + + when: + params.gnomad + + input: + val g from params.gencode_url + + output: + file("gencode.v19.pc_transcripts.fa") into gencode_fasta + file("gencode.v19.annotation.gtf") into gencode_gtf + + script: + """ + wget ${g}/gencode.v19.pc_transcripts.fa.gz + wget ${g}/gencode.v19.annotation.gtf.gz + gunzip *.gz + """ +} + +/** + * Download gnomAD variants (VCF) - requires gsutil + */ +process gnomad_download { + + when: + params.gnomad + + input: + val g from params.gnomad_file_url + + output: + file "*.vcf.bgz" into gnomad_vcf_bgz + + script: + """ + gsutil cp $g . + """ +} + +/** + * Extract gnomAD VCF + */ +process extract_gnomad_vcf { + + when: + params.gnomad + + input: + file g from gnomad_vcf_bgz.flatten().map{ file(it) } + + output: + file "*.vcf" into gnomad_vcf_files + + script: + """ + zcat $g > ${g}.vcf + """ +} + +/** + * Generate gmomAD proteinDB + */ +process gnomad_proteindb { + + when: + params.gnomad + + input: + file v from gnomad_vcf_files + file f from gencode_fasta + file g from gencode_gtf + file e from ensembl_config + + output: + file "${v}_proteinDB.fa" into gnomad_vcf_proteindb + + script: + """ + pypgatk_cli.py vcf-to-proteindb \\ + --config_file $e \\ + --vcf $v \\ + --input_fasta $f \\ + --gene_annotations_gtf $g \\ + --output_proteindb "${v}_proteinDB.fa" \\ + --af_field controls_AF \\ + --transcript_index 6 \\ + --annotation_field_name vep \\ + --var_prefix gnomadvar + """ +} + +//concatenate all gnomad proteindbs into one +gnomad_vcf_proteindb.collectFile(name: 'gnomad_proteindb.fa', newLine: false, storeDir: "${projectDir}/result") + .set {gnomad_vcf_proteindb_final} + +merged_databases = merged_databases.mix(gnomad_vcf_proteindb_final) + +/****** cBioPortal mutations *****/ +/** + * Download GRCh37 CDS file from ENSEMBL release 75 + */ +process cds_GRCh37_download { + + when: + params.cbioportal + + output: + file("Homo_sapiens.GRCh37.75.cds.all.fa") into ch_GRCh37_cds + + script: + """ + wget ftp://ftp.ensembl.org/pub/release-75/fasta/homo_sapiens/cds/Homo_sapiens.GRCh37.75.cds.all.fa.gz + gunzip *.gz + """ +} + +/** + * Download all cBioPortal studies using git-lfs +*/ +process download_all_cbioportal { + + when: + params.cbioportal + + output: + file('cbioportal_allstudies_data_mutations_mskcc.txt') into cbio_mutations + file('cbioportal_allstudies_data_clinical_sample.txt') into cbio_samples + + script: + if (params.cbioportal_study_id == "all") + """ + git clone https://github.com/cBioPortal/datahub.git . + git lfs install --local --skip-smudge + git lfs pull -I public --include "data*clinical*sample.txt" + git lfs pull -I public --include "data_mutations_mskcc.txt" + cat public/*/data_mutations_mskcc.txt > cbioportal_allstudies_data_mutations_mskcc.txt + cat public/*/*data*clinical*sample.txt | \\ + awk 'BEGIN{FS=OFS="\\t"}{if(\$1!~"#SAMPLE_ID"){gsub("#SAMPLE_ID", "\\nSAMPLE_ID");} print}' | \\ + awk 'BEGIN{FS=OFS="\\t"}{s=0; j=0; \\ + for(i=1;i<=NF;i++){ \\ + if(\$i=="CANCER_TYPE_DETAILED") j=1; \\ + if(\$i=="CANCER_TYPE") s=1; \\ + } \\ + if(j==1 && s==0){ \\ + gsub("CANCER_TYPE_DETAILED", "CANCER_TYPE"); \\ + } \\ + print; \\ + }' \\ + > cbioportal_allstudies_data_clinical_sample.txt + """ + else + """ + pypgatk_cli.py cbioportal-downloader \\ + --config_file "$cbioportal_config" \\ + -d "$params.cbioportal_study_id" + + tar -xzvf database_cbioportal/${params.cbioportal_study_id}.tar.gz + cat ${params.cbioportal_study_id}/data_mutations_mskcc.txt > cbioportal_allstudies_data_mutations_mskcc.txt + cat ${params.cbioportal_study_id}/data_clinical_sample.txt | \\ + awk 'BEGIN{FS=OFS="\\t"}{if(\$1!~"#SAMPLE_ID"){gsub("#SAMPLE_ID", "\\nSAMPLE_ID");} print}' | \\ + awk 'BEGIN{FS=OFS="\\t"}{s=0; j=0; \\ + for(i=1;i<=NF;i++){ \\ + if(\$i=="CANCER_TYPE_DETAILED") j=1; if(\$i=="CANCER_TYPE") s=1; \\ + } \\ + if(j==1 && s==0){gsub("CANCER_TYPE_DETAILED", "CANCER_TYPE");} print;}' \\ + > cbioportal_allstudies_data_clinical_sample.txt + """ +} + +/** + * Generate proteinDB from cBioPortal mutations + */ +process cbioportal_proteindb { + + when: + params.cbioportal + + input: + file g from ch_GRCh37_cds + file m from cbio_mutations + file s from cbio_samples + file cbioportal_config + + output: + file 'cbioPortal_proteinDB*.fa' into cBioportal_proteindb + + script: + """ + pypgatk_cli.py cbioportal-to-proteindb \\ + --config_file $cbioportal_config \\ + --input_mutation $m \\ + --input_cds $g \\ + --clinical_sample_file $s \\ + --filter_column $params.cbioportal_filter_column \\ + --accepted_values $params.cbioportal_accepted_values \\ + --output_db cbioPortal_proteinDB.fa + """ +} + +merged_databases = merged_databases.mix(cBioportal_proteindb) + +/** + * Concatenate all generated databases from merged_databases channel to the final_database_protein file + */ +process merge_proteindbs { + + publishDir "${params.outdir}/", mode: params.publish_dir_mode, + // Final step if not cleaning or creating a decoy database - save output to params.final_database_protein saveAs: { filename -> - filename.indexOf(".zip") > 0 ? "zips/$filename" : "$filename" - } + params.clean_database || params.decoy ? null : params.final_database_protein + } input: - set val(name), file(reads) from ch_read_files_fastqc + file("proteindb*") from merged_databases.collect() output: - file "*_fastqc.{zip,html}" into ch_fastqc_results + file 'merged_databases.fa' into to_clean_ch script: """ - fastqc --quiet --threads $task.cpus $reads + cat proteindb* > merged_databases.fa """ } -/* - * STEP 2 - MultiQC +/** + * clean the database for stop codons, and unwanted AA like: *, also remove proteins with less than 6 AA + */ +process clean_protein_database { + + publishDir "${params.outdir}/", mode: params.publish_dir_mode, + // Final step if not creating a decoy database - save output to params.final_database_protein + saveAs: { filename -> + params.decoy ? null : params.final_database_protein + } + + when: + params.clean_database + + input: + file file from to_clean_ch + file e from ensembl_config + + output: + file 'database_clean.fa' into clean_database_sh + + script: + stop_codons = '' + if (params.add_stop_codons){ + stop_codons = "--add_stop_codons" + } + + """ + pypgatk_cli.py ensembl-check \\ + -in "$file" \\ + --config_file "$e" \\ + -out database_clean.fa \\ + --num_aa "$params.minimum_aa" \\ + "$stop_codons" + """ +} + +to_protein_decoy_ch = params.clean_database ? clean_database_sh : to_clean_ch + +/** + * Create the decoy database using DecoyPYrat + * Decoy sequences will have "DECOY_" prefix tag to the protein accession. */ -process multiqc { - publishDir "${params.outdir}/MultiQC", mode: params.publish_dir_mode +process decoy { + + publishDir "${params.outdir}/", mode: params.publish_dir_mode, + saveAs: { filename -> params.final_database_protein } + + when: + params.decoy input: - file (multiqc_config) from ch_multiqc_config - file (mqc_custom_config) from ch_multiqc_custom_config.collect().ifEmpty([]) - // TODO nf-core: Add in log files from your new processes for MultiQC to find! - file ('fastqc/*') from ch_fastqc_results.collect().ifEmpty([]) - file ('software_versions/*') from ch_software_versions_yaml.collect() - file workflow_summary from ch_workflow_summary.collectFile(name: "workflow_summary_mqc.yaml") + file f from to_protein_decoy_ch + file protein_decoy_config output: - file "*multiqc_report.html" into ch_multiqc_report - file "*_data" - file "multiqc_plots" + file 'decoy_database.fa' into fasta_decoy_db_ch script: - rtitle = custom_runName ? "--title \"$custom_runName\"" : '' - rfilename = custom_runName ? "--filename " + custom_runName.replaceAll('\\W','_').replaceAll('_+','_') + "_multiqc_report" : '' - custom_config_file = params.multiqc_config ? "--config $mqc_custom_config" : '' - // TODO nf-core: Specify which MultiQC modules to use with -m for a faster run time """ - multiqc -f $rtitle $rfilename $custom_config_file . + pypgatk_cli.py generate-decoy \\ + --method "$params.decoy_method" \\ + --enzyme "$params.decoy_enzyme" \\ + --config_file $protein_decoy_config \\ + --input_database $f \\ + --decoy_prefix "$params.decoy_prefix" \\ + --output_database decoy_database.fa """ } + /* - * STEP 3 - Output Description HTML + * Output Description HTML */ process output_documentation { + publishDir "${params.outdir}/pipeline_info", mode: params.publish_dir_mode input: @@ -262,7 +832,7 @@ process output_documentation { file images from ch_output_docs_images output: - file "results_description.html" + file 'results_description.html' script: """ @@ -282,7 +852,7 @@ workflow.onComplete { } def email_fields = [:] email_fields['version'] = workflow.manifest.version - email_fields['runName'] = custom_runName ?: workflow.runName + email_fields['runName'] = workflow.runName email_fields['success'] = workflow.success email_fields['dateComplete'] = workflow.complete email_fields['duration'] = workflow.duration @@ -303,21 +873,6 @@ workflow.onComplete { email_fields['summary']['Nextflow Build'] = workflow.nextflow.build email_fields['summary']['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp - // TODO nf-core: If not using MultiQC, strip out this code (including params.max_multiqc_email_size) - // On success try attach the multiqc report - def mqc_report = null - try { - if (workflow.success) { - mqc_report = ch_multiqc_report.getVal() - if (mqc_report.getClass() == ArrayList) { - log.warn "[nf-core/pgdb] Found multiple reports from process 'multiqc', will use only one" - mqc_report = mqc_report[0] - } - } - } catch (all) { - log.warn "[nf-core/pgdb] Could not attach MultiQC report to summary email" - } - // Check if we are only sending emails on failure email_address = params.email if (!params.email && params.email_on_fail && !workflow.success) { @@ -352,7 +907,7 @@ workflow.onComplete { // Catch failures and try with plaintext def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] if ( mqc_report.size() <= params.max_multiqc_email_size.toBytes() ) { - mail_cmd += [ '-A', mqc_report ] + mail_cmd += [ '-A', mqc_report ] } mail_cmd.execute() << email_html log.info "[nf-core/pgdb] Sent summary e-mail to $email_address (mail)" @@ -389,28 +944,9 @@ workflow.onComplete { } - -def nfcoreHeader() { - // Log colors ANSI codes - c_black = params.monochrome_logs ? '' : "\033[0;30m"; - c_blue = params.monochrome_logs ? '' : "\033[0;34m"; - c_cyan = params.monochrome_logs ? '' : "\033[0;36m"; - c_dim = params.monochrome_logs ? '' : "\033[2m"; - c_green = params.monochrome_logs ? '' : "\033[0;32m"; - c_purple = params.monochrome_logs ? '' : "\033[0;35m"; - c_reset = params.monochrome_logs ? '' : "\033[0m"; - c_white = params.monochrome_logs ? '' : "\033[0;37m"; - c_yellow = params.monochrome_logs ? '' : "\033[0;33m"; - - return """ -${c_dim}--------------------------------------------------${c_reset}- - ${c_green},--.${c_black}/${c_green},-.${c_reset} - ${c_blue} ___ __ __ __ ___ ${c_green}/,-._.--~\'${c_reset} - ${c_blue} |\\ | |__ __ / ` / \\ |__) |__ ${c_yellow}} {${c_reset} - ${c_blue} | \\| | \\__, \\__/ | \\ |___ ${c_green}\\`-._,-`-,${c_reset} - ${c_green}`._,._,\'${c_reset} - ${c_purple} nf-core/pgdb v${workflow.manifest.version}${c_reset} - -${c_dim}--------------------------------------------------${c_reset}- - """.stripIndent() +workflow.onError { + // Print unexpected parameters - easiest is to just rerun validation + NfcoreSchema.validateParameters(params, json_schema, log) } def checkHostname() { @@ -419,15 +955,15 @@ def checkHostname() { def c_red = params.monochrome_logs ? '' : "\033[1;91m" def c_yellow_bold = params.monochrome_logs ? '' : "\033[1;93m" if (params.hostnames) { - def hostname = "hostname".execute().text.trim() + def hostname = 'hostname'.execute().text.trim() params.hostnames.each { prof, hnames -> hnames.each { hname -> if (hostname.contains(hname) && !workflow.profile.contains(prof)) { - log.error "====================================================\n" + + log.error '====================================================\n' + " ${c_red}WARNING!${c_reset} You are running with `-profile $workflow.profile`\n" + " but your machine hostname is ${c_white}'$hostname'${c_reset}\n" + " ${c_yellow_bold}It's highly recommended that you use `-profile $prof${c_reset}`\n" + - "============================================================" + '============================================================' } } } diff --git a/nextflow.config b/nextflow.config index 4e58e935..64687ac2 100644 --- a/nextflow.config +++ b/nextflow.config @@ -8,32 +8,96 @@ // Global default params, used in configs params { - // Workflow flags - // TODO nf-core: Specify your pipeline's command line flags - genome = false - input = "data/*{1,2}.fastq.gz" - single_end = false + // process flag variables + ncrna = false + pseudogenes = false + altorfs = false + vcf = false + cbioportal = false + cosmic = false + cosmic_celllines = false + ensembl = false + gnomad = false + add_reference = true + + // Output results outdir = './results' + + // Clean database options + clean_database = false + minimum_aa = 6 + add_stop_codons = true + + // data download variables + cosmic_user_name = null + cosmic_password = null + + // config files + ensembl_downloader_config = "$projectDir/conf/ensembl_downloader_config.yaml" + ensembl_config = "$projectDir/conf/ensembl_config.yaml" + cosmic_config = "$projectDir/conf/cosmic_config.yaml" + cbioportal_config = "$projectDir/conf/cbioportal_config.yaml" + protein_decoy_config = "$projectDir/conf/protein_decoy.yaml" + + // ENSEMBL parameters + ensembl_name = 'homo_sapiens' + + /* Biotype groups according to: + * https://www.ensembl.org/Help/Faq?id=468 and + * http://vega.archive.ensembl.org/info/about/gene_and_transcript_types.html + */ + + biotypes = [ + 'protein_coding': "protein_coding,polymorphic_pseudogene,non_stop_decay,nonsense_mediated_decay,IG_C_gene,IG_D_gene,IG_J_gene,IG_V_gene,TR_C_gene,TR_D_gene,TR_J_gene,TR_V_gene,TEC", + 'pseudogene': "pseudogene,IG_C_pseudogene,IG_J_pseudogene,IG_V_pseudogene,IG_pseudogene,TR_V_pseudogene,TR_J_pseudogene,processed_pseudogene,rRNA_pseudogene,transcribed_processed_pseudogene,transcribed_unitary_pseudogene,transcribed_unprocessed_pseudogene,translated_unprocessed_pseudogene,unitary_pseudogene,unprocessed_pseudogene,translated_processed_pseudogene", + 'ncRNA': "lncRNA,Mt_rRNA,Mt_tRNA,miRNA,misc_RNA,rRNA,retained_intron,ribozyme,sRNA,scRNA,scaRNA,snRNA,snoRNA,vaultRNA", + ] + + // vcf-to-proteindb parameters + vcf = false + vcf_file = false + cosmic_cancer_type = 'all' + cosmic_cellline_name = 'all' + cbioportal_study_id = 'all' + cbioportal_accepted_values = 'all' + cbioportal_filter_column = 'CANCER_TYPE' + af_field = "" // set to empty when AF_field does not exist in the INFO filed or filtering on AF is not desired + + + // Output parameters + final_database_protein = "final_proteinDB.fa" + + // Decoy options + decoy_prefix = "Decoy_" + decoy = false + decoy_method = "decoypyrat" + decoy_enzyme = "Trypsin" + + // gencode download parameters + gencode_url = "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19" + gnomad_file_url = "gs://gnomad-public/release/2.1.1/vcf/genomes/gnomad.genomes.r2.1.1.sites.*.vcf.bgz" + gnomad_file_url = "gs://gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz" // use for testing the pipeline, smaller file - only exomes + publish_dir_mode = 'copy' // Boilerplate options - name = false - multiqc_config = false email = false email_on_fail = false max_multiqc_email_size = 25.MB plaintext_email = false monochrome_logs = false help = false - igenomes_base = 's3://ngi-igenomes/igenomes/' tracedir = "${params.outdir}/pipeline_info" - igenomes_ignore = false custom_config_version = 'master' custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" hostnames = false - config_profile_description = false - config_profile_contact = false - config_profile_url = false + config_profile_name = null + config_profile_description = null + config_profile_contact = null + config_profile_url = null + validate_params = true + show_hidden_params = false + schema_ignore_params = 'biotypes' // Defaults only, expecting to be overwritten max_memory = 128.GB @@ -44,7 +108,7 @@ params { // Container slug. Stable releases should specify release tag! // Developmental code should specify :dev -process.container = 'nfcore/pgdb:dev' +process.container = 'nfcore/pgdb:1.0.0' // Load base.config by default for all pipelines includeConfig 'conf/base.config' @@ -57,10 +121,22 @@ try { } profiles { - conda { process.conda = "$projectDir/environment.yml" } + conda { + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud = false + conda.createTimeout = '1 h' + process.conda = "$projectDir/environment.yml" + } debug { process.beforeScript = 'echo $HOSTNAME' } docker { docker.enabled = true + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false // Avoid this error: // WARNING: Your kernel does not support swap limit capabilities or the cgroup is not mounted. Memory limited without swap. // Testing this in nf-core after discussion here https://github.com/nf-core/tools/pull/351 @@ -68,19 +144,37 @@ profiles { docker.runOptions = '-u \$(id -u):\$(id -g)' } singularity { + docker.enabled = false singularity.enabled = true + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false singularity.autoMounts = true } podman { + singularity.enabled = false + docker.enabled = false podman.enabled = true + shifter.enabled = false + charliecloud = false + } + shifter { + singularity.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = true + charliecloud.enabled = false + } + charliecloud { + singularity.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = true } test { includeConfig 'conf/test.config' } test_full { includeConfig 'conf/test_full.config' } -} - -// Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' + dev { includeConfig 'conf/dev.config' } } // Export these variables to prevent local Python/R libraries from conflicting with those in the container @@ -114,10 +208,10 @@ manifest { name = 'nf-core/pgdb' author = 'Husen M. Umer & Yasset Perez-Riverol' homePage = 'https://github.com/nf-core/pgdb' - description = 'The ProteoGenomics database generation workflow (pgdb) use the pypgatk and nextflow to create different protein databases for ProteoGenomics data analysis.' + description = 'Proteogenomics database creation workflow using pypgatk framework. ' mainScript = 'main.nf' nextflowVersion = '>=20.04.0' - version = '1.0dev' + version = '1.0.0' } // Function to ensure that resource requirements don't go beyond diff --git a/nextflow_schema.json b/nextflow_schema.json index 86a061f4..a456208b 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -2,76 +2,249 @@ "$schema": "http://json-schema.org/draft-07/schema", "$id": "https://raw.githubusercontent.com/nf-core/pgdb/master/nextflow_schema.json", "title": "nf-core/pgdb pipeline parameters", - "description": "The ProteoGenomics database generation workflow (pgdb) use the pypgatk and nextflow to create different protein databases for ProteoGenomics data analysis.", + "description": "Proteogenomics database creation workflow using pypgatk framework. ", "type": "object", "definitions": { - "input_output_options": { - "title": "Input/output options", + "ensembl_canonical_proteomes": { + "title": "ENSEMBL canonical proteomes", "type": "object", - "fa_icon": "fas fa-terminal", - "description": "Define where the pipeline should find input data and save output data.", - "required": [ - "input" - ], + "description": "Add ENSEMBL canonical proteomes", + "default": "", "properties": { - "input": { + "add_reference": { + "type": "boolean", + "default": true, + "description": "Add the reference proteome to the file" + }, + "ensembl_downloader_config": { + "type": "string", + "description": "Path to configuration file for ENSEMBL download parameters" + }, + "ensembl_config": { + "type": "string", + "description": "Path to configuration file for parameters in generating protein databases from ENSMEBL sequences" + }, + "gencode_url": { "type": "string", - "fa_icon": "fas fa-dna", - "description": "Input FastQ files.", - "help_text": "Use this to specify the location of your input FastQ files. For example:\n\n```bash\n--input 'path/to/data/sample_*_{1,2}.fastq'\n```\n\nPlease note the following requirements:\n\n1. The path must be enclosed in quotes\n2. The path must have at least one `*` wildcard character\n3. When using the pipeline with paired end data, the path must use `{1,2}` notation to specify read pairs.\n\nIf left unspecified, a default pattern is used: `data/*{1,2}.fastq.gz`" + "default": "ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_19", + "description": "URL for downloading GENCODE datafiles" }, - "single_end": { + "ensembl_name": { + "type": "string", + "default": "homo_sapiens", + "description": "Taxonomic term for the species to download from ENSEMBL" + } + } + }, + "non_canonical_proteome_parameters": { + "title": "Non canonical proteome parameters", + "type": "object", + "description": "Non canonical proteins generation parameters", + "default": "", + "properties": { + "ncrna": { "type": "boolean", - "description": "Specifies that the input is single-end reads.", - "fa_icon": "fas fa-align-center", - "help_text": "By default, the pipeline expects paired-end data. If you have single-end data, you need to specify `--single_end` on the command line when you launch the pipeline. A normal glob pattern, enclosed in quotation marks, can then be used for `--input`. For example:\n\n```bash\n--single_end --input '*.fastq'\n```\n\nIt is not possible to run a mixture of single-end and paired-end files in one run." + "description": "Generate protein database from non-coding RNA" }, - "outdir": { + "pseudogenes": { + "type": "boolean", + "description": "Generate protein database from pseudogenes" + }, + "altorfs": { + "type": "boolean", + "description": "Generate alternative ORFs from canonical proteins" + }, + "ensembl": { + "type": "boolean", + "description": "Download ENSEMBL variants and generate protein database" + } + } + }, + "custom_vcf_based_variant_proteomes": { + "title": "Custom VCF-based variant proteomes", + "type": "object", + "description": "Proteins generated using an input VCF", + "default": "", + "properties": { + "vcf": { + "type": "boolean", + "description": "Enable translation of a given VCF file" + }, + "vcf_file": { "type": "string", - "description": "The output directory where the results will be saved.", - "default": "./results", - "fa_icon": "fas fa-folder-open" + "description": "VCF file path to be translated. Generate variants proteins by modifying sequences of affected transcripts." }, - "email": { + "af_field": { "type": "string", - "description": "Email address for completion summary.", - "fa_icon": "fas fa-envelope", - "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", - "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" + "description": "Allele frequency identifier string in VCF Info column, if no AF info is given set it to empty." } } }, - "reference_genome_options": { - "title": "Reference genome options", + "cbioportal_variant_proteomes": { + "title": "cBioportal variant proteomes", "type": "object", - "fa_icon": "fas fa-dna", - "description": "Options for the reference genome indices used to align reads.", + "description": "cBioportal variant parameters", + "default": "", "properties": { - "genome": { + "cbioportal": { + "type": "boolean", + "description": "Download cBioPortal studies and generate protein database" + }, + "cbioportal_accepted_values": { "type": "string", - "description": "Name of iGenomes reference.", - "fa_icon": "fas fa-book", - "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`.\n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." + "default": "all", + "description": "Specify a tissue type to limit the cBioPortal mutations to a particular caner type" }, - "fasta": { + "cbioportal_filter_column": { "type": "string", - "fa_icon": "fas fa-font", - "description": "Path to FASTA genome file.", - "help_text": "If you have no genome reference available, the pipeline can build one using a FASTA file. This requires additional time and resources, so it's better to use a pre-build index if possible." + "default": "CANCER_TYPE", + "description": "Specify a column from the clinical sample file to be used for filtering records" }, - "igenomes_base": { + "cbioportal_study_id": { "type": "string", - "description": "Directory / URL base for iGenomes references.", - "default": "s3://ngi-igenomes/igenomes/", - "fa_icon": "fas fa-cloud-download-alt", - "hidden": true + "description": "Download mutations from a specific study in cbiportal default is all which downloads mutations from all studies" }, - "igenomes_ignore": { + "cbioportal_config": { + "type": "string", + "description": "cBioPortal configuration file" + } + } + }, + "cosmic_variant_proteomes": { + "title": "COSMIC variant proteomes", + "type": "object", + "description": "COSMIC variant proteins parameters", + "default": "", + "properties": { + "cosmic": { "type": "boolean", - "description": "Do not load the iGenomes reference config.", - "fa_icon": "fas fa-ban", - "hidden": true, - "help_text": "Do not load `igenomes.config` when running the pipeline. You may choose this option if you observe clashes between custom parameters and those supplied in `igenomes.config`." + "description": "Download COSMIC mutation files and generate protein database" + }, + "cosmic_celllines": { + "type": "string", + "description": "Download COSMIC cell line files and generate protein database" + }, + "cosmic_user_name": { + "type": "string", + "description": "User name (or email) for COSMIC account" + }, + "cosmic_password": { + "type": "string", + "description": "Password for COSMIC account" + }, + "cosmic_config": { + "type": "string", + "description": "Path to configuration file for parameters in generating" + }, + "cosmic_cancer_type": { + "type": "string", + "default": "all", + "description": "Specify a tissue type to limit the COSMIC mutations to a particular caner type" + }, + "cosmic_cellline_name": { + "type": "string", + "default": "all", + "description": "Specify a sample name to limit the COSMIC cell line mutations to a particular cell line" + } + } + }, + "gnomad_variant_proteomes": { + "title": "GNOMAD variant proteomes", + "type": "object", + "description": "", + "default": "", + "properties": { + "gnomad": { + "type": "boolean", + "description": "Add gNOMAD variants to the database" + }, + "gnomad_file_url": { + "type": "string", + "default": "gs://gnomad-public/release/2.1.1/vcf/exomes/gnomad.exomes.r2.1.1.sites.vcf.bgz", + "description": "gNOMAD url" + } + } + }, + "decoy_generation": { + "title": "Decoy generation", + "type": "object", + "description": "Generate decoy proteins and attach them to the final protein database", + "default": "", + "properties": { + "decoy": { + "type": "boolean", + "description": "Append the decoy proteins to the database" + }, + "decoy_prefix": { + "type": "string", + "default": "Decoy_", + "description": "String to be used as prefix for the generated decoy sequences" + }, + "decoy_method": { + "type": "string", + "default": "decoypyrat", + "description": "Method used to generate the decoy database", + "enum": [ + "protein-reverse", + "protein-shuffle", + "decoypyrat" + ] + }, + "decoy_enzyme": { + "type": "string", + "default": "Trypsin", + "description": "Enzyme used to generate the decoy" + }, + "protein_decoy_config": { + "type": "string", + "description": "Configuration file to perform the decoy generation" + } + } + }, + "clean_and_process_database": { + "title": "Clean and process database", + "type": "object", + "description": "Clean and process the resulted database", + "default": "", + "properties": { + "clean_database": { + "type": "boolean", + "description": "Clean the database for stop codons, short protein sequences" + }, + "minimum_aa": { + "type": "integer", + "default": 6, + "description": "Minimum number of AminoAcids for a protein to be included in the database" + }, + "add_stop_codons": { + "type": "boolean", + "description": "If an stop codons is found, create two proteins from it" + } + } + }, + "input_output_options": { + "title": "Input/output options", + "type": "object", + "fa_icon": "fas fa-terminal", + "description": "Define where the pipeline should find input data and save output data.", + "properties": { + "outdir": { + "type": "string", + "description": "The output directory where the results will be saved.", + "default": "./results", + "fa_icon": "fas fa-folder-open" + }, + "email": { + "type": "string", + "description": "Email address for completion summary.", + "fa_icon": "fas fa-envelope", + "help_text": "Set this parameter to your e-mail address to get a summary e-mail with details of the run sent to you when the workflow exits. If set in your user config file (`~/.nextflow/config`) then you don't need to specify this on the command line for every run.", + "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" + }, + "final_database_protein": { + "type": "string", + "default": "final_proteinDB.fa", + "description": "Filename for the final protein database" } } }, @@ -104,12 +277,12 @@ "move" ] }, - "name": { - "type": "string", - "description": "Workflow name.", - "fa_icon": "fas fa-fingerprint", - "hidden": true, - "help_text": "A custom name for the pipeline run. Unlike the core nextflow `-name` option with one hyphen this parameter can be reused multiple times, for example if using `-resume`. Passed through to steps such as MultiQC and used for things like report filenames and titles." + "validate_params": { + "type": "boolean", + "description": "Boolean whether to validate parameters against the schema at runtime", + "default": true, + "fa_icon": "fas fa-check-square", + "hidden": true }, "email_on_fail": { "type": "string", @@ -141,18 +314,19 @@ "hidden": true, "help_text": "Set to disable colourful command line output and live life in monochrome." }, - "multiqc_config": { - "type": "string", - "description": "Custom config file to supply to MultiQC.", - "fa_icon": "fas fa-cog", - "hidden": true - }, "tracedir": { "type": "string", "description": "Directory to keep pipeline Nextflow logs and reports.", "default": "${params.outdir}/pipeline_info", "fa_icon": "fas fa-cogs", "hidden": true + }, + "show_hidden_params": { + "type": "boolean", + "fa_icon": "far fa-eye-slash", + "description": "Show all params when using `--help`", + "hidden": true, + "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." } } }, @@ -176,6 +350,7 @@ "description": "Maximum amount of memory that can be requested for any single job.", "default": "128.GB", "fa_icon": "fas fa-memory", + "pattern": "^[\\d\\.]+\\s*.(K|M|G|T)?B$", "hidden": true, "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" }, @@ -184,6 +359,7 @@ "description": "Maximum amount of time that can be requested for any single job.", "default": "240.h", "fa_icon": "far fa-clock", + "pattern": "^(\\d+(\\.\\d+)?(?:\\s*|\\.?)(s|m|h|d)\\s*)+$", "hidden": true, "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" } @@ -218,6 +394,12 @@ "hidden": true, "fa_icon": "fas fa-users-cog" }, + "config_profile_name": { + "type": "string", + "description": "Institutional config name.", + "hidden": true, + "fa_icon": "fas fa-users-cog" + }, "config_profile_description": { "type": "string", "description": "Institutional config description.", @@ -241,10 +423,31 @@ }, "allOf": [ { - "$ref": "#/definitions/input_output_options" + "$ref": "#/definitions/ensembl_canonical_proteomes" + }, + { + "$ref": "#/definitions/non_canonical_proteome_parameters" + }, + { + "$ref": "#/definitions/custom_vcf_based_variant_proteomes" + }, + { + "$ref": "#/definitions/cbioportal_variant_proteomes" }, { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/definitions/cosmic_variant_proteomes" + }, + { + "$ref": "#/definitions/gnomad_variant_proteomes" + }, + { + "$ref": "#/definitions/decoy_generation" + }, + { + "$ref": "#/definitions/clean_and_process_database" + }, + { + "$ref": "#/definitions/input_output_options" }, { "$ref": "#/definitions/generic_options"