From 0ab9f89d76d4bba72f7b630ec98d2269fad6647e Mon Sep 17 00:00:00 2001 From: Florian De Temmerman Date: Wed, 15 May 2024 10:07:30 +0200 Subject: [PATCH] Merge branch 'dev' into nf-core-template-merge-2.14.1 --- .github/workflows/awsfulltest.yml | 3 - .github/workflows/ci.yml | 3 - .github/workflows/release-announcments.yml | 68 +++ .gitignore | 2 + .nf-core.yml | 11 + .pre-commit-config.yaml | 7 + .prettierignore | 1 + CHANGELOG.md | 65 ++- CITATIONS.md | 12 +- README.md | 57 +-- assets/methods_description_template.yml | 29 -- assets/multiqc_config.yml | 17 - assets/samplesheet.csv | 7 +- assets/schema_input.json | 31 +- assets/test_samplesheet.csv | 4 + bin/collect_metadata.py | 83 ++++ conf/base.config | 4 +- conf/igenomes.config | 440 ------------------ conf/modules.config | 129 ++++- conf/test.config | 19 +- conf/test_full.config | 9 +- docs/images/mqc_fastqc_adapter.png | Bin 23458 -> 0 bytes docs/images/mqc_fastqc_counts.png | Bin 33918 -> 0 bytes docs/images/mqc_fastqc_quality.png | Bin 55769 -> 0 bytes docs/images/nf-core-pixelator-metromap.svg | 246 ++++++++++ docs/output.md | 233 ++++++++-- docs/usage.md | 140 ++++-- main.nf | 23 +- modules.json | 6 +- modules/local/pixelator/collect_metadata.nf | 79 ++++ modules/local/pixelator/list_options.nf | 31 ++ .../pixelator/single-cell/amplicon/main.nf | 45 ++ .../pixelator/single-cell/analysis/main.nf | 47 ++ .../pixelator/single-cell/annotate/main.nf | 53 +++ .../pixelator/single-cell/collapse/main.nf | 54 +++ .../local/pixelator/single-cell/demux/main.nf | 54 +++ .../local/pixelator/single-cell/graph/main.nf | 48 ++ .../local/pixelator/single-cell/qc/main.nf | 78 ++++ .../pixelator/single-cell/report/main.nf | 57 +++ modules/local/rename_reads.nf | 45 ++ .../{fastqc => cat/fastq}/environment.yml | 4 +- modules/nf-core/cat/fastq/main.nf | 79 ++++ modules/nf-core/cat/fastq/meta.yml | 42 ++ modules/nf-core/cat/fastq/tests/main.nf.test | 138 ++++++ .../nf-core/cat/fastq/tests/main.nf.test.snap | 169 +++++++ modules/nf-core/cat/fastq/tests/tags.yml | 2 + .../dumpsoftwareversions}/environment.yml | 4 +- .../custom/dumpsoftwareversions/main.nf | 24 + .../custom/dumpsoftwareversions/meta.yml | 37 ++ .../templates/dumpsoftwareversions.py | 103 ++++ .../dumpsoftwareversions/tests/main.nf.test | 43 ++ .../tests/main.nf.test.snap | 33 ++ .../dumpsoftwareversions/tests/tags.yml | 2 + modules/nf-core/fastqc/main.nf | 61 --- modules/nf-core/fastqc/meta.yml | 57 --- modules/nf-core/fastqc/tests/main.nf.test | 212 --------- .../nf-core/fastqc/tests/main.nf.test.snap | 88 ---- modules/nf-core/fastqc/tests/tags.yml | 2 - modules/nf-core/multiqc/main.nf | 55 --- modules/nf-core/multiqc/meta.yml | 58 --- modules/nf-core/multiqc/tests/main.nf.test | 84 ---- modules/nf-core/multiqc/tests/tags.yml | 2 - nextflow.config | 167 ++++--- nextflow_schema.json | 348 +++++++++++--- samplesheet.csv | 3 + subworkflows/local/generate_reports.nf | 134 ++++++ .../utils_nfcore_pixelator_pipeline/main.nf | 216 ++++++++- tower.yml | 6 +- workflows/pixelator.nf | 263 +++++++++-- 69 files changed, 3232 insertions(+), 1444 deletions(-) create mode 100644 .github/workflows/release-announcments.yml delete mode 100644 assets/methods_description_template.yml delete mode 100644 assets/multiqc_config.yml create mode 100644 assets/test_samplesheet.csv create mode 100755 bin/collect_metadata.py delete mode 100644 conf/igenomes.config delete mode 100755 docs/images/mqc_fastqc_adapter.png delete mode 100755 docs/images/mqc_fastqc_counts.png delete mode 100755 docs/images/mqc_fastqc_quality.png create mode 100644 docs/images/nf-core-pixelator-metromap.svg create mode 100644 modules/local/pixelator/collect_metadata.nf create mode 100644 modules/local/pixelator/list_options.nf create mode 100644 modules/local/pixelator/single-cell/amplicon/main.nf create mode 100644 modules/local/pixelator/single-cell/analysis/main.nf create mode 100644 modules/local/pixelator/single-cell/annotate/main.nf create mode 100644 modules/local/pixelator/single-cell/collapse/main.nf create mode 100644 modules/local/pixelator/single-cell/demux/main.nf create mode 100644 modules/local/pixelator/single-cell/graph/main.nf create mode 100644 modules/local/pixelator/single-cell/qc/main.nf create mode 100644 modules/local/pixelator/single-cell/report/main.nf create mode 100644 modules/local/rename_reads.nf rename modules/nf-core/{fastqc => cat/fastq}/environment.yml (57%) create mode 100644 modules/nf-core/cat/fastq/main.nf create mode 100644 modules/nf-core/cat/fastq/meta.yml create mode 100644 modules/nf-core/cat/fastq/tests/main.nf.test create mode 100644 modules/nf-core/cat/fastq/tests/main.nf.test.snap create mode 100644 modules/nf-core/cat/fastq/tests/tags.yml rename modules/nf-core/{multiqc => custom/dumpsoftwareversions}/environment.yml (51%) create mode 100644 modules/nf-core/custom/dumpsoftwareversions/main.nf create mode 100644 modules/nf-core/custom/dumpsoftwareversions/meta.yml create mode 100755 modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap create mode 100644 modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml delete mode 100644 modules/nf-core/fastqc/main.nf delete mode 100644 modules/nf-core/fastqc/meta.yml delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test delete mode 100644 modules/nf-core/fastqc/tests/main.nf.test.snap delete mode 100644 modules/nf-core/fastqc/tests/tags.yml delete mode 100644 modules/nf-core/multiqc/main.nf delete mode 100644 modules/nf-core/multiqc/meta.yml delete mode 100644 modules/nf-core/multiqc/tests/main.nf.test delete mode 100644 modules/nf-core/multiqc/tests/tags.yml create mode 100644 samplesheet.csv create mode 100644 subworkflows/local/generate_reports.nf diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index bd9c15db..831c60e8 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -15,9 +15,6 @@ jobs: steps: - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 - # 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 with: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index a7db22d2..4168fb0f 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -39,8 +39,5 @@ jobs: uses: jlumbroso/free-disk-space@54081f138730dfa15788a46383842cd2f914a1be # v1.3.1 - 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 --outdir ./results diff --git a/.github/workflows/release-announcments.yml b/.github/workflows/release-announcments.yml new file mode 100644 index 00000000..6ad33927 --- /dev/null +++ b/.github/workflows/release-announcments.yml @@ -0,0 +1,68 @@ +name: release-announcements +# Automatic release toot and tweet anouncements +on: + release: + types: [published] + workflow_dispatch: + +jobs: + toot: + runs-on: ubuntu-latest + steps: + - uses: rzr/fediverse-action@master + with: + access-token: ${{ secrets.MASTODON_ACCESS_TOKEN }} + host: "mstdn.science" # custom host if not "mastodon.social" (default) + # GitHub event payload + # https://docs.github.com/en/developers/webhooks-and-events/webhooks/webhook-events-and-payloads#release + message: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + + send-tweet: + runs-on: ubuntu-latest + + steps: + - uses: actions/setup-python@v4 + with: + python-version: "3.10" + - name: Install dependencies + run: pip install tweepy==4.14.0 + - name: Send tweet + shell: python + run: | + import os + import tweepy + + client = tweepy.Client( + access_token=os.getenv("TWITTER_ACCESS_TOKEN"), + access_token_secret=os.getenv("TWITTER_ACCESS_TOKEN_SECRET"), + consumer_key=os.getenv("TWITTER_CONSUMER_KEY"), + consumer_secret=os.getenv("TWITTER_CONSUMER_SECRET"), + ) + tweet = os.getenv("TWEET") + client.create_tweet(text=tweet) + env: + TWEET: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + TWITTER_CONSUMER_KEY: ${{ secrets.TWITTER_CONSUMER_KEY }} + TWITTER_CONSUMER_SECRET: ${{ secrets.TWITTER_CONSUMER_SECRET }} + TWITTER_ACCESS_TOKEN: ${{ secrets.TWITTER_ACCESS_TOKEN }} + TWITTER_ACCESS_TOKEN_SECRET: ${{ secrets.TWITTER_ACCESS_TOKEN_SECRET }} + + bsky-post: + runs-on: ubuntu-latest + steps: + - uses: zentered/bluesky-post-action@v0.0.2 + with: + post: | + Pipeline release! ${{ github.repository }} v${{ github.event.release.tag_name }} - ${{ github.event.release.name }}! + + Please see the changelog: ${{ github.event.release.html_url }} + env: + BSKY_IDENTIFIER: ${{ secrets.BSKY_IDENTIFIER }} + BSKY_PASSWORD: ${{ secrets.BSKY_PASSWORD }} + # diff --git a/.gitignore b/.gitignore index 5124c9ac..d0538e85 100644 --- a/.gitignore +++ b/.gitignore @@ -6,3 +6,5 @@ results/ testing/ testing* *.pyc +.idea +.vscode diff --git a/.nf-core.yml b/.nf-core.yml index e0b85a77..f447682f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,2 +1,13 @@ repository_type: pipeline nf_core_version: "2.14.1" +lint: + # No multiqc support for now + multiqc_config: false + files_exist: + - assets/multiqc_config.yml + - conf/igenomes.config + files_unchanged: + - lib/NfcoreTemplate.groovy + - .prettierignore + # Skip warning for a removed a reference to nf-test + - .github/PULL_REQUEST_TEMPLATE.md diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 4dc0f1dc..b92f13dc 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -1,3 +1,5 @@ +exclude: ^(.*.test.snap)$ + repos: - repo: https://github.com/pre-commit/mirrors-prettier rev: "v3.1.0" @@ -11,3 +13,8 @@ repos: hooks: - id: editorconfig-checker alias: ec + + - repo: https://github.com/psf/black + rev: 24.2.0 + hooks: + - id: black diff --git a/.prettierignore b/.prettierignore index 437d763d..651a8862 100644 --- a/.prettierignore +++ b/.prettierignore @@ -1,6 +1,7 @@ email_template.html adaptivecard.json slackreport.json +.devcontainer/devcontainer.json .nextflow* work/ data/ diff --git a/CHANGELOG.md b/CHANGELOG.md index f7f10319..bf5d953d 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,14 +3,67 @@ 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). -## v1.1.0 - [date] +## [[1.2.0](https://github.com/nf-core/pixelator/releases/tag/1.2.0)] - UNRELEASED -Initial release of nf-core/pixelator, created with the [nf-core](https://nf-co.re/) template. +### Enhancements & fixes -### `Added` +- [[PR #89](https://github.com/nf-core/pixelator/pull/89)] - Template update for nf-core/tools v2.14.1 -### `Fixed` +## [[1.1.0](https://github.com/nf-core/pixelator/releases/tag/1.1.0)] - 2024-03-29 -### `Dependencies` +### Enhancements & fixes -### `Deprecated` +- [[PR #83](https://github.com/nf-core/pixelator/pull/83)] - Template update for nf-core/tools v2.13 +- [[PR #84](https://github.com/nf-core/pixelator/pull/84)] - Update pixelator to 0.16.2, collapse`and`graph` step now return parquet files +- [[PR #85](https://github.com/nf-core/pixelator/pull/85)] - Remove a workaround for container issues, silence some warnings, update default resources + +### Software dependencies + +| Dependency | Old version | New version | +| ----------- | ----------- | ----------- | +| `pixelator` | 0.15.2 | 0.16.2 | + +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. + +## [[1.0.3](https://github.com/nf-core/pixelator/releases/tag/1.0.3)] - 2024-01-19 + +### Enhancements & fixes + +- [[PR #74](https://github.com/nf-core/pixelator/pull/74)] - Template update for nf-core/tools v2.11 +- [[e196431](https://github.com/nf-core/pixelator/commit/e196431842b039cbf5c299c7a3e568f6a3e30e33)] - Workaround a tool issue by removing `docker.runOptions` user and group flags +- [[PR #76](https://github.com/nf-core/pixelator/pull/76)] - Use `adapterqc` output as main output of PIXELATOR_QC +- [[PR #77](https://github.com/nf-core/pixelator/pull/77)] - Fix some style issues in nextflow_schema.json + +## [[1.0.2](https://github.com/nf-core/pixelator/releases/tag/1.0.2)] - 2023-11-20 + +### Enhancements & fixes + +- [[PR #70](https://github.com/nf-core/pixelator/pull/70)] - Fix loading of absolute paths and urls in input samplesheet + +## [[1.0.1](https://github.com/nf-core/pixelator/releases/tag/1.0.1)] - 2023-10-27 + +### Enhancements & fixes + +- [[PR #66](https://github.com/nf-core/pixelator/pull/66)] - Add a warning and workaround for singularity & apptainer +- Cleanup some linting warnings +- Update docker image in RENAME_READS to match the singularity container + +### Software dependencies + +| Dependency | Old version | New version | +| ----------- | ----------- | ----------- | +| `pixelator` | 0.15.0 | 0.15.2 | + +> **NB:** Dependency has been **updated** if both old and new version information is present. +> +> **NB:** Dependency has been **added** if just the new version information is present. +> +> **NB:** Dependency has been **removed** if new version information isn't present. + +## [[1.0.0](https://github.com/nf-core/pixelator/releases/tag/1.0.0)] - 2023-10-17 + +Initial release of nf-core/pixelator. diff --git a/CITATIONS.md b/CITATIONS.md index ca3444ff..49b37b62 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -10,13 +10,17 @@ ## Pipeline tools -- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) +- [pixelator](https://doi.org/10.1101/2023.06.05.543770) - > Andrews, S. (2010). FastQC: A Quality Control Tool for High Throughput Sequence Data [Online]. + > Karlsson, Filip, Tomasz Kallas, Divya Thiagarajan, Max Karlsson, Maud Schweitzer, Jose Fernandez Navarro, Louise Leijonancker, et al. “Molecular Pixelation: Single Cell Spatial Proteomics by Sequencing.” bioRxiv, June 8, 2023. https://doi.org/10.1101/2023.06.05.543770. -- [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) +- [cutadapt](http://dx.doi.org/10.14806/ej.17.1.200) - > Ewels P, Magnusson M, Lundin S, Käller M. MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics. 2016 Oct 1;32(19):3047-8. doi: 10.1093/bioinformatics/btw354. Epub 2016 Jun 16. PubMed PMID: 27312411; PubMed Central PMCID: PMC5039924. + > Martin, Marcel. “Cutadapt Removes Adapter Sequences from High-Throughput Sequencing Reads.” EMBnet.Journal 17, no. 1 (May 2, 2011): 10–12. https://doi.org/10.14806/ej.17.1.200. + +- [fastp](https://doi.org/10.1002/imt2.107) + + > Chen, Shifu. “Ultrafast One-Pass FASTQ Data Preprocessing, Quality Control, and Deduplication Using Fastp.” IMeta 2, no. 2 (2023): e107. https://doi.org/10.1002/imt2.107. ## Software packaging/containerisation tools diff --git a/README.md b/README.md index fdbb131a..1c8d8fe5 100644 --- a/README.md +++ b/README.md @@ -5,9 +5,8 @@ -[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/pixelator/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) -[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) +[![GitHub Actions CI Status](https://github.com/nf-core/pixelator/workflows/nf-core%20CI/badge.svg)](https://github.com/nf-core/pixelator/actions?query=workflow%3A%22nf-core+CI%22) +[![GitHub Actions Linting Status](https://github.com/nf-core/pixelator/workflows/nf-core%20linting/badge.svg)](https://github.com/nf-core/pixelator/actions?query=workflow%3A%22nf-core+linting%22)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/pixelator/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.10015112-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.10015112) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) @@ -19,46 +18,43 @@ ## Introduction -**nf-core/pixelator** is a bioinformatics pipeline that ... +**nf-core/pixelator** is a bioinformatics best-practice analysis pipeline for analysis of Molecular Pixelation assays. +It takes a samplesheet as input and will process your data using `pixelator` to produce final antibody counts. - +![](./docs/images/nf-core-pixelator-metromap.svg) - - +1. Build amplicon from input reads ([`pixelator amplicon`](https://github.com/PixelgenTechnologies/pixelator)) +2. Read QC and filtering, correctness of the pixel binding sequence sequences ([`pixelator preqc | pixelator adapterqc`](https://github.com/PixelgenTechnologies/pixelator)) +3. Assign a marker (barcode) to each read ([`pixelator demux`](https://github.com/PixelgenTechnologies/pixelator)) +4. Error correction, duplicate removal, compute read counts ([`pixelator collapse`](https://github.com/PixelgenTechnologies/pixelator)) +5. Compute the components of the graph from the edge list in order to create putative cells ([`pixelator graph`](https://github.com/PixelgenTechnologies/pixelator)) +6. Call and annotate cells ([`pixelator annotate`](https://github.com/PixelgenTechnologies/pixelator)) +7. Analyze the cells for polarization and colocalization ([`pixelator analysis`](https://github.com/PixelgenTechnologies/pixelator)) +8. Report generation ([`pixelator report`](https://github.com/PixelgenTechnologies/pixelator)) -1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)) -2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/)) +> [!WARNING] +> Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity. +> This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable +> `NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline. ## Usage > [!NOTE] > If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. - +Each row represents a sample and gives the design, a panel file and the input fastq files. Now, you can run the pipeline using: - - ```bash nextflow run nf-core/pixelator \ -profile \ @@ -80,11 +76,11 @@ For more details about the output files and reports, please refer to the ## Credits -nf-core/pixelator was originally written by Pixelgen Technologies AB. - -We thank the following people for their extensive assistance in the development of this pipeline: +nf-core/pixelator was originally written for [Pixelgen Technologies AB](https://www.pixelgen.com/) by: - +- Florian De Temmerman +- Johan Dahlberg +- Alvaro Martinez Barrio ## Contributions and Support @@ -94,10 +90,7 @@ For further information or help, don't hesitate to get in touch on the [Slack `# ## Citations - - - - +If you use nf-core/pixelator for your analysis, please cite it using the following doi: [10.5281/zenodo.10015112](https://doi.org/10.5281/zenodo.10015112) 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/methods_description_template.yml b/assets/methods_description_template.yml deleted file mode 100644 index 2b6ed3cd..00000000 --- a/assets/methods_description_template.yml +++ /dev/null @@ -1,29 +0,0 @@ -id: "nf-core-pixelator-methods-description" -description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "nf-core/pixelator Methods Description" -section_href: "https://github.com/nf-core/pixelator" -plot_type: "html" -## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline -## You inject any metadata in the Nextflow '${workflow}' object -data: | -

Methods

-

Data was processed using nf-core/pixelator v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020), utilising reproducible software environments from the Bioconda (Grüning et al., 2018) and Biocontainers (da Veiga Leprevost et al., 2017) projects.

-

The pipeline was executed with Nextflow v${workflow.nextflow.version} (Di Tommaso et al., 2017) with the following command:

- 
${workflow.commandLine}
-

${tool_citations}

-

References

- -
-
Notes:
-
    - ${nodoi_text} -
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • -
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • -
-
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml deleted file mode 100644 index a67694de..00000000 --- a/assets/multiqc_config.yml +++ /dev/null @@ -1,17 +0,0 @@ -report_comment: > - - This report has been generated by the nf-core/pixelator - analysis pipeline. For information about how to interpret these results, please see the - documentation. - -report_section_order: - "nf-core-pixelator-methods-description": - order: -1000 - software_versions: - order: -1001 - "nf-core-pixelator-summary": - order: -1002 - -export_plots: true - -disable_version_detection: true diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index 5f653ab7..e50611a7 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,3 +1,4 @@ -sample,fastq_1,fastq_2 -SAMPLE_PAIRED_END,/path/to/fastq/files/AEG588A1_S1_L002_R1_001.fastq.gz,/path/to/fastq/files/AEG588A1_S1_L002_R2_001.fastq.gz -SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz, +sample,design,panel,fastq_1,fastq_2 +uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L001_R1_001.fastq.gz,uropod_control_S1_L001_R2_001.fastq.gz +uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L002_R1_001.fastq.gz,uropod_control_S1_L002_R2_001.fastq.gz +uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L003_R1_001.fastq.gz,uropod_control_S1_L003_R2_001.fastq.gz diff --git a/assets/schema_input.json b/assets/schema_input.json index 0b6b7dd1..463396c3 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -6,6 +6,7 @@ "type": "array", "items": { "type": "object", + "required": ["sample", "design", "fastq_1"], "properties": { "sample": { "type": "string", @@ -13,21 +14,39 @@ "errorMessage": "Sample name must be provided and cannot contain spaces", "meta": ["id"] }, + "design": { + "type": "string", + "meta": ["design"], + "errorMessage": "Design must be specified" + }, + "panel": { + "errorMessage": "Panel name must be specified", + "type": "string", + "meta": ["panel"] + }, + "panel_file": { + "errorMessage": "Panel file must either be left empty or cannot contain spaces and must have extension '.csv', '.tsv' or '.yaml'", + "anyOf": [ + { + "type": "string", + "pattern": "^\\S+.(csv|tsv|ya?ml)$" + }, + { + "type": "string", + "maxLength": 0 + } + ] + }, "fastq_1": { "type": "string", - "format": "file-path", - "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" }, "fastq_2": { "type": "string", - "format": "file-path", - "exists": true, "pattern": "^\\S+\\.f(ast)?q\\.gz$", "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" } - }, - "required": ["sample", "fastq_1"] + } } } diff --git a/assets/test_samplesheet.csv b/assets/test_samplesheet.csv new file mode 100644 index 00000000..9ad1694e --- /dev/null +++ b/assets/test_samplesheet.csv @@ -0,0 +1,4 @@ +sample,design,panel,panel_file,fastq_1,fastq_2 +uropod_control_1,D21,,UNO_D21.csv,uropod_control_300k_S1_R1_001.part_001.fastq.gz,uropod_control_300k_S1_R2_001.part_001.fastq.gz +uropod_control_1,D21,,UNO_D21.csv,uropod_control_300k_S1_R1_001.part_002.fastq.gz,uropod_control_300k_S1_R2_001.part_002.fastq.gz +uropod_control_2,D21,human-sc-immunology-spatial-proteomics,,uropod_control_300k_S1_R1_001.fastq.gz,uropod_control_300k_S1_R2_001.fastq.gz diff --git a/bin/collect_metadata.py b/bin/collect_metadata.py new file mode 100755 index 00000000..8eef3d74 --- /dev/null +++ b/bin/collect_metadata.py @@ -0,0 +1,83 @@ +#!/usr/bin/env python + +""" +Collect version information about the pixelator python environment. + +Written by Florian De Temmerman (https://github.com/fbdtemme) +Copyright (c) 2023 Pixelgen Technologies AB. +""" + +import sys +import subprocess +from pathlib import Path +import importlib.metadata +import json +import argparse +import ruamel.yaml as yaml + + +installed_packages = {d.name: d.version for d in importlib.metadata.distributions()} + + +def subtool_versions(): + cutadapt_proc = subprocess.run( + ["cutadapt", "--version"], capture_output=True, text=True + ) + fastp_proc = subprocess.run(["fastp", "--version"], capture_output=True, text=True) + + cutadapt_version = cutadapt_proc.stdout.strip("\n") + fastp_version = fastp_proc.stderr.strip("\n").split(" ")[-1] + + return {"cutadapt_version": cutadapt_version, "fastp_version": fastp_version} + + +def main(args): + dep_versions = subtool_versions() + root = { + "platform": sys.platform, + "python": { + "version": { + "major": sys.version_info.major, + "minor": sys.version_info.minor, + "micro": sys.version_info.micro, + "releaselevel": sys.version_info.releaselevel, + "serial": sys.version_info.serial, + }, + "packages": installed_packages, + }, + "fastp": {"version": dep_versions["fastp_version"]}, + "cutadapt": {"version": dep_versions["cutadapt_version"]}, + } + + workflow_data = None + if args.workflow_data is not None and args.workflow_data.exists(): + with open(str(args.workflow_data)) as f: + workflow_data = json.load(f) + + if workflow_data: + root = {**root, **workflow_data} + + with open("metadata.json", "w") as f: + json.dump(root, f, indent=4) + + with open("versions.yml", "w") as f: + yaml.dump( + data={ + args.process_name: { + "python": f"{sys.version_info.major}.{sys.version_info.minor}.{sys.version_info.micro}" + } + }, + stream=f, + ) + + +if __name__ == "__main__": + parser = argparse.ArgumentParser() + + parser.add_argument("--process-name", dest="process_name", type=str) + parser.add_argument( + "--workflow-data", dest="workflow_data", type=Path, default=None + ) + args = parser.parse_args() + + main(args) diff --git a/conf/base.config b/conf/base.config index 4d00103e..c3596e9c 100644 --- a/conf/base.config +++ b/conf/base.config @@ -10,7 +10,6 @@ process { - // TODO nf-core: Check the defaults for all processes cpus = { check_max( 1 * task.attempt, 'cpus' ) } memory = { check_max( 6.GB * task.attempt, 'memory' ) } time = { check_max( 4.h * task.attempt, 'time' ) } @@ -24,7 +23,6 @@ process { // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. // If possible, it would be nice to keep the same label naming convention when // adding in your local modules too. - // TODO nf-core: Customise requirements for specific processes. // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors withLabel:process_single { cpus = { check_max( 1 , 'cpus' ) } @@ -38,7 +36,7 @@ process { } withLabel:process_medium { cpus = { check_max( 6 * task.attempt, 'cpus' ) } - memory = { check_max( 36.GB * task.attempt, 'memory' ) } + memory = { check_max( 32.GB * task.attempt, 'memory' ) } time = { check_max( 8.h * task.attempt, 'time' ) } } withLabel:process_high { diff --git a/conf/igenomes.config b/conf/igenomes.config deleted file mode 100644 index 3f114377..00000000 --- a/conf/igenomes.config +++ /dev/null @@ -1,440 +0,0 @@ -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Nextflow config file for iGenomes paths -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Defines reference genomes using iGenome paths. - Can be used by any config that customises the base path using: - $params.igenomes_base / --igenomes_base ----------------------------------------------------------------------------------------- -*/ - -params { - // illumina iGenomes reference file paths - genomes { - 'GRCh37' { - fasta = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/Ensembl/GRCh37/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/GRCh37-blacklist.bed" - } - 'GRCh38' { - fasta = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/NCBI/GRCh38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'CHM13' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAIndex/" - bwamem2 = "${params.igenomes_base}/Homo_sapiens/UCSC/CHM13/Sequence/BWAmem2Index/" - gtf = "${params.igenomes_base}/Homo_sapiens/NCBI/CHM13/Annotation/Genes/genes.gtf" - gff = "ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCF/009/914/755/GCF_009914755.1_T2T-CHM13v2.0/GCF_009914755.1_T2T-CHM13v2.0_genomic.gff.gz" - mito_name = "chrM" - } - 'GRCm38' { - fasta = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/Ensembl/GRCm38/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/GRCm38-blacklist.bed" - } - 'TAIR10' { - fasta = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Arabidopsis_thaliana/Ensembl/TAIR10/Annotation/README.txt" - mito_name = "Mt" - } - 'EB2' { - fasta = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bacillus_subtilis_168/Ensembl/EB2/Annotation/README.txt" - } - 'UMD3.1' { - fasta = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Bos_taurus/Ensembl/UMD3.1/Annotation/README.txt" - mito_name = "MT" - } - 'WBcel235' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/Ensembl/WBcel235/Annotation/Genes/genes.bed" - mito_name = "MtDNA" - macs_gsize = "9e7" - } - 'CanFam3.1' { - fasta = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/Ensembl/CanFam3.1/Annotation/README.txt" - mito_name = "MT" - } - 'GRCz10' { - fasta = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/Ensembl/GRCz10/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'BDGP6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/Ensembl/BDGP6/Annotation/Genes/genes.bed" - mito_name = "M" - macs_gsize = "1.2e8" - } - 'EquCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/Ensembl/EquCab2/Annotation/README.txt" - mito_name = "MT" - } - 'EB1' { - fasta = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Escherichia_coli_K_12_DH10B/Ensembl/EB1/Annotation/README.txt" - } - 'Galgal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/Ensembl/Galgal4/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Gm01' { - fasta = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Glycine_max/Ensembl/Gm01/Annotation/README.txt" - } - 'Mmul_1' { - fasta = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Macaca_mulatta/Ensembl/Mmul_1/Annotation/README.txt" - mito_name = "MT" - } - 'IRGSP-1.0' { - fasta = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Oryza_sativa_japonica/Ensembl/IRGSP-1.0/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'CHIMP2.1.4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/Ensembl/CHIMP2.1.4/Annotation/README.txt" - mito_name = "MT" - } - 'Rnor_5.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_5.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'Rnor_6.0' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/Ensembl/Rnor_6.0/Annotation/Genes/genes.bed" - mito_name = "MT" - } - 'R64-1-1' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Saccharomyces_cerevisiae/Ensembl/R64-1-1/Annotation/Genes/genes.bed" - mito_name = "MT" - macs_gsize = "1.2e7" - } - 'EF2' { - fasta = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Schizosaccharomyces_pombe/Ensembl/EF2/Annotation/README.txt" - mito_name = "MT" - macs_gsize = "1.21e7" - } - 'Sbi1' { - fasta = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sorghum_bicolor/Ensembl/Sbi1/Annotation/README.txt" - } - 'Sscrofa10.2' { - fasta = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/Ensembl/Sscrofa10.2/Annotation/README.txt" - mito_name = "MT" - } - 'AGPv3' { - fasta = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Zea_mays/Ensembl/AGPv3/Annotation/Genes/genes.bed" - mito_name = "Mt" - } - 'hg38' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg38/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg38-blacklist.bed" - } - 'hg19' { - fasta = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Homo_sapiens/UCSC/hg19/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "2.7e9" - blacklist = "${projectDir}/assets/blacklists/hg19-blacklist.bed" - } - 'mm10' { - fasta = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Mus_musculus/UCSC/mm10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.87e9" - blacklist = "${projectDir}/assets/blacklists/mm10-blacklist.bed" - } - 'bosTau8' { - fasta = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Bos_taurus/UCSC/bosTau8/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'ce10' { - fasta = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Caenorhabditis_elegans/UCSC/ce10/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "9e7" - } - 'canFam3' { - fasta = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Canis_familiaris/UCSC/canFam3/Annotation/README.txt" - mito_name = "chrM" - } - 'danRer10' { - fasta = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Danio_rerio/UCSC/danRer10/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.37e9" - } - 'dm6' { - fasta = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Drosophila_melanogaster/UCSC/dm6/Annotation/Genes/genes.bed" - mito_name = "chrM" - macs_gsize = "1.2e8" - } - 'equCab2' { - fasta = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Equus_caballus/UCSC/equCab2/Annotation/README.txt" - mito_name = "chrM" - } - 'galGal4' { - fasta = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Gallus_gallus/UCSC/galGal4/Annotation/README.txt" - mito_name = "chrM" - } - 'panTro4' { - fasta = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Pan_troglodytes/UCSC/panTro4/Annotation/README.txt" - mito_name = "chrM" - } - 'rn6' { - fasta = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Rattus_norvegicus/UCSC/rn6/Annotation/Genes/genes.bed" - mito_name = "chrM" - } - 'sacCer3' { - fasta = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Sequence/BismarkIndex/" - readme = "${params.igenomes_base}/Saccharomyces_cerevisiae/UCSC/sacCer3/Annotation/README.txt" - mito_name = "chrM" - macs_gsize = "1.2e7" - } - 'susScr3' { - fasta = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/WholeGenomeFasta/genome.fa" - bwa = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BWAIndex/version0.6.0/" - bowtie2 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/Bowtie2Index/" - star = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/STARIndex/" - bismark = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Sequence/BismarkIndex/" - gtf = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.gtf" - bed12 = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/Genes/genes.bed" - readme = "${params.igenomes_base}/Sus_scrofa/UCSC/susScr3/Annotation/README.txt" - mito_name = "chrM" - } - } -} diff --git a/conf/modules.config b/conf/modules.config index d203d2b6..b1872182 100644 --- a/conf/modules.config +++ b/conf/modules.config @@ -10,6 +10,7 @@ ---------------------------------------------------------------------------------------- */ + process { publishDir = [ @@ -18,17 +19,131 @@ process { saveAs: { filename -> filename.equals('versions.yml') ? null : filename } ] - withName: FASTQC { - ext.args = '--quiet' + withName: "PIXELATOR.*" { + publishDir = [ + [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, + mode: params.publish_dir_mode, + saveAs: { filename -> (filename.endsWith('.log') || filename.equals('versions.yml')) ? null : filename } + ], + [ + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}/logs" }, + mode: params.publish_dir_mode, + pattern: "*.log" + ] + ] + + if (params.pixelator_container) { + container = params.pixelator_container + } + } + + withName: PIXELATOR_LIST_OPTIONS { + publishDir = [ enabled: false ] + } + + withName: "CAT_FASTQ" { + publishDir = [ enabled: false ] } - withName: 'MULTIQC' { - ext.args = { params.multiqc_title ? "--title \"$params.multiqc_title\"" : '' } + withName: RENAME_READS { publishDir = [ - path: { "${params.outdir}/multiqc" }, - mode: params.publish_dir_mode, - saveAs: { filename -> filename.equals('versions.yml') ? null : filename } + enabled: false, + path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, ] } + + // use explicit (params.my_option instanceof Integer) checks to avoid issues with 0 evaluating false + // since most pixelator flags do accept zero as a value + + withName: PIXELATOR_AMPLICON { + ext.args = { + [ + "--design ${meta.design}", + ].join(' ').trim() + } + } + + withName: PIXELATOR_QC { + // Options for pixelator preqc + ext.args = { + [ + "--design ${meta.design}", + (params.trim_front instanceof Integer)? "--trim-front ${params.trim_front}": '', + (params.trim_tail instanceof Integer) ? "--trim-tail ${params.trim_tail}": '', + (params.max_length instanceof Integer) ? "--max-length ${params.max_length}": '', + (params.min_length instanceof Integer) ? "--min-length ${params.min_length}": '', + (params.max_n_bases instanceof Integer) ? "--max-n-bases ${params.max_n_bases}": '', + (params.avg_qual instanceof Integer)? "--avg-qual ${params.avg_qual}": '', + params.dedup ? "--dedup": '', + params.remove_polyg ? "--remove_polyg": '', + ].join(' ').trim() + } + + // Options for pixelator adapterqc + ext.args2 = { [ + "--design ${meta.design}", + params.adapterqc_mismatches ? "--mismatches ${params.adapterqc_mismatches}": '', + ].join(' ').trim() + } + } + + withName: PIXELATOR_DEMUX { + ext.args = { + [ + "--design ${meta.design}", + (params.demux_mismatches != null) ? "--mismatches ${params.demux_mismatches}": '', + (params.demux_min_length instanceof Integer) ? "--mismatches ${params.demux_min_length}": '', + ].join(' ').trim() + } + } + + withName: PIXELATOR_COLLAPSE { + ext.args = [ + params.markers_ignore ? "--markers_ignore ${params.markers_ignore}": + params.algorithm ? "--algorithm ${params.algorithm}": '', + params.max_neighbours ? "--max-neighbours ${params.max_neighbours}": '', + params.collapse_mismatches ? "--mismatches ${params.collapse_mismatches}": '', + params.collapse_min_count ? "--min-count ${params.collapse_min_count}": '', + params.collapse_use_counts ? "--use-counts": '', + ].join(' ').trim() + } + + withName: PIXELATOR_GRAPH { + ext.args = [ + params.multiplet_recovery ? "--multiplet-recovery" : '', + params.leiden_iterations ? "--leiden-iterations ${params.leiden_iterations}" : '', + params.graph_min_count ? "--min-count ${params.graph_min_count}" : '', + ].join(' ').trim() + } + + withName: PIXELATOR_ANNOTATE { + ext.args = [ + (params.min_size instanceof Integer) ? "--min-size ${params.min_size}" : '', + (params.max_size instanceof Integer) ? "--max-size ${params.max_size}" : '', + params.dynamic_filter ? "--dynamic-filter ${params.dynamic_filter}" : '', + params.aggregate_calling ? "--aggregate-calling" : '', + ].join(' ').trim() + } + + withName: PIXELATOR_ANALYSIS { + ext.when = { !params.skip_analysis } + ext.args = [ + params.compute_polarization ? "--compute-polarization" : '', + params.compute_colocalization ? "--compute-colocalization" : '', + params.use_full_bipartite ? "--use-full-bipartite " : '', + params.polarization_normalization ? "--polarization-normalization ${params.polarization_normalization}" : '', + params.polarization_binarization ? "--polarization-binarization" : '', + params.colocalization_transformation ? "--colocalization-transformation ${params.colocalization_transformation}" : '', + (params.colocalization_neighbourhood_size instanceof Integer) ? "--colocalization-neighbourhood-size ${params.colocalization_neighbourhood_size}" : '', + (params.colocalization_n_permutations instanceof Integer) ? "--colocalization-n-permutations ${params.colocalization_n_permutations}" : '', + (params.colocalization_min_region_count instanceof Integer) ? "--colocalization-min-region-count ${params.colocalization_min_region_count}" : '', + ].join(' ').trim() + } + + withName: PIXELATOR_REPORT { + ext.when = { !params.skip_report } + } + } diff --git a/conf/test.config b/conf/test.config index 8f96a616..5bd688e8 100644 --- a/conf/test.config +++ b/conf/test.config @@ -10,6 +10,10 @@ ---------------------------------------------------------------------------------------- */ + +aws.client.downloadParallel = true + + params { config_profile_name = 'Test profile' config_profile_description = 'Minimal test dataset to check pipeline function' @@ -20,10 +24,15 @@ params { max_time = '6.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 - input = params.pipelines_testdata_base_path + 'viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' + input = params.pipelines_testdata_base_path + 'pixelator/samplesheet/samplesheet.csv' + input_basedir = "https://raw.githubusercontent.com/nf-core/test-datasets/pixelator/testdata" - // Genome references - genome = 'R64-1-1' + multiplet_recovery = true + min_size = 2 + max_size = 100000 + compute_polarization = true + use_full_bipartite = true + colocalization_min_region_count = 0 + colocalization_n_permutations = 10 + colocalization_neighbourhood_size = 1 } diff --git a/conf/test_full.config b/conf/test_full.config index b8f7cf2a..2690a944 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -14,11 +14,6 @@ params { config_profile_name = 'Full test profile' config_profile_description = 'Full test dataset to check pipeline function' - // 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 - input = 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/docs/output.md b/docs/output.md index dc8682df..5590fee4 100644 --- a/docs/output.md +++ b/docs/output.md @@ -2,58 +2,238 @@ ## 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 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. - - ## 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 processes data using multiple subcommands +of [`pixelator`](https://github.com/PixelgenTechnologies/pixelator). + +The pipeline consists of the following steps: + +- [Preprocessing](#Preprocessing) +- [Quality control](#quality-control) +- [Demultiplexing](#demultiplexing) +- [Duplicate removal and error correction](#duplicate-removal-and-error-correction) +- [Compute connected components](#compute-connected-components) +- [Filtering, annotation, cell-calling](#cell-calling-filtering-and-annotation) +- [Downstream analysis](#downstream-analysis) +- [Generate reports](#generate-reports) + +### Preprocessing + +
+Output files + +- `pixelator` + + - `amplicon` + + - `.merged.fastq.gz`: + Combine R1 and R2 reads into full amplicon reads and calculate Q30 scores for the amplicon regions. + - `.report.json`: Q30 metrics of the amplicon. + - `.meta.json`: Command invocation metadata. + + - `logs` + - `.pixelator-amplicon.log`: pixelator log output. + +
+ +The preprocessing step uses `pixelator single-cell amplicon` to create full-length amplicon sequences from both single-end and paired-end data. +It returns a single fastq file per sample containing fixed length amplicons. +This step will also calculate Q30 quality scores for different regions of the library. + +### Quality control + +
+Output files + +- `pixelator` + + - `preqc` + - `.processed.fastq.gz`: Processed reads. + - `.failed.fastq.gz`: Discarded reads. + - `.report.json`: Fastp json report. + - `.meta.json`: Command invocation metadata. + - `adapterqc` + + - `.processed.fastq.gz`: Processed reads. + - `.failed.fastq.gz`: Discarded reads. + - `.report.json`: Cutadapt json report. + - `.meta.json`: Command invocation metadata. + + - `logs` + - `.pixelator-preqc.log`: pixelator log output. + +
+ +Quality control is performed using `pixelator single-cell preqc` and `pixelator single-cell adapterqc`. + +The preqc stage performs QC and quality filtering of the raw sequencing data. +It also generates a QC report in HTML and JSON formats. It saves processed reads as well as reads that were +discarded (i.e. were too short, had too many Ns, or too low quality, etc.). Internally `preqc` +uses [Fastp](https://github.com/OpenGene/fastp), and `adapterqc` +uses [Cutadapt](https://cutadapt.readthedocs.io/en/stable/). + +The `adapterqc` stage checks for the presence and correctness of the pixel binding sequences. It also generates a QC report in JSON format. It saves processed reads as well as discarded reads (i.e. reads that did not have a match for both pixel binding sequences). + +### Demultiplexing + +
+Output files + +- `pixelator` + + - `demux` + + - `.processed-.fastq.gz`: Reads demultiplexed per antibody. + - `.failed.fastq.gz`: Discarded reads that do not match an antibody barcode. + - `.report.json`: Cutadapt json report. + - `.meta.json`: Command invocation metadata. + + - `logs` + - `.pixelator-demultiplex.log`: pixelator log output. + +
-- [FastQC](#fastqc) - Raw read QC -- [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline -- [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution +The `pixelator single-cell demux` command assigns a marker (barcode) to each read. It also generates QC report in +JSON format. It saves processed reads (one per antibody) as well as discarded reads with no match to the +given barcodes/antibodies. -### FastQC +### Duplicate removal and error correction
Output files -- `fastqc/` - - `*_fastqc.html`: FastQC report containing quality metrics. - - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. +- `pixelator` + + - `collapse` + + - `.collapsed.parquet`: Edgelist of the graph. + - `.report.json`: Statistics for the collapse step. + - `.meta.json`: Command invocation metadata. + + - `logs` + - `.pixelator-collapse.log`: pixelator log output.
-[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. For further reading and documentation see the [FastQC help pages](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/). +This step uses the `pixelator single-cell collapse` command. + +The `collapse` command removes duplicate reads and performs error correction. +This is achieved using the unique pixel identifier and unique molecular identifier sequences to check for +uniqueness, collapse and compute a read count. The command generates a QC report in JSON format. +Errors are allowed when collapsing reads if `--algorithm` is set to `adjacency` (this is the default option). -![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) +The output format of this command is an edge list in CSV format. -![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) +### Compute connected components -![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) +
+Output files + +- `pixelator` -:::note -The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. -::: + - `graph` -### MultiQC + - `.edgelist.parquet`: + Edge list dataframe after recovering technical multiplets. + - `.components_recovered.csv`: + List of new components recovered (when using `--multiple-recovery`) + - `.meta.json`: Command invocation metadata. + - `.report.json`: Metrics with useful information about the clustering. + - `*.meta.json`: Command invocation metadata. + + - `logs` + - `.pixelator-cluster.log`: pixelator log output. + +
+ +This step uses the `pixelator single-cell graph` command. +The input is the edge list dataframe (CSV) generated in the collapse step and after filtering it +by count (`--graph_min_count`), the connected components of the graph (graphs) are computed and +added to the edge list in a column called "component". + +The graph command has the option to recover components (technical multiplets) into smaller +components using community detection to find and remove problematic edges. +(See `--multiplet_recovery`). The information to keep track of the original and +newly recovered components are stored in a file (components_recovered.csv). + +### Cell-calling, filtering, and annotation
Output files -- `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. +- `pixelator` + + - `annotate` + - `.dataset.pxl` + - `.meta.json`: Command invocation metadata. + - `.rank_vs_size.png` + - `.raw_components_metrics.csv` + - `.report.json`: Statistics for the analysis step. + - `.umap.png` + - `logs` + - `.pixelator-annotate.log`: pixelator log output. +
+ +This step uses the `pixelator single-cell annotate` command. + +The annotate command takes as input the edge list (CSV) file generated in the graph command. It parses, and filters the +edgelist to find putative cells, and it will generate a pxl file containing the edgelist, and an +(AnnData object)[https://anndata.readthedocs.io/en/latest/] as well as some useful metadata. + +### Downstream analysis + +
+Output files + +- `pixelator` + + - `analysis` + + - `.dataset.pxl`: PXL file with the analysis results added to it. + - `.meta.json`: Command invocation metadata. + - `.report.json`: Statistics for the analysis step. + + - `logs` + - `.pixelator-analysis.log`: pixelator log output. + +
+ +This step uses the `pixelator single-cell analysis` command. +Downstream analysis is performed on the `pxl` file generated by the previous stage. +The results of the analysis is added to the pxl file. + +Currently, the following analysis are performed: + +- polarization scores (enable with `--compute_polarization`) +- co-localization scores (enable with `--compute_colocalization`) + +Each analysis can be disabled by using respectively `--compute_polarization false` or `--compute_colocalization false`. +This entire step can also be skipped using the `--skip_analysis` option. + +### Generate reports + +
+Output files + +- `pixelator` + - `report` + - `_report.html`: Pixelator summary report. + - `logs` + - `.pixelator-report.log`: Pixelator log output.
-[MultiQC](http://multiqc.info) is a visualization tool that generates a single HTML report summarising 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. +This step uses the `pixelator single-cell report` command. +This step will collect metrics and outputs generated by previous stages +and generate a report in HTML format for each sample. + +This step can be skipped using the `--skip_report` option. -Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQC. The pipeline has special steps which also allow the software versions to be reported in the MultiQC output for future traceability. For more information about how to use MultiQC reports, see . +More information on the report can be found in the [pixelator documentation](https://software.pixelgen.com/pixelator/outputs/web-report/) ### Pipeline information @@ -64,6 +244,7 @@ Results generated by MultiQC collate pipeline QC from supported tools e.g. FastQ - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. - Reports generated by the pipeline: `pipeline_report.html`, `pipeline_report.txt` and `software_versions.yml`. The `pipeline_report*` files will only be present if the `--email` / `--email_on_fail` parameter's are used when running the pipeline. - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. + - Metadata file with software versions, environment information and pipeline configuration for debugging: `metadata.json` - Parameters used by the pipeline run: `params.json`. diff --git a/docs/usage.md b/docs/usage.md index 20bcc59d..f6337e55 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -6,58 +6,137 @@ ## Introduction - - ## Samplesheet input -You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row as shown in the examples below. +You will need to create a samplesheet with information about the samples you would like to analyse before running the pipeline. +Use this parameter to specify its location. ```bash --input '[path to samplesheet file]' ``` +An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. + +### Format + +The samplesheet is a CSV or TSV formatted file with a few required and some optional columns. +You can export to CSV from spreadsheet programs such as Microsoft Excel, Google Sheets and LibreOffice Calc. + +Following table provides an overview of all possible columns in the samplesheet. +The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 5 columns +to match those defined in the table below. + +Below is an example of a simple samplesheet with two samples. + +```csv +sample,design,panel,fastq_1,fastq_2 +uropod_control,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_R1_001.fastq.gz,uropod_control_S1_R2_001.fastq.gz +uropod_stimulated,D21,human-sc-immunology-spatial-proteomics,uropod_stimulated_S1_R1_001.fastq.gz,uropod_stimulated_S1_R2_001.fastq.gz +``` + +Columns not defined in the table below are ignored by the pipeline but can be useful +to add extra information for downstream processing. + +| Column | Required | Description | +| ----------------------------------- | -------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| `sample` | Yes | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | +| `design` | Yes | The name of the pixelator design configuration. | +| `panel`
or
`panel_file` | Yes | Name of the panel to use.
or
Path to a CSV file containing a custom panel. | +| `fastq_1` | Yes | Path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +| `fastq_2` | No | Path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". Parameter only used if you are running paired-end. | + +The `panel` and `panel_file` options are mutually exclusive. If both are specified, the pipeline will throw an error. +One of them has to be specified. + +The pipeline will auto-detect whether a sample is single- or paired-end based on if both `fastq_1` and `fastq_2` or only `fastq_1` is present in the samplesheet. + ### Multiple runs of the same sample The `sample` identifiers have to be the same when you have re-sequenced the same sample more than once e.g. to increase sequencing depth. The pipeline will concatenate the raw reads before performing any downstream analysis. Below is an example for the same sample sequenced across 3 lanes: ```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L003_R1_001.fastq.gz,AEG588A1_S1_L003_R2_001.fastq.gz -CONTROL_REP1,AEG588A1_S1_L004_R1_001.fastq.gz,AEG588A1_S1_L004_R2_001.fastq.gz +sample,design,panel,fastq_1,fastq_2 +uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L001_R1_001.fastq.gz,uropod_control_S1_L001_R2_001.fastq.gz +uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L002_R1_001.fastq.gz,uropod_control_S1_L002_R2_001.fastq.gz +uropod_control_1,D21,human-sc-immunology-spatial-proteomics,uropod_control_S1_L003_R1_001.fastq.gz,uropod_control_S1_L003_R2_001.fastq.gz ``` -### Full samplesheet +### Relative paths + +Using relative paths in a samplesheet is supported. +This make it easier to relocate data since you do not have to edit the paths to files in the samplesheet. + +The default behavior is to resolve relative paths based on the directory the samplesheet file is located in. -The pipeline will auto-detect whether a sample is single- or paired-end using the information provided in the samplesheet. The samplesheet can have as many columns as you desire, however, there is a strict requirement for the first 3 columns to match those defined in the table below. +Given following directory structure: -A final samplesheet file consisting of both single- and paired-end data may look something like the one below. This is for 6 samples, where `TREATMENT_REP3` has been sequenced twice. +- data + - samplesheet.csv + - fastq + - sample1_R1.fq.gz + - sample1_R2.fq.gz + +You can use following samplesheet: ```csv title="samplesheet.csv" -sample,fastq_1,fastq_2 -CONTROL_REP1,AEG588A1_S1_L002_R1_001.fastq.gz,AEG588A1_S1_L002_R2_001.fastq.gz -CONTROL_REP2,AEG588A2_S2_L002_R1_001.fastq.gz,AEG588A2_S2_L002_R2_001.fastq.gz -CONTROL_REP3,AEG588A3_S3_L002_R1_001.fastq.gz,AEG588A3_S3_L002_R2_001.fastq.gz -TREATMENT_REP1,AEG588A4_S4_L003_R1_001.fastq.gz, -TREATMENT_REP2,AEG588A5_S5_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L003_R1_001.fastq.gz, -TREATMENT_REP3,AEG588A6_S6_L004_R1_001.fastq.gz, +sample,design,panel,panel_file,fastq_1,fastq_2 +sample1,D21,human-sc-immunology-spatial-proteomics,,fastq/sample1_R1.fq.gz,fastq/sample1_R2.fq.gz ``` -| Column | Description | -| --------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| `sample` | Custom sample name. This entry will be identical for multiple sequencing libraries/runs from the same sample. Spaces in sample names are automatically converted to underscores (`_`). | -| `fastq_1` | Full path to FastQ file for Illumina short reads 1. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | -| `fastq_2` | Full path to FastQ file for Illumina short reads 2. File has to be gzipped and have the extension ".fastq.gz" or ".fq.gz". | +Using the `--input_basedir` option you can specify a different location that will be used to resolve relative paths. +This location can be a local or a remote path. -An [example samplesheet](../assets/samplesheet.csv) has been provided with the pipeline. +For example, using the same samplesheet as above, but with the samplesheet on the local machine and the input data located on an AWS S3 bucket: + +- s3://my-company-data/experiment-1/fastq + - sample1_R1.fq.gz + - sample1_R2.fq.gz + +```shell +nextflow run nf-core/pixelator --input samplesheet.csv --input_basedir s3://my-company-data/experiment-1/ +``` + +### Design + +The `design` column specifies the name of the pixelator assay design configuration to use. + +A list of available designs can be listed by running following command: + +```shell +pixelator single-cell --list-designs +``` + +Currently, a single design is available: + +- `D21` + +### Panels + +The panel file contains all information used to link antibodies barcodes to their respective targets. +Panel files can be specified in two ways: + +- Using a predefined panel name to use the default build in panels. +- Passing a csv file with a customized panel. + +Predefined panels can be passed in the `panel` field. Custom panels can be passed in the `panel_file` field. +Every sample should have either `panel` or `panel_file` specified. + +A list of available panels can be listed by running following command: + +```shell +pixelator single-cell --list-panels +``` + +Currently, a single built-in panel is available: + +- `human-sc-immunology-spatial-proteomics` ## Running the pipeline The typical command for running the pipeline is as follows: ```bash -nextflow run nf-core/pixelator --input ./samplesheet.csv --outdir ./results --genome GRCh37 -profile docker +nextflow run nf-core/pixelator --input samplesheet.csv --outdir -profile docker ``` This will launch the pipeline with the `docker` configuration profile. See below for more information about profiles. @@ -90,10 +169,11 @@ with `params.yaml` containing: ```yaml input: './samplesheet.csv' outdir: './results/' -genome: 'GRCh37' <...> ``` +You can find an extensive example of a `params.yaml` file with all options and +documentation in comments [here](../assets/params-file.yml). You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-co.re/launch). ### Updating the pipeline @@ -112,7 +192,7 @@ First, go to the [nf-core/pixelator releases page](https://github.com/nf-core/pi This version number will be logged in reports when you run the pipeline, so that you'll know what you used when you look back in the future. For example, at the bottom of the MultiQC reports. -To further assist in reproducbility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. +To further assist in reproducibility, you can use share and re-use [parameter files](#running-the-pipeline) to repeat pipeline runs with the same settings without having to write out a command with every single parameter. :::tip If you wish to share such profile (such as upload as supplementary material for academic publications), make sure to NOT include cluster specific paths to files, nor institutional specific profiles. @@ -161,6 +241,12 @@ If `-profile` is not specified, the pipeline will run locally and expect all sof - `conda` - A generic configuration profile to be used with [Conda](https://conda.io/docs/). Please only use Conda as a last resort i.e. when it's not possible to run the pipeline with Docker, Singularity, Podman, Shifter, Charliecloud, or Apptainer. +:::warning +Since Nextflow 23.07.0-edge, Nextflow no longer mounts the host's home directory when using Apptainer or Singularity. +This causes issues in some dependencies. As a workaround, you can revert to the old behavior by setting the environment variable +`NXF_APPTAINER_HOME_MOUNT` or `NXF_SINGULARITY_HOME_MOUNT` to `true` in the machine from which you launch the pipeline. +::: + ### `-resume` Specify this when restarting a pipeline. Nextflow will use cached results from any pipeline steps where the inputs are the same, continuing from where it got to previously. For input to be considered the same, not only the names must be identical but the files' contents as well. For more info about this parameter, see [this blog post](https://www.nextflow.io/blog/2019/demystifying-nextflow-resume.html). diff --git a/main.nf b/main.nf index 268be7c8..759cf0a2 100644 --- a/main.nf +++ b/main.nf @@ -17,23 +17,10 @@ nextflow.enable.dsl = 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { PIXELATOR } from './workflows/pixelator' +include { PIXELATOR } from './workflows/pixelator' include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_pixelator_pipeline' include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_pixelator_pipeline' -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_pixelator_pipeline' - -/* -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - GENOME PARAMETER VALUES -~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ -*/ - -// TODO nf-core: Remove this line if you don't need a FASTA file -// This is an example of how to use getGenomeAttribute() to fetch parameters -// from igenomes.config using `--genome` -params.fasta = getGenomeAttribute('fasta') - /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ NAMED WORKFLOWS FOR PIPELINE @@ -57,9 +44,6 @@ workflow NFCORE_PIXELATOR { samplesheet ) - emit: - multiqc_report = PIXELATOR.out.multiqc_report // channel: /path/to/multiqc_report.html - } /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -81,7 +65,8 @@ workflow { params.monochrome_logs, args, params.outdir, - params.input + params.input, + params.input_basedir ) // @@ -101,7 +86,7 @@ workflow { params.outdir, params.monochrome_logs, params.hook_url, - NFCORE_PIXELATOR.out.multiqc_report + [] ) } diff --git a/modules.json b/modules.json index 6cb9bbd1..5cf0d6b3 100644 --- a/modules.json +++ b/modules.json @@ -5,14 +5,14 @@ "https://github.com/nf-core/modules.git": { "modules": { "nf-core": { - "fastqc": { + "cat/fastq": { "branch": "master", "git_sha": "285a50500f9e02578d90b3ce6382ea3c30216acd", "installed_by": ["modules"] }, - "multiqc": { + "custom/dumpsoftwareversions": { "branch": "master", - "git_sha": "b7ebe95761cd389603f9cc0e0dc384c0f663815a", + "git_sha": "de45447d060b8c8b98575bc637a4a575fd0638e1", "installed_by": ["modules"] } } diff --git a/modules/local/pixelator/collect_metadata.nf b/modules/local/pixelator/collect_metadata.nf new file mode 100644 index 00000000..6f0f0ac1 --- /dev/null +++ b/modules/local/pixelator/collect_metadata.nf @@ -0,0 +1,79 @@ +import groovy.json.JsonOutput + + + +process PIXELATOR_COLLECT_METADATA { + label 'process_single' + cache false + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + + output: + path "metadata.json", emit: metadata + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + + Map nextflow_dict = [ + version: workflow.nextflow.version, + build: workflow.nextflow.build, + timestamp: workflow.nextflow.timestamp?.toString(), + ] + Map manifest_dict = [ + author: workflow.manifest.getAuthor(), + defaultBranch: workflow.manifest.getDefaultBranch(), + description: workflow.manifest.getDescription(), + homePage: workflow.manifest.getHomePage(), + gitmodules: workflow.manifest.getGitmodules(), + mainScript: workflow.manifest.getMainScript(), + version: workflow.manifest.getVersion(), + nextflowVersion: workflow.manifest.getNextflowVersion(), + doi: workflow.manifest.getDoi(), + ] + + Map workflow_dict = [ + scriptId: workflow.scriptId, + scriptName: workflow.scriptName, + scriptFile: workflow.scriptFile.toString(), + repository: workflow.repository, + commitId: workflow.commitId, + revision: workflow.revision, + projectDir: workflow.projectDir.toString(), + launchDir: workflow.launchDir.toString(), + workDir: workflow.workDir.toString(), + homeDir: workflow.homeDir.toString(), + userName: workflow.userName, + configFiles: workflow.configFiles.collect { it.toString() }, + container: workflow.container.collectEntries { [it.key, it.value?.toString()] }, + containerEngine: workflow.containerEngine, + commandLine: workflow.commandLine, + profile: workflow.profile, + runName: workflow.runName, + sessionId: workflow.sessionId, + resume: workflow.resume, + stubRun: workflow.stubRun, + start: workflow.start?.toString(), + ] + + def metadata = [ + nextflow: nextflow_dict, + manifest: manifest_dict, + workflow : workflow_dict, + parameters: params + ] + + def nextflowJson = JsonOutput.toJson(metadata) + + """ + echo '${nextflowJson}' > nextflow-metadata.json + collect_metadata.py --process-name ${task.process} --workflow-data "nextflow-metadata.json" + """ +} diff --git a/modules/local/pixelator/list_options.nf b/modules/local/pixelator/list_options.nf new file mode 100644 index 00000000..fe59c369 --- /dev/null +++ b/modules/local/pixelator/list_options.nf @@ -0,0 +1,31 @@ +process PIXELATOR_LIST_OPTIONS { + label 'process_single' + + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + output: + path "design_options.txt" , emit: designs + path "panel_options.txt" , emit: panels + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def args2 = task.ext.args2 ?: '' + + """ + pixelator single-cell --list-designs $args > design_options.txt + pixelator single-cell --list-panels $args2 > panel_options.txt + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell/amplicon/main.nf b/modules/local/pixelator/single-cell/amplicon/main.nf new file mode 100644 index 00000000..bdd60d2a --- /dev/null +++ b/modules/local/pixelator/single-cell/amplicon/main.nf @@ -0,0 +1,45 @@ +process PIXELATOR_AMPLICON { + tag "$meta.id" + label 'process_low' + + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("amplicon/*.merged.{fq,fastq}.gz"), emit: merged + tuple val(meta), path("amplicon/*.report.json") , emit: report_json + tuple val(meta), path("amplicon/*.meta.json") , emit: metadata + tuple val(meta), path("*pixelator-amplicon.log") , emit: log + + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + + """ + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-amplicon.log \\ + --verbose \\ + single-cell \\ + amplicon \\ + --output . \\ + $args \\ + ${reads} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell/analysis/main.nf b/modules/local/pixelator/single-cell/analysis/main.nf new file mode 100644 index 00000000..0ad705e0 --- /dev/null +++ b/modules/local/pixelator/single-cell/analysis/main.nf @@ -0,0 +1,47 @@ +process PIXELATOR_ANALYSIS { + tag "$meta.id" + label 'process_medium' + + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(data) + + output: + tuple val(meta), path("analysis/*dataset.pxl") , emit: dataset + tuple val(meta), path("analysis/*report.json") , emit: report_json + tuple val(meta), path("analysis/*.meta.json") , emit: metadata + tuple val(meta), path("analysis/*") , emit: all_results + tuple val(meta), path("*pixelator-analysis.log"), emit: log + + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + + prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + + """ + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-analysis.log \\ + --verbose \\ + single-cell \\ + analysis \\ + --output . \\ + $args \\ + $data + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell/annotate/main.nf b/modules/local/pixelator/single-cell/annotate/main.nf new file mode 100644 index 00000000..c7a44e82 --- /dev/null +++ b/modules/local/pixelator/single-cell/annotate/main.nf @@ -0,0 +1,53 @@ +process PIXELATOR_ANNOTATE { + tag "$meta.id" + label 'process_medium' + + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(dataset), path(panel_file), val(panel) + + output: + tuple val(meta), path("annotate/*.dataset.pxl") , emit: dataset + tuple val(meta), path("annotate/*.report.json") , emit: report_json + tuple val(meta), path("annotate/*.meta.json") , emit: metadata + tuple val(meta), path("annotate/*") , emit: all_results + tuple val(meta), path("*pixelator-annotate.log"), emit: log + + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + + prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def panelOpt = ( + panel ? "--panel $panel" : + panel_file ? "--panel $panel_file" : + "" + ) + + """ + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-annotate.log \\ + --verbose \\ + single-cell \\ + annotate \\ + --output . \\ + $panelOpt \\ + $args \\ + $dataset \\ + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell/collapse/main.nf b/modules/local/pixelator/single-cell/collapse/main.nf new file mode 100644 index 00000000..17918e76 --- /dev/null +++ b/modules/local/pixelator/single-cell/collapse/main.nf @@ -0,0 +1,54 @@ +process PIXELATOR_COLLAPSE { + tag "$meta.id" + label 'process_medium' + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(reads), path(panel_file), val(panel) + + output: + tuple val(meta), path("collapse/*.collapsed.parquet"), emit: collapsed + tuple val(meta), path("collapse/*.report.json") , emit: report_json + tuple val(meta), path("collapse/*.meta.json") , emit: metadata + tuple val(meta), path("*pixelator-collapse.log") , emit: log + + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + assert meta.design != null + + prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def readsArg = reads.join(' ') + def panelOpt = ( + panel ? "--panel $panel" : + panel_file ? "--panel $panel_file" : + "" + ) + + """ + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-collapse.log \\ + --verbose \\ + single-cell \\ + collapse \\ + --output . \\ + --design ${meta.design} \\ + $panelOpt \\ + $args \\ + $readsArg + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell/demux/main.nf b/modules/local/pixelator/single-cell/demux/main.nf new file mode 100644 index 00000000..6a02b0ac --- /dev/null +++ b/modules/local/pixelator/single-cell/demux/main.nf @@ -0,0 +1,54 @@ +process PIXELATOR_DEMUX { + tag "$meta.id" + label 'process_medium' + + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(reads), path(panel_file), val(panel) + + output: + tuple val(meta), path("demux/*processed*.{fq,fastq}.gz"), emit: processed + tuple val(meta), path("demux/*failed.{fq,fastq}.gz") , emit: failed + tuple val(meta), path("demux/*.report.json") , emit: report_json + tuple val(meta), path("demux/*.meta.json") , emit: metadata + tuple val(meta), path("*pixelator-demux.log") , emit: log + + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + // --design is passed in meta and added to args through modules.conf + + prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def panelOpt = ( + panel ? "--panel $panel" : + panel_file ? "--panel $panel_file" : + "" + ) + + """ + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-demux.log \\ + --verbose \\ + single-cell \\ + demux \\ + --output . \\ + $panelOpt \\ + $args \\ + ${reads} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell/graph/main.nf b/modules/local/pixelator/single-cell/graph/main.nf new file mode 100644 index 00000000..96e56324 --- /dev/null +++ b/modules/local/pixelator/single-cell/graph/main.nf @@ -0,0 +1,48 @@ +process PIXELATOR_GRAPH { + tag "$meta.id" + label 'process_medium' + + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(edge_list) + + output: + tuple val(meta), path("graph/*.edgelist.parquet") , emit: edgelist + tuple val(meta), path("graph/*.components_recovered.csv"), emit: components_recovered, optional: true + tuple val(meta), path("graph/*.report.json") , emit: report_json + tuple val(meta), path("graph/*.meta.json") , emit: input_params + tuple val(meta), path("graph/*") , emit: all_results + tuple val(meta), path("*pixelator-graph.log") , emit: log + + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + + prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + + """ + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-graph.log \\ + --verbose \\ + single-cell \\ + graph \\ + --output . \\ + $args \\ + ${edge_list} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell/qc/main.nf b/modules/local/pixelator/single-cell/qc/main.nf new file mode 100644 index 00000000..2650e5c4 --- /dev/null +++ b/modules/local/pixelator/single-cell/qc/main.nf @@ -0,0 +1,78 @@ +process PIXELATOR_QC { + tag "$meta.id" + label 'process_medium' + + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("adapterqc/*.processed.{fq,fastq}.gz") , emit: processed + + tuple val(meta), path("adapterqc/*.processed.{fq,fastq}.gz") , emit: adapterqc_processed + tuple val(meta), path("preqc/*.processed.{fq,fastq}.gz") , emit: preqc_processed + + tuple val(meta), path("adapterqc/*.failed.{fq,fastq}.gz") , emit: adapterqc_failed + tuple val(meta), path("preqc/*.failed.{fq,fastq}.gz") , emit: preqc_failed + tuple val(meta), path("{adapterqc,preqc}/*.failed.{fq,fastq}.gz"), emit: failed + + tuple val(meta), path("adapterqc/*.report.json") , emit: adapterqc_report_json + tuple val(meta), path("preqc/*.report.json") , emit: preqc_report_json + tuple val(meta), path("{adapterqc,preqc}/*.report.json") , emit: report_json + + tuple val(meta), path("adapterqc/*.meta.json") , emit: adapterqc_metadata + tuple val(meta), path("preqc/*.meta.json") , emit: preqc_metadata + tuple val(meta), path("{adapterqc,preqc}/*.meta.json") , emit: metadata + + tuple val(meta), path("*pixelator-*.log") , emit: log + + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + assert meta.design + + prefix = task.ext.prefix ?: "${meta.id}" + def preqc_args = task.ext.args ?: '' + def adapterqc_args = task.ext.args2 ?: '' + + // --design is passed in meta and added to args and args2 through modules.conf + """ + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-qc.log \\ + --verbose \\ + single-cell \\ + preqc \\ + --output . \\ + ${preqc_args} \\ + ${reads} + + shopt -s nullglob + preqc_results=( preqc/*.processed.* ) + echo \${preqc_results[@]} + shopt -u nullglob # Turn off nullglob to make sure it doesn't interfere with anything later + + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-qc.log \\ + --verbose \\ + single-cell \\ + adapterqc \\ + --output . \\ + ${adapterqc_args} \\ + \${preqc_results[@]} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/pixelator/single-cell/report/main.nf b/modules/local/pixelator/single-cell/report/main.nf new file mode 100644 index 00000000..c71b9749 --- /dev/null +++ b/modules/local/pixelator/single-cell/report/main.nf @@ -0,0 +1,57 @@ +process PIXELATOR_REPORT { + tag "$meta.id" + label 'process_low' + + + conda "bioconda::pixelator=0.16.2" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/pixelator:0.16.2--pyhdfd78af_0' : + 'biocontainers/pixelator:0.16.2--pyhdfd78af_0' }" + + input: + tuple val(meta), path(panel_file), val(panel) + path amplicon_data , stageAs: "results/amplicon/*" + path preqc_data , stageAs: "results/preqc/*" + path adapterqc_data , stageAs: "results/adapterqc/*" + path demux_data , stageAs: "results/demux/*" + path collapse_data , stageAs: "results/collapse/*" + path graph_data , stageAs: "results/graph/*" + path annotate_data , stageAs: "results/annotate/*" + path analysis_data , stageAs: "results/analysis/*" + + + output: + path "report/*.html" , emit: reports + path "versions.yml" , emit: versions + path "*pixelator-*.log" , emit: log + + when: + task.ext.when == null || task.ext.when + + script: + def prefix = task.ext.prefix ?: "${meta.id}" + def args = task.ext.args ?: '' + def panelOpt = ( + panel ? "--panel $panel" : + panel_file ? "--panel $panel_file" : + "" + ) + + """ + pixelator \\ + --cores $task.cpus \\ + --log-file ${prefix}.pixelator-report.log \\ + --verbose \\ + single-cell \\ + report \\ + --output . \\ + $panelOpt \\ + $args \\ + results + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + pixelator: \$(echo \$(pixelator --version 2>/dev/null) | sed 's/pixelator, version //g' ) + END_VERSIONS + """ +} diff --git a/modules/local/rename_reads.nf b/modules/local/rename_reads.nf new file mode 100644 index 00000000..024bd2de --- /dev/null +++ b/modules/local/rename_reads.nf @@ -0,0 +1,45 @@ +process RENAME_READS { + tag "$meta.id" + label 'process_single' + + conda "conda-forge::sed=4.7" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" + + + input: + tuple val(meta), path(reads) + + output: + tuple val(meta), path("${meta.id}{,_R1,_R2}*"), emit: reads + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + + if (reads in List) { + """ + r1_ext=\$(echo ${reads[0]} | grep -E -o "f(ast)?q.gz") + r2_ext=\$(echo ${reads[1]} | grep -E -o "f(ast)?q.gz") + + mv ${reads[0]} ${meta.id}_R1.\${r1_ext} + mv ${reads[1]} ${meta.id}_R2.\${r2_ext} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": {} + END_VERSIONS + """ + } else { + """ + r1_ext=\$(echo ${reads} | grep -E -o "f(ast)?q.gz") + mv ${reads} ${meta.id}.\${r1_ext} + + cat <<-END_VERSIONS > versions.yml + "${task.process}": {} + END_VERSIONS + """ + } +} diff --git a/modules/nf-core/fastqc/environment.yml b/modules/nf-core/cat/fastq/environment.yml similarity index 57% rename from modules/nf-core/fastqc/environment.yml rename to modules/nf-core/cat/fastq/environment.yml index 1787b38a..8c69b121 100644 --- a/modules/nf-core/fastqc/environment.yml +++ b/modules/nf-core/cat/fastq/environment.yml @@ -1,7 +1,7 @@ -name: fastqc +name: cat_fastq channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::fastqc=0.12.1 + - conda-forge::coreutils=8.30 diff --git a/modules/nf-core/cat/fastq/main.nf b/modules/nf-core/cat/fastq/main.nf new file mode 100644 index 00000000..f132b2ad --- /dev/null +++ b/modules/nf-core/cat/fastq/main.nf @@ -0,0 +1,79 @@ +process CAT_FASTQ { + tag "$meta.id" + label 'process_single' + + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/ubuntu:20.04' : + 'nf-core/ubuntu:20.04' }" + + input: + tuple val(meta), path(reads, stageAs: "input*/*") + + output: + tuple val(meta), path("*.merged.fastq.gz"), emit: reads + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] + if (meta.single_end) { + if (readList.size >= 1) { + """ + cat ${readList.join(' ')} > ${prefix}.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } else { + if (readList.size >= 2) { + def read1 = [] + def read2 = [] + readList.eachWithIndex{ v, ix -> ( ix & 1 ? read2 : read1 ) << v } + """ + cat ${read1.join(' ')} > ${prefix}_1.merged.fastq.gz + cat ${read2.join(' ')} > ${prefix}_2.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } + + stub: + def prefix = task.ext.prefix ?: "${meta.id}" + def readList = reads instanceof List ? reads.collect{ it.toString() } : [reads.toString()] + if (meta.single_end) { + if (readList.size > 1) { + """ + touch ${prefix}.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } else { + if (readList.size > 2) { + """ + touch ${prefix}_1.merged.fastq.gz + touch ${prefix}_2.merged.fastq.gz + + cat <<-END_VERSIONS > versions.yml + "${task.process}": + cat: \$(echo \$(cat --version 2>&1) | sed 's/^.*coreutils) //; s/ .*\$//') + END_VERSIONS + """ + } + } +} diff --git a/modules/nf-core/cat/fastq/meta.yml b/modules/nf-core/cat/fastq/meta.yml new file mode 100644 index 00000000..db4ac3c7 --- /dev/null +++ b/modules/nf-core/cat/fastq/meta.yml @@ -0,0 +1,42 @@ +name: cat_fastq +description: Concatenates fastq files +keywords: + - cat + - fastq + - concatenate +tools: + - cat: + description: | + The cat utility reads files sequentially, writing them to the standard output. + documentation: https://www.gnu.org/software/coreutils/manual/html_node/cat-invocation.html + licence: ["GPL-3.0-or-later"] +input: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: | + List of input FastQ files to be concatenated. +output: + - meta: + type: map + description: | + Groovy Map containing sample information + e.g. [ id:'test', single_end:false ] + - reads: + type: file + description: Merged fastq file + pattern: "*.{merged.fastq.gz}" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@joseespinosa" + - "@drpatelh" +maintainers: + - "@joseespinosa" + - "@drpatelh" diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test b/modules/nf-core/cat/fastq/tests/main.nf.test new file mode 100644 index 00000000..dab2e14c --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test @@ -0,0 +1,138 @@ +nextflow_process { + + name "Test Process CAT_FASTQ" + script "../main.nf" + process "CAT_FASTQ" + tag "modules" + tag "modules_nfcore" + tag "cat" + tag "cat/fastq" + + test("test_cat_fastq_single_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_same_name") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_paired_end_same_name") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:false ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), + file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } + + test("test_cat_fastq_single_end_single_file") { + + when { + params { + outdir = "$outputDir" + } + process { + """ + input[0] = Channel.of([ + [ id:'test', single_end:true ], // meta map + [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true)] + ]) + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot(process.out).match() } + ) + } + } +} diff --git a/modules/nf-core/cat/fastq/tests/main.nf.test.snap b/modules/nf-core/cat/fastq/tests/main.nf.test.snap new file mode 100644 index 00000000..43dfe28f --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/main.nf.test.snap @@ -0,0 +1,169 @@ +{ + "test_cat_fastq_single_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,ee314a9bd568d06617171b0c85f508da" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:30:39.816981" + }, + "test_cat_fastq_single_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:32:35.229332" + }, + "test_cat_fastq_single_end_single_file": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": true + }, + "test.merged.fastq.gz:md5,4161df271f9bfcd25d5845a1e220dbec" + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:34:00.058829" + }, + "test_cat_fastq_paired_end_same_name": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:33:33.031555" + }, + "test_cat_fastq_paired_end": { + "content": [ + { + "0": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "1": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ], + "reads": [ + [ + { + "id": "test", + "single_end": false + }, + [ + "test_1.merged.fastq.gz:md5,3ad9406595fafec8172368f9cd0b6a22", + "test_2.merged.fastq.gz:md5,a52cab0b840c7178b0ea83df1fdbe8d5" + ] + ] + ], + "versions": [ + "versions.yml:md5,d42d6e24d67004608495883e00bd501b" + ] + } + ], + "timestamp": "2024-01-17T17:32:02.270935" + } +} \ No newline at end of file diff --git a/modules/nf-core/cat/fastq/tests/tags.yml b/modules/nf-core/cat/fastq/tests/tags.yml new file mode 100644 index 00000000..6ac43614 --- /dev/null +++ b/modules/nf-core/cat/fastq/tests/tags.yml @@ -0,0 +1,2 @@ +cat/fastq: + - modules/nf-core/cat/fastq/** diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/custom/dumpsoftwareversions/environment.yml similarity index 51% rename from modules/nf-core/multiqc/environment.yml rename to modules/nf-core/custom/dumpsoftwareversions/environment.yml index ca39fb67..b48ced26 100644 --- a/modules/nf-core/multiqc/environment.yml +++ b/modules/nf-core/custom/dumpsoftwareversions/environment.yml @@ -1,7 +1,7 @@ -name: multiqc +name: custom_dumpsoftwareversions channels: - conda-forge - bioconda - defaults dependencies: - - bioconda::multiqc=1.21 + - bioconda::multiqc=1.20 diff --git a/modules/nf-core/custom/dumpsoftwareversions/main.nf b/modules/nf-core/custom/dumpsoftwareversions/main.nf new file mode 100644 index 00000000..105f9265 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/main.nf @@ -0,0 +1,24 @@ +process CUSTOM_DUMPSOFTWAREVERSIONS { + label 'process_single' + + // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container + conda "${moduleDir}/environment.yml" + container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? + 'https://depot.galaxyproject.org/singularity/multiqc:1.20--pyhdfd78af_0' : + 'biocontainers/multiqc:1.20--pyhdfd78af_0' }" + + input: + path versions + + output: + path "software_versions.yml" , emit: yml + path "software_versions_mqc.yml", emit: mqc_yml + path "versions.yml" , emit: versions + + when: + task.ext.when == null || task.ext.when + + script: + def args = task.ext.args ?: '' + template 'dumpsoftwareversions.py' +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/meta.yml b/modules/nf-core/custom/dumpsoftwareversions/meta.yml new file mode 100644 index 00000000..5f15a5fd --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/meta.yml @@ -0,0 +1,37 @@ +# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/meta-schema.json +name: custom_dumpsoftwareversions +description: Custom module used to dump software versions within the nf-core pipeline template +keywords: + - custom + - dump + - version +tools: + - custom: + description: Custom module used to dump software versions within the nf-core pipeline template + homepage: https://github.com/nf-core/tools + documentation: https://github.com/nf-core/tools + licence: ["MIT"] +input: + - versions: + type: file + description: YML file containing software versions + pattern: "*.yml" +output: + - yml: + type: file + description: Standard YML file containing software versions + pattern: "software_versions.yml" + - mqc_yml: + type: file + description: MultiQC custom content YML file containing software versions + pattern: "software_versions_mqc.yml" + - versions: + type: file + description: File containing software versions + pattern: "versions.yml" +authors: + - "@drpatelh" + - "@grst" +maintainers: + - "@drpatelh" + - "@grst" diff --git a/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py new file mode 100755 index 00000000..4a993608 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py @@ -0,0 +1,103 @@ +#!/usr/bin/env python + + +"""Provide functions to merge multiple versions.yml files.""" + + +import yaml +import platform +from textwrap import dedent + + +def _make_versions_html(versions): + """Generate a tabular HTML output of all versions for MultiQC.""" + html = [ + dedent( + """\\ + + + + + + + + + + """ + ) + ] + for process, tmp_versions in sorted(versions.items()): + html.append("") + for i, (tool, version) in enumerate(sorted(tmp_versions.items())): + html.append( + dedent( + f"""\\ + + + + + + """ + ) + ) + html.append("") + html.append("
Process Name Software Version
{process if (i == 0) else ''}{tool}{version}
") + return "\\n".join(html) + + +def main(): + """Load all version files and generate merged output.""" + versions_this_module = {} + versions_this_module["${task.process}"] = { + "python": platform.python_version(), + "yaml": yaml.__version__, + } + + with open("$versions") as f: + versions_by_process = ( + yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module + ) + + # aggregate versions by the module name (derived from fully-qualified process name) + versions_by_module = {} + for process, process_versions in versions_by_process.items(): + module = process.split(":")[-1] + try: + if versions_by_module[module] != process_versions: + raise AssertionError( + "We assume that software versions are the same between all modules. " + "If you see this error-message it means you discovered an edge-case " + "and should open an issue in nf-core/tools. " + ) + except KeyError: + versions_by_module[module] = process_versions + + versions_by_module["Workflow"] = { + "Nextflow": "$workflow.nextflow.version", + "$workflow.manifest.name": "$workflow.manifest.version", + } + + versions_mqc = { + "id": "software_versions", + "section_name": "${workflow.manifest.name} Software Versions", + "section_href": "https://github.com/${workflow.manifest.name}", + "plot_type": "html", + "description": "are collected at run time from the software output.", + "data": _make_versions_html(versions_by_module), + } + + with open("software_versions.yml", "w") as f: + yaml.dump(versions_by_module, f, default_flow_style=False) + with open("software_versions_mqc.yml", "w") as f: + yaml.dump(versions_mqc, f, default_flow_style=False) + + with open("versions.yml", "w") as f: + yaml.dump(versions_this_module, f, default_flow_style=False) + + +if __name__ == "__main__": + main() diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test new file mode 100644 index 00000000..b1e1630b --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test @@ -0,0 +1,43 @@ +nextflow_process { + + name "Test Process CUSTOM_DUMPSOFTWAREVERSIONS" + script "../main.nf" + process "CUSTOM_DUMPSOFTWAREVERSIONS" + tag "modules" + tag "modules_nfcore" + tag "custom" + tag "dumpsoftwareversions" + tag "custom/dumpsoftwareversions" + + test("Should run without failures") { + when { + process { + """ + def tool1_version = ''' + TOOL1: + tool1: 0.11.9 + '''.stripIndent() + + def tool2_version = ''' + TOOL2: + tool2: 1.9 + '''.stripIndent() + + input[0] = Channel.of(tool1_version, tool2_version).collectFile() + """ + } + } + + then { + assertAll( + { assert process.success }, + { assert snapshot( + process.out.versions, + file(process.out.mqc_yml[0]).readLines()[0..10], + file(process.out.yml[0]).readLines()[0..7] + ).match() + } + ) + } + } +} diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap new file mode 100644 index 00000000..5f59a936 --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/main.nf.test.snap @@ -0,0 +1,33 @@ +{ + "Should run without failures": { + "content": [ + [ + "versions.yml:md5,76d454d92244589d32455833f7c1ba6d" + ], + [ + "data: \"\\n\\n \\n \\n \\n \\n \\n \\n \\n\\", + " \\n\\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n \\n \\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\", + " \\ \\n\\n\\n\\n\\n\\n \\n\\", + " \\ \\n \\n\\n\\n\\n\\", + " \\n\\n \\n \\n\\" + ], + [ + "CUSTOM_DUMPSOFTWAREVERSIONS:", + " python: 3.11.7", + " yaml: 5.4.1", + "TOOL1:", + " tool1: 0.11.9", + "TOOL2:", + " tool2: '1.9'", + "Workflow:" + ] + ], + "timestamp": "2024-01-09T23:01:18.710682" + } +} \ No newline at end of file diff --git a/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml new file mode 100644 index 00000000..405aa24a --- /dev/null +++ b/modules/nf-core/custom/dumpsoftwareversions/tests/tags.yml @@ -0,0 +1,2 @@ +custom/dumpsoftwareversions: + - modules/nf-core/custom/dumpsoftwareversions/** diff --git a/modules/nf-core/fastqc/main.nf b/modules/nf-core/fastqc/main.nf deleted file mode 100644 index d79f1c86..00000000 --- a/modules/nf-core/fastqc/main.nf +++ /dev/null @@ -1,61 +0,0 @@ -process FASTQC { - tag "$meta.id" - label 'process_medium' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/fastqc:0.12.1--hdfd78af_0' : - 'biocontainers/fastqc:0.12.1--hdfd78af_0' }" - - input: - tuple val(meta), path(reads) - - output: - tuple val(meta), path("*.html"), emit: html - tuple val(meta), path("*.zip") , emit: zip - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def prefix = task.ext.prefix ?: "${meta.id}" - // Make list of old name and new name pairs to use for renaming in the bash while loop - def old_new_pairs = reads instanceof Path || reads.size() == 1 ? [[ reads, "${prefix}.${reads.extension}" ]] : reads.withIndex().collect { entry, index -> [ entry, "${prefix}_${index + 1}.${entry.extension}" ] } - def rename_to = old_new_pairs*.join(' ').join(' ') - def renamed_files = old_new_pairs.collect{ old_name, new_name -> new_name }.join(' ') - - def memory_in_mb = MemoryUnit.of("${task.memory}").toUnit('MB') - // FastQC memory value allowed range (100 - 10000) - def fastqc_memory = memory_in_mb > 10000 ? 10000 : (memory_in_mb < 100 ? 100 : memory_in_mb) - - """ - printf "%s %s\\n" $rename_to | while read old_name new_name; do - [ -f "\${new_name}" ] || ln -s \$old_name \$new_name - done - - fastqc \\ - $args \\ - --threads $task.cpus \\ - --memory $fastqc_memory \\ - $renamed_files - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ - - stub: - def prefix = task.ext.prefix ?: "${meta.id}" - """ - touch ${prefix}.html - touch ${prefix}.zip - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - fastqc: \$( fastqc --version | sed '/FastQC v/!d; s/.*v//' ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/fastqc/meta.yml b/modules/nf-core/fastqc/meta.yml deleted file mode 100644 index ee5507e0..00000000 --- a/modules/nf-core/fastqc/meta.yml +++ /dev/null @@ -1,57 +0,0 @@ -name: fastqc -description: Run FastQC on sequenced reads -keywords: - - quality control - - qc - - adapters - - fastq -tools: - - fastqc: - description: | - FastQC gives general quality metrics about your reads. - It provides information about the quality score distribution - across your reads, the per base sequence content (%A/C/G/T). - You get information about adapter contamination and other - overrepresented sequences. - homepage: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ - documentation: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/Help/ - licence: ["GPL-2.0-only"] -input: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - reads: - type: file - description: | - List of input FastQ files of size 1 and 2 for single-end and paired-end data, - respectively. -output: - - meta: - type: map - description: | - Groovy Map containing sample information - e.g. [ id:'test', single_end:false ] - - html: - type: file - description: FastQC report - pattern: "*_{fastqc.html}" - - zip: - type: file - description: FastQC report archive - pattern: "*_{fastqc.zip}" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" -maintainers: - - "@drpatelh" - - "@grst" - - "@ewels" - - "@FelixKrueger" diff --git a/modules/nf-core/fastqc/tests/main.nf.test b/modules/nf-core/fastqc/tests/main.nf.test deleted file mode 100644 index 70edae4d..00000000 --- a/modules/nf-core/fastqc/tests/main.nf.test +++ /dev/null @@ -1,212 +0,0 @@ -nextflow_process { - - name "Test Process FASTQC" - script "../main.nf" - process "FASTQC" - - tag "modules" - tag "modules_nfcore" - tag "fastqc" - - test("sarscov2 single-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - // NOTE The report contains the date inside it, which means that the md5sum is stable per day, but not longer than that. So you can't md5sum it. - // looks like this:
Mon 2 Oct 2023
test.gz
- // https://github.com/nf-core/modules/pull/3903#issuecomment-1743620039 - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_single") } - ) - } - } - - test("sarscov2 paired-end [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_paired") } - ) - } - } - - test("sarscov2 interleaved [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_interleaved.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_interleaved") } - ) - } - } - - test("sarscov2 paired-end [bam]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/bam/test.paired_end.sorted.bam', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/test_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/test_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_bam") } - ) - } - } - - test("sarscov2 multiple [fastq]") { - - when { - process { - """ - input[0] = Channel.of([ - [id: 'test', single_end: false], // meta map - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_2.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_1.fastq.gz', checkIfExists: true), - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test2_2.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1][0] ==~ ".*/test_1_fastqc.html" }, - { assert process.out.html[0][1][1] ==~ ".*/test_2_fastqc.html" }, - { assert process.out.html[0][1][2] ==~ ".*/test_3_fastqc.html" }, - { assert process.out.html[0][1][3] ==~ ".*/test_4_fastqc.html" }, - { assert process.out.zip[0][1][0] ==~ ".*/test_1_fastqc.zip" }, - { assert process.out.zip[0][1][1] ==~ ".*/test_2_fastqc.zip" }, - { assert process.out.zip[0][1][2] ==~ ".*/test_3_fastqc.zip" }, - { assert process.out.zip[0][1][3] ==~ ".*/test_4_fastqc.zip" }, - { assert path(process.out.html[0][1][0]).text.contains("") }, - { assert path(process.out.html[0][1][1]).text.contains("") }, - { assert path(process.out.html[0][1][2]).text.contains("") }, - { assert path(process.out.html[0][1][3]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_multiple") } - ) - } - } - - test("sarscov2 custom_prefix") { - - when { - process { - """ - input[0] = Channel.of([ - [ id:'mysample', single_end:true ], // meta map - file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - - { assert process.out.html[0][1] ==~ ".*/mysample_fastqc.html" }, - { assert process.out.zip[0][1] ==~ ".*/mysample_fastqc.zip" }, - { assert path(process.out.html[0][1]).text.contains("") }, - - { assert snapshot(process.out.versions).match("fastqc_versions_custom_prefix") } - ) - } - } - - test("sarscov2 single-end [fastq] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of([ - [ id: 'test', single_end:true ], - [ file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastq/test_1.fastq.gz', checkIfExists: true) ] - ]) - """ - } - } - - then { - assertAll ( - { assert process.success }, - { assert snapshot(process.out.html.collect { file(it[1]).getName() } + - process.out.zip.collect { file(it[1]).getName() } + - process.out.versions ).match("fastqc_stub") } - ) - } - } - -} diff --git a/modules/nf-core/fastqc/tests/main.nf.test.snap b/modules/nf-core/fastqc/tests/main.nf.test.snap deleted file mode 100644 index 86f7c311..00000000 --- a/modules/nf-core/fastqc/tests/main.nf.test.snap +++ /dev/null @@ -1,88 +0,0 @@ -{ - "fastqc_versions_interleaved": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:07.293713" - }, - "fastqc_stub": { - "content": [ - [ - "test.html", - "test.zip", - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:31:01.425198" - }, - "fastqc_versions_multiple": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:55.797907" - }, - "fastqc_versions_bam": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:40:26.795862" - }, - "fastqc_versions_single": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:39:27.043675" - }, - "fastqc_versions_paired": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:39:47.584191" - }, - "fastqc_versions_custom_prefix": { - "content": [ - [ - "versions.yml:md5,e1cc25ca8af856014824abd842e93978" - ] - ], - "meta": { - "nf-test": "0.8.4", - "nextflow": "23.10.1" - }, - "timestamp": "2024-01-31T17:41:14.576531" - } -} \ No newline at end of file diff --git a/modules/nf-core/fastqc/tests/tags.yml b/modules/nf-core/fastqc/tests/tags.yml deleted file mode 100644 index 7834294b..00000000 --- a/modules/nf-core/fastqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -fastqc: - - modules/nf-core/fastqc/** diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf deleted file mode 100644 index 47ac352f..00000000 --- a/modules/nf-core/multiqc/main.nf +++ /dev/null @@ -1,55 +0,0 @@ -process MULTIQC { - label 'process_single' - - conda "${moduleDir}/environment.yml" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/multiqc:1.21--pyhdfd78af_0' : - 'biocontainers/multiqc:1.21--pyhdfd78af_0' }" - - input: - path multiqc_files, stageAs: "?/*" - path(multiqc_config) - path(extra_multiqc_config) - path(multiqc_logo) - - output: - path "*multiqc_report.html", emit: report - path "*_data" , emit: data - path "*_plots" , optional:true, emit: plots - path "versions.yml" , emit: versions - - when: - task.ext.when == null || task.ext.when - - script: - def args = task.ext.args ?: '' - def config = multiqc_config ? "--config $multiqc_config" : '' - def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' - def logo = multiqc_logo ? /--cl-config 'custom_logo: "${multiqc_logo}"'/ : '' - """ - multiqc \\ - --force \\ - $args \\ - $config \\ - $extra_config \\ - $logo \\ - . - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ - - stub: - """ - mkdir multiqc_data - touch multiqc_plots - touch multiqc_report.html - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) - END_VERSIONS - """ -} diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml deleted file mode 100644 index 45a9bc35..00000000 --- a/modules/nf-core/multiqc/meta.yml +++ /dev/null @@ -1,58 +0,0 @@ -name: multiqc -description: Aggregate results from bioinformatics analyses across many samples into a single report -keywords: - - QC - - bioinformatics tools - - Beautiful stand-alone HTML report -tools: - - multiqc: - description: | - MultiQC searches a given directory for analysis logs and compiles a HTML report. - It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. - homepage: https://multiqc.info/ - documentation: https://multiqc.info/docs/ - licence: ["GPL-3.0-or-later"] -input: - - multiqc_files: - type: file - description: | - List of reports / files recognised by MultiQC, for example the html and zip output of FastQC - - multiqc_config: - type: file - description: Optional config yml for MultiQC - pattern: "*.{yml,yaml}" - - extra_multiqc_config: - type: file - description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. - pattern: "*.{yml,yaml}" - - multiqc_logo: - type: file - description: Optional logo file for MultiQC - pattern: "*.{png}" -output: - - report: - type: file - description: MultiQC report file - pattern: "multiqc_report.html" - - data: - type: directory - description: MultiQC data dir - pattern: "multiqc_data" - - plots: - type: file - description: Plots created by MultiQC - pattern: "*_data" - - versions: - type: file - description: File containing software versions - pattern: "versions.yml" -authors: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" -maintainers: - - "@abhi18av" - - "@bunop" - - "@drpatelh" - - "@jfy133" diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test deleted file mode 100644 index f1c4242e..00000000 --- a/modules/nf-core/multiqc/tests/main.nf.test +++ /dev/null @@ -1,84 +0,0 @@ -nextflow_process { - - name "Test Process MULTIQC" - script "../main.nf" - process "MULTIQC" - - tag "modules" - tag "modules_nfcore" - tag "multiqc" - - test("sarscov2 single-end [fastqc]") { - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_single") } - ) - } - - } - - test("sarscov2 single-end [fastqc] [config]") { - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true)) - input[2] = [] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert process.out.report[0] ==~ ".*/multiqc_report.html" }, - { assert process.out.data[0] ==~ ".*/multiqc_data" }, - { assert snapshot(process.out.versions).match("multiqc_versions_config") } - ) - } - } - - test("sarscov2 single-end [fastqc] - stub") { - - options "-stub" - - when { - process { - """ - input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true)) - input[1] = [] - input[2] = [] - input[3] = [] - """ - } - } - - then { - assertAll( - { assert process.success }, - { assert snapshot(process.out.report.collect { file(it).getName() } + - process.out.data.collect { file(it).getName() } + - process.out.plots.collect { file(it).getName() } + - process.out.versions ).match("multiqc_stub") } - ) - } - - } -} diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml deleted file mode 100644 index bea6c0d3..00000000 --- a/modules/nf-core/multiqc/tests/tags.yml +++ /dev/null @@ -1,2 +0,0 @@ -multiqc: - - modules/nf-core/multiqc/** diff --git a/nextflow.config b/nextflow.config index ebfdbf55..eb09e930 100644 --- a/nextflow.config +++ b/nextflow.config @@ -6,23 +6,67 @@ ---------------------------------------------------------------------------------------- */ + // Global default params, used in configs params { - // TODO nf-core: Specify your pipeline's command line flags // Input options - input = null - // References - genome = null - igenomes_base = 's3://ngi-igenomes/igenomes/' - igenomes_ignore = false - - // MultiQC options - multiqc_config = null - multiqc_title = null - multiqc_logo = null - max_multiqc_email_size = '25.MB' - multiqc_methods_description = null + input = null + input_basedir = null + + // Preqc options + trim_front = 0 + trim_tail = 0 + max_length = null + min_length = null + max_n_bases = 0 + avg_qual = 20 + dedup = false + remove_polyg = false + + // adapterqc options + adapterqc_mismatches = 0.1 + + // demux options + demux_mismatches = 0.1 + demux_min_length = null + + // collapse options + markers_ignore = null + algorithm = 'adjacency' + max_neighbours = 60 + collapse_mismatches = 2 + collapse_min_count = 2 + collapse_use_counts = false + + // graph options + multiplet_recovery = true + leiden_iterations = 10 + graph_min_count = 2 + + // annotate options + min_size = null + max_size = null + dynamic_filter = 'min' + aggregate_calling = true + + // analysis options + compute_polarization = true + compute_colocalization = true + use_full_bipartite = false + polarization_normalization = "clr" + polarization_binarization = false + colocalization_transformation = "log1p" + colocalization_neighbourhood_size = 1 + colocalization_n_permutations = 50 + colocalization_min_region_count = 5 + + // skip options + skip_report = false + skip_analysis = false + + // Main pixelator container override + pixelator_container = null // Boilerplate options outdir = null @@ -56,7 +100,6 @@ params { validationSchemaIgnoreParams = 'genomes,igenomes_base' validationShowHiddenParams = false validate_params = true - } // Load base.config by default for all pipelines @@ -70,11 +113,19 @@ try { } // Load nf-core/pixelator custom profiles from different institutions. -try { - includeConfig "${params.custom_config_base}/pipeline/pixelator.config" -} catch (Exception e) { - System.err.println("WARNING: Could not load nf-core/config/pixelator profiles: ${params.custom_config_base}/pipeline/pixelator.config") -} +// Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! +// try { +// includeConfig "${params.custom_config_base}/pipeline/pixelator.config" +// } catch (Exception e) { +// System.err.println("WARNING: Could not load nf-core/config/pixelator profiles: ${params.custom_config_base}/pipeline/pixelator.config") +// } + + +def container_env_options = [ + "MPLCONFIGDIR": '/tmp/.config/matplotlib', + "NUMBA_CACHE_DIR": "/tmp/.numba_cache", +] + profiles { debug { dumpHashes = true @@ -103,36 +154,40 @@ profiles { apptainer.enabled = false } docker { - docker.enabled = true - conda.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false - docker.runOptions = '-u $(id -u):$(id -g)' + docker.enabled = true + conda.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + docker.runOptions = '-u $(id -u):$(id -g)' + env = container_env_options } arm { docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' } singularity { - singularity.enabled = true - singularity.autoMounts = true - conda.enabled = false - docker.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + singularity.enabled = true + singularity.autoMounts = true + conda.enabled = false + docker.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + env = container_env_options } podman { - podman.enabled = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - shifter.enabled = false - charliecloud.enabled = false - apptainer.enabled = false + podman.enabled = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + shifter.enabled = false + charliecloud.enabled = false + apptainer.enabled = false + podman.runOptions = '--userns=keep-id' + env = container_env_options } shifter { shifter.enabled = true @@ -142,6 +197,7 @@ profiles { podman.enabled = false charliecloud.enabled = false apptainer.enabled = false + env = container_env_options } charliecloud { charliecloud.enabled = true @@ -153,14 +209,15 @@ profiles { apptainer.enabled = false } apptainer { - apptainer.enabled = true - apptainer.autoMounts = true - conda.enabled = false - docker.enabled = false - singularity.enabled = false - podman.enabled = false - shifter.enabled = false - charliecloud.enabled = false + apptainer.enabled = true + apptainer.autoMounts = true + conda.enabled = false + docker.enabled = false + singularity.enabled = false + podman.enabled = false + shifter.enabled = false + charliecloud.enabled = false + env = container_env_options } wave { apptainer.ociAutoPull = true @@ -191,12 +248,6 @@ plugins { id 'nf-validation@1.1.3' // Validation of pipeline parameters and creation of an input channel from a sample sheet } -// Load igenomes.config if required -if (!params.igenomes_ignore) { - includeConfig 'conf/igenomes.config' -} else { - params.genomes = [:] -} // Export these variables to prevent local Python/R libraries from conflicting with those in the container // The JULIA depot path has been adjusted to a fixed path `/usr/local/share/julia` that needs to be used for packages in the container. // See https://apeltzer.github.io/post/03-julia-lang-nextflow/ for details on that. Once we have a common agreement on where to keep Julia packages, this is adjustable. @@ -239,8 +290,8 @@ manifest { description = """Pipeline for analysis of Molecular Pixelation assays""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' - version = '1.1.0' - doi = '' + version = '1.2.0' + doi = '10.1101/2023.06.05.543770' } // Load modules.config for DSL2 module specific options diff --git a/nextflow_schema.json b/nextflow_schema.json index 77b2a8e1..e58178a9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -18,11 +18,18 @@ "exists": true, "schema": "assets/schema_input.json", "mimetype": "text/csv", - "pattern": "^\\S+\\.csv$", + "pattern": "^\\S+\\.(csv|tsv)$", "description": "Path to comma-separated file containing information about the samples in the experiment.", "help_text": "You will need to create a design file with information about the samples in your experiment before running the pipeline. Use this parameter to specify its location. It has to be a comma-separated file with 3 columns, and a header row. See [usage docs](https://nf-co.re/pixelator/usage#samplesheet-input).", "fa_icon": "fas fa-file-csv" }, + "input_basedir": { + "type": "string", + "format": "directory-path", + "exists": false, + "description": "Path to a local or remote directory that is the \"current working directory\" for relative paths defined in the input samplesheet", + "fa_icon": "fas fa-folder" + }, "outdir": { "type": "string", "format": "directory-path", @@ -35,42 +42,277 @@ "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})$" + } + } + }, + "preqc_options": { + "title": "QC/Filtering/Trimming options", + "type": "object", + "fa_icon": "fas fa-terminal", + "properties": { + "trim_front": { + "fa_icon": "fas backward-step", + "type": "integer", + "description": "Trim N bases from the front of the reads", + "default": 0 }, - "multiqc_title": { - "type": "string", - "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", - "fa_icon": "fas fa-file-signature" + "trim_tail": { + "fa_icon": "fas forward-step", + "type": "integer", + "description": "Trim N bases from the tail of the reads", + "default": 0 + }, + "max_length": { + "fa_icon": "fas up-right-and-down-left-from-center", + "type": "integer", + "description": "The maximum length of a read", + "help_text": "Reads longer then given length will be trimmed to the given length. If you set this argument it will overrule the value from the chosen design" + }, + "min_length": { + "fa_icon": "fas down-left-and-up-right-to-center", + "type": "integer", + "description": "The minimum length (bases) of a read", + "help_text": "Reads shorter then given length will be discarded. If you set this argument it will overrule the value from the chosen design." + }, + "max_n_bases": { + "fa_icon": "fas n", + "description": "The maximum number of Ns allowed in a read", + "help_text": "The default value of 0 means any reads with N in it will be filtered out", + "type": "integer", + "default": 0 + }, + "avg_qual": { + "fa_icon": "fas gauge", + "description": "Minimum avg. quality a read must have (0 will disable the filter)", + "type": "integer", + "default": 20 + }, + "dedup": { + "fa_icon": "fas clone", + "description": "Remove duplicated reads (exact same sequence)", + "type": "boolean" + }, + "remove_polyg": { + "fa_icon": "fas g", + "description": "Remove PolyG sequences (length of 10 or more)", + "type": "boolean" + } + } + }, + "adapterqc_options": { + "title": "Adapter QC Options", + "type": "object", + "properties": { + "adapterqc_mismatches": { + "fa_icon": "fas not-equal", + "description": "The number of mismatches allowed (in percentage) [default: 0.1; 0.0<=x<=0.9]", + "type": "number", + "default": 0.1, + "minimum": 0.0, + "maximum": 0.9 + } + } + }, + "demux_options": { + "title": "Demux options", + "type": "object", + "properties": { + "demux_mismatches": { + "fa_icon": "fas not-equal", + "description": "The number of mismatches allowed (as a fraction)", + "type": "number", + "default": 0.1, + "minimum": 0.0, + "maximum": 0.9 + }, + "demux_min_length": { + "fa_icon": "fas down-left-and-up-right-to-center", + "description": "The minimum length of the barcode that must overlap when matching", + "help_text": "If you set this argument it will overrule the value from the chosen design", + "type": "integer" } } }, - "reference_genome_options": { - "title": "Reference genome options", + "collapse_options": { + "title": "Collapse options", "type": "object", - "fa_icon": "fas fa-dna", - "description": "Reference genome related files and options required for the workflow.", "properties": { - "genome": { + "markers_ignore": { + "fa_icon": "fas fa-list", + "description": "A list of comma separated antibodies to discard", "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." + "pattern": "(\\S+)?(,\\S+)*" + }, + "algorithm": { + "fa_icon": "fas code-fork", + "description": "The algorithm to use for collapsing (adjacency will perform error correction using the number of mismatches given)", + "default": "adjacency", + "enum": ["adjacency", "unique"], + "type": "string" + }, + "max_neighbours": { + "fa_icon": "fas circle-nodes", + "description": "The maximum number of neighbors to use when searching for similar sequences. This number depends on the sequence depth and the ratio of erroneous molecules expected. A high value can make the algorithm slower. This is only used when algorithm is set to 'adjacency'", + "default": 60, + "minimum": 1, + "maximum": 250, + "type": "integer", + "hidden": true + }, + "collapse_mismatches": { + "fa_icon": "fas not-equal", + "description": "The number of mismatches allowed when collapsing (adjacency)", + "type": "integer", + "default": 2, + "minimum": 0, + "maximum": 5 + }, + "collapse_min_count": { + "fa_icon": "fas more-than-equal", + "description": "Discard molecules with with a count (reads) lower than this value", + "default": 2, + "minimum": 1, + "type": "integer" + }, + "collapse_use_counts": { + "description": "Use counts when collapsing (the difference in counts between two molecules must be more than double in order to be collapsed)", + "type": "boolean" + } + } + }, + "graph_options": { + "title": "Options for pixelator graph command.", + "type": "object", + "properties": { + "multiplet_recovery": { + "description": "Activate the multiplet recovery using leiden community detection", + "type": "boolean", + "default": true }, - "fasta": { + "leiden_iterations": { + "fa_icon": "fas repeat", + "description": "Number of iterations for the leiden algorithm, high values will decrease the variance of the results but increase the runtime [default: 10; 1<=x<=100]", + "type": "integer", + "minimum": 1, + "maximum": 100, + "default": 10, + "hidden": true + }, + "graph_min_count": { + "fa_icon": "fas less-than-equal", + "description": "Discard edges (pixels) with a count (reads) lower than this, use 1 to disable", + "type": "integer", + "default": 2, + "minimum": 1, + "maximum": 50, + "hidden": true + } + } + }, + "annotate_options": { + "title": "Options for pixelator annotate command.", + "type": "object", + "properties": { + "min_size": { + "description": "The minimum size (pixels) a component/cell can have (disabled by default)", + "type": "integer" + }, + "max_size": { + "description": "The maximum size (pixels) a component/cell can have (disabled by default)", + "type": "integer" + }, + "dynamic_filter": { + "description": " Enable the estimation of dynamic size filters using a log-rank approach both: estimate both min and max size, min: estimate min size (--min-size), max: estimate max size (--max-size)", "type": "string", - "format": "file-path", - "exists": true, - "mimetype": "text/plain", - "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", - "description": "Path to FASTA genome file.", - "help_text": "This parameter is *mandatory* if `--genome` is not specified. If you don't have a BWA index available this will be generated for you automatically. Combine with `--save_reference` to save BWA index for future runs.", - "fa_icon": "far fa-file-code" + "enum": ["both", "min", "max"], + "default": "min" }, - "igenomes_ignore": { + "aggregate_calling": { + "description": "Enable aggregate calling, information on potential aggregates will be added to the output data", "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`." + "default": true + } + } + }, + "analysis_options": { + "title": "Options for pixelator analysis command.", + "type": "object", + "properties": { + "skip_analysis": { + "description": "Skip analysis step", + "type": "boolean" + }, + "compute_polarization": { + "description": "Compute polarization scores matrix (clusters by markers)", + "type": "boolean", + "default": true + }, + "compute_colocalization": { + "description": " Compute colocalization scores (marker by marker) for each component", + "type": "boolean", + "default": true + }, + "use_full_bipartite": { + "description": "Use the bipartite graph instead of the one-node projection when computing polarization, coabundance and colocalization scores", + "type": "boolean" + }, + "polarization_normalization": { + "description": "Which approach to use to normalize the antibody counts.", + "help_text": "- `raw`: use the raw counts.\n- `CLR`: use the CLR-transformed counts.\n- `denoise`: use CLR-transformed counts and subtract the counts of control antibodies", + "type": "string", + "enum": ["raw", "clr", "denoise"], + "default": "clr" + }, + "polarization_binarization": { + "fa_icon": "fas binary", + "description": "Transform the antibody counts to 0-1 (binarize) when computing polarization", + "type": "boolean" + }, + "colocalization_transformation": { + "type": "string", + "enum": ["raw", "clr", "log1p", "relative"], + "default": "log1p", + "description": "Select the type of transformation to use on the node by antibody counts matrix when computing colocalization" + }, + "colocalization_neighbourhood_size": { + "type": "integer", + "description": "Select the size of the neighborhood to use when computing colocalization metrics on each component", + "default": 1, + "minimum": 0 + }, + "colocalization_n_permutations": { + "type": "integer", + "description": "Set the number of permutations use to compute the empirical p-value for the colocalization score", + "default": 50, + "minimum": 5 + }, + "colocalization_min_region_count": { + "type": "integer", + "description": "The minimum number of counts in a region for it to be considered valid for computing colocalization", + "default": 5, + "minimum": 0 + } + } + }, + "report_options": { + "title": "Options for pixelator report command.", + "type": "object", + "properties": { + "skip_report": { + "description": "Skip report generation", + "type": "boolean" + } + } + }, + "global_config_options": { + "title": "Global options", + "type": "object", + "description": "Global configuration options specific to nf-core/pixelator.", + "properties": { + "pixelator_container": { + "type": "string", + "description": "Override the container image reference to use for all steps using the `pixelator` command.", + "help_text": "Use this to force the pipeline to use a different image version in all steps that use the pixelator command.\nThe pipeline is not guaranteed to work when using different pixelator versions." } } }, @@ -199,14 +441,6 @@ "fa_icon": "fas fa-remove-format", "hidden": true }, - "max_multiqc_email_size": { - "type": "string", - "description": "File size limit when attaching MultiQC reports to summary emails.", - "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", - "default": "25.MB", - "fa_icon": "fas fa-file-upload", - "hidden": true - }, "monochrome_logs": { "type": "boolean", "description": "Do not use coloured log outputs.", @@ -220,24 +454,6 @@ "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", "hidden": true }, - "multiqc_config": { - "type": "string", - "format": "file-path", - "description": "Custom config file to supply to MultiQC.", - "fa_icon": "fas fa-cog", - "hidden": true - }, - "multiqc_logo": { - "type": "string", - "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", - "fa_icon": "fas fa-image", - "hidden": true - }, - "multiqc_methods_description": { - "type": "string", - "description": "Custom MultiQC yaml file containing HTML including a methods description.", - "fa_icon": "fas fa-cog" - }, "validate_params": { "type": "boolean", "description": "Boolean whether to validate parameters against the schema at runtime", @@ -257,7 +473,7 @@ "fa_icon": "far fa-check-circle", "description": "Validation of parameters fails when an unrecognised parameter is found.", "hidden": true, - "help_text": "By default, when an unrecognised parameter is found, it returns a warinig." + "help_text": "By default, when an unrecognised parameter is found, it returns a warning." }, "validationLenientMode": { "type": "boolean", @@ -281,7 +497,31 @@ "$ref": "#/definitions/input_output_options" }, { - "$ref": "#/definitions/reference_genome_options" + "$ref": "#/definitions/preqc_options" + }, + { + "$ref": "#/definitions/adapterqc_options" + }, + { + "$ref": "#/definitions/demux_options" + }, + { + "$ref": "#/definitions/collapse_options" + }, + { + "$ref": "#/definitions/graph_options" + }, + { + "$ref": "#/definitions/annotate_options" + }, + { + "$ref": "#/definitions/analysis_options" + }, + { + "$ref": "#/definitions/report_options" + }, + { + "$ref": "#/definitions/global_config_options" }, { "$ref": "#/definitions/institutional_config_options" diff --git a/samplesheet.csv b/samplesheet.csv new file mode 100644 index 00000000..da37578e --- /dev/null +++ b/samplesheet.csv @@ -0,0 +1,3 @@ +sample,design,panel,panel_file,fastq_1,fastq_2 +uropod_control,D21,human-sc-immunology-spatial-proteomics,,uropod_control_300k_R1_001.fastq.gz,uropod_control_300k_R2_001.fastq.gz +pbmcs_unstimulated,D21,human-sc-immunology-spatial-proteomics,,Sample01_human_pbmcs_unstimulated_200k_R1_001.fastq.gz,Sample01_human_pbmcs_unstimulated_200k_R2_001.fastq.gz diff --git a/subworkflows/local/generate_reports.nf b/subworkflows/local/generate_reports.nf new file mode 100644 index 00000000..dc5fb42c --- /dev/null +++ b/subworkflows/local/generate_reports.nf @@ -0,0 +1,134 @@ +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT MODULES / SUBWORKFLOWS / FUNCTIONS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +include { PIXELATOR_REPORT } from '../../modules/local/pixelator/single-cell/report/main' + + +/* +======================================================================================== + SUBWORKFLOW TO GENERATE PIXELATOR REPORTS +======================================================================================== +*/ + +workflow GENERATE_REPORTS { + take: + panel_files // channel: [meta, path(panel_file) | []] + amplicon_data // channel: [meta, [path, ...]] + preqc_data // channel: [meta, [path, ...]] + adapterqc_data // channel: [meta, [path, ...]] + demux_data // channel: [meta, [path, ...]] + collapse_data // channel: [meta, [path, ...]] + graph_data // channel: [meta, [path, ...]] + annotate_data // channel: [meta, [path, ...]] + analysis_data // channel: [meta, [path, ...]] + + main: + ch_versions = Channel.empty() + + ch_meta_col = panel_files + .map { meta, data -> [ meta.id, meta] } + .groupTuple() + .map { id, data -> + if (data instanceof List) { + def newMeta = [:] + for (item in data) { + newMeta += item + } + return [id, newMeta] + } + return [id, data] + } + + ch_panel_col = panel_files + .map { meta, data -> [ meta.id, data] } + + // + // These first subcommands each return two files per sample used by the reporting + // A json file with stats and a command invocation metadata json file + // + ch_amplicon_col = amplicon_data.map { meta, data -> [ meta.id, data] } + ch_preqc_col = preqc_data.map { meta, data -> [ meta.id, data] } + ch_adapterqc_col = adapterqc_data.map { meta, data -> [ meta.id, data] } + ch_demux_col = demux_data.map { meta, data -> [ meta.id, data] } + ch_collapse_col = collapse_data.map { meta, data -> [ meta.id, data] } + ch_graph_col = graph_data.map { meta, data -> [meta.id, data] } + ch_annotate_col = annotate_data.map { meta, data -> [meta.id, data] } + ch_analysis_col = analysis_data.map { meta, data -> [meta.id, data] } + + // + // Combine all inputs and group them, then split them up again. + // This is neded to have the per subcommand outputs in the sample order + // + // ch_report_data: [ + // [ + // meta, panel_files, + // [amplicon files...], + // [preqc files...], + // [adapterqc files...], + // [demux files...], + // [collapse files...], + // [cluster files], + // [annotate files...], + // [analysis files...] + // ], + // [ same structure repeated for each sample ] + // ] + + ch_report_data = ch_meta_col + .concat ( ch_panel_col ) + .concat ( ch_amplicon_col ) + .concat ( ch_preqc_col ) + .concat ( ch_adapterqc_col ) + .concat ( ch_demux_col ) + .concat ( ch_collapse_col ) + .concat ( ch_graph_col ) + .concat ( ch_annotate_col ) + .concat ( ch_analysis_col ) + .groupTuple (size: 10) + + // + // Split up everything per stage so we can recreate the expected directory structure for + // `pixelator single-cell report` using stageAs for each stage + // + // These ch__grouped channels all emit a list of input files for each sample in the samplesheet + // The channels will emit values in the same order so eg. the first list of files from each ch__grouped + // channel will match the same sample from the samplesheet. + + // If no `panel_file` (data[1]) is given we need to pass in `panel` from the samplesheet instead + // + ch_panel_files_grouped = ch_report_data.map { id, data -> [ data[0], data[1], data[1] ? null : data[0].panel ] } + ch_amplicon_grouped = ch_report_data.map { id, data -> data[2] ? data[2].flatten() : [] } + ch_preqc_grouped = ch_report_data.map { id, data -> data[3] ? data[3].flatten() : [] } + ch_adapterqc_grouped = ch_report_data.map { id, data -> data[4] ? data[4].flatten() : [] } + ch_demux_grouped = ch_report_data.map { id, data -> data[5] ? data[5].flatten() : [] } + ch_collapse_grouped = ch_report_data.map { id, data -> data[6] ? data[6].flatten() : [] } + ch_graph_grouped = ch_report_data.map { id, data -> data[7] ? data[7].flatten() : [] } + ch_annotate_grouped = ch_report_data.map { id, data -> data[8] ? data[8].flatten() : [] } + ch_analysis_grouped = ch_report_data.map { id, data -> data[9] ? data[9].flatten() : [] } + + // + // MODULE: Run pixelator single-cell report for each samples + // + // NB: These channels need to be split per stage to allow PIXELATOR_REPORT to + // use stageAs directives to reorder the inputs and prevent filename collisions + PIXELATOR_REPORT ( + ch_panel_files_grouped, + ch_amplicon_grouped, + ch_preqc_grouped, + ch_adapterqc_grouped, + ch_demux_grouped, + ch_collapse_grouped, + ch_graph_grouped, + ch_annotate_grouped, + ch_analysis_grouped, + ) + + ch_versions = ch_versions.mix(PIXELATOR_REPORT.out.versions.first()) + + emit: + pixelator_reports = PIXELATOR_REPORT.out.reports + versions = ch_versions +} diff --git a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf index 5d96f1f8..3a61820a 100644 --- a/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_pixelator_pipeline/main.nf @@ -20,6 +20,8 @@ include { imNotification } from '../../nf-core/utils_nfcore_pipeline' include { UTILS_NFCORE_PIPELINE } from '../../nf-core/utils_nfcore_pipeline' include { workflowCitation } from '../../nf-core/utils_nfcore_pipeline' +include { PIXELATOR_LIST_OPTIONS } from '../../../modules/local/pixelator/list_options.nf' + /* ======================================================================================== SUBWORKFLOW TO INITIALISE PIPELINE @@ -36,6 +38,7 @@ workflow PIPELINE_INITIALISATION { nextflow_cli_args // array: List of positional nextflow CLI args outdir // string: The output directory where the results will be saved input // string: Path to input samplesheet + input_basedir // string: Path to the base directory for relative paths resolving main: @@ -80,25 +83,57 @@ workflow PIPELINE_INITIALISATION { // // Create channel from input file provided through params.input // - Channel - .fromSamplesheet("input") - .map { - meta, fastq_1, fastq_2 -> - if (!fastq_2) { - return [ meta.id, meta + [ single_end:true ], [ fastq_1 ] ] - } else { - return [ meta.id, meta + [ single_end:false ], [ fastq_1, fastq_2 ] ] - } - } - .groupTuple() + ch_versions = Channel.empty() + + // + // Resolve relative paths and validate fastq files existence + // + def samplesheet_uri = file(input).toUri() + def inputBaseDir = get_data_basedir(samplesheet_uri, input_basedir) + + log.info "Resolving relative paths in samplesheet relative to: ${inputBaseDir}" + + ch_input = Channel.fromSamplesheet("input") .map { - validateInputSamplesheet(it) + validate_input_samplesheet(inputBaseDir, it) } + + + // + // Validate design and panel samplesheet fields agains a dynamic set of allowed values + // + PIXELATOR_LIST_OPTIONS() + ch_versions = ch_versions.mix(PIXELATOR_LIST_OPTIONS.out.versions) + + // Create a set of valid pixelator options to pass to --design + ch_design_options = PIXELATOR_LIST_OPTIONS.out.designs + .splitText() + .map( text -> text.trim()) + .reduce( new HashSet() ) { prev, curr -> prev << curr } + + // Create a set of valid pixelator panel keys to pass using --panel + ch_panel_options = PIXELATOR_LIST_OPTIONS.out.panels + .splitText() + .map( text -> text.trim()) + .reduce( new HashSet() ) { prev, curr -> prev << curr } + + + + // + // Combine the validated inputs again in a single channel + // + ch_samplesheet = ch_input + .map { it -> it[0] } + .combine(ch_panel_options) + .combine(ch_design_options) .map { - meta, fastqs -> - return [ meta, fastqs.flatten() ] + meta, panel_options, design_options -> { + meta = validate_panel(meta, panel_options) + meta = validate_design(meta, design_options) + return meta + } } - .set { ch_samplesheet } + .join(ch_input) emit: samplesheet = ch_samplesheet @@ -155,7 +190,8 @@ workflow PIPELINE_COMPLETION { // Check and validate pipeline parameters // def validateInputParameters() { - genomeExistsError() + // Keep this commented here to closely follow the template + // genomeExistsError() } // @@ -261,3 +297,151 @@ def methodsDescriptionText(mqc_methods_yaml) { return description_html.toString() } + + + +// +// Resolve relative paths relative to the samplesheet parent directory. +// +def resolve_relative_path(relative_path, URI samplesheet_path) { + if (!(relative_path instanceof String)) { + return relative_path + } + + // Try to create a java.net.UR object out of it. If it is not a proper URL, a MalformedURLException will be t + URI uri; + + try { + uri = new URI(relative_path) + } catch (URISyntaxException exc) { + return relative_path + } + + // If a scheme is given we keep it as given + if (uri.getScheme() != null) { + return relative_path + } + + def path = new File(relative_path) + if (path.isAbsolute()) { + return relative_path + } + + // Resolve relative paths agains the samplesheet_path + def resolvedPath = samplesheet_path.resolve(relative_path); + + def stringPath = resolvedPath.toString() + return stringPath +} + +// +// Validate a given panel key if present against the (dynamic) set of panel options retrieved from pixelator +// +def validate_panel(LinkedHashMap meta, HashSet options) { + if (meta.panel == null) { + return + } + + if (!options.contains(meta.panel)) { + options_list_str = " - ${options.join("\n - ")}" + exit 1, "Please check input samplesheet -> panel field does not contains a valid key!\n\nInput: ${meta.panel}\nValid options:\n${options_list_str}" + } + + return meta +} + + +// +// Validate a given design key if present against the (dynamic) set of design options retrieved from pixelator +// +def validate_design(LinkedHashMap meta, HashSet options) { + if (meta.design == null) { + return + } + + if (!options.contains(meta.design)) { + options_list_str = " - ${options.join("\n - ")}" + exit 1, "Please check input samplesheet -> design field does not contains a valid key!\n\nInput: ${meta.design}\nValid options:\n${options_list_str}" + } + + return meta +} + +// +// Determine the path/url that will be used as the root for relative paths in the samplesheet +// +def get_data_basedir(URI samplesheet, String input_basedir) { + + URI uri; + + // nothing given to --input_data so we use the samplesheet as root directory + // for resolving relative paths + if (!input_basedir) { + return samplesheet + } + + try { + uri = new URI(input_basedir) + } catch (URISyntaxException exc) { + return samplesheet + } + + // If a scheme is given we keep check that it is a directory (trailing-slash) + if (uri.getScheme() != null) { + if (!uri.path.endsWith('/')) { + def newUrl = new URI( + uri.getScheme(), uri.getUserInfo(), uri.getHost(), + uri.getPort(), uri.getPath() + '/', uri.getQuery(), uri.getFragment() + ) + return newUrl + } + return uri + } + + f = file(input_basedir) + if (!f.exists()) { + exit 1, "ERROR: data path passed with --input_basedir does not exist!" + } + if (f.isDirectory()) { + data_root = new URI(f.toString() + '/') + } else { + data_root = new URI(f.toString()) + } + + return data_root +} + +// +// Resolve relative paths and check that all files exist. +// +def validate_input_samplesheet(URI samplesheetUrl, items) { + def meta = items[0] + def panel_file = items[1] + def fq = items[2..-1] + + def paired_end = fq.size() == 2 + def panel_file_abs = resolve_relative_path(panel_file, samplesheetUrl) + def fq1_abs = resolve_relative_path(fq[0], samplesheetUrl) + + if (panel_file_abs && !file(panel_file_abs).exists()) { + exit 1, "ERROR: Please check input samplesheet -> panel_file does not exist!\n${panel_file_abs}" + } + + if (!file(fq1_abs).exists()) { + exit 1, "ERROR: Please check input samplesheet -> fastq_1 does not exist!\n${fq1_abs}" + } + + def reads = [ fq1_abs ] + + if (paired_end) { + def fq2_abs = resolve_relative_path(fq[1], samplesheetUrl) + + if (fq2_abs && !file(fq2_abs).exists()) { + exit 1, "ERROR: Please check input samplesheet -> fastq_2 does not exist!\n${fq2_abs}" + } + + reads += [ fq2_abs] + } + + return [ meta, panel_file_abs, reads ] +} diff --git a/tower.yml b/tower.yml index 787aedfe..c67d4691 100644 --- a/tower.yml +++ b/tower.yml @@ -1,5 +1,3 @@ reports: - multiqc_report.html: - display: "MultiQC HTML report" - samplesheet.csv: - display: "Auto-created samplesheet with collated metadata and FASTQ paths" + "**/report/*_report.html": + display: "Pixelator HTML report" diff --git a/workflows/pixelator.nf b/workflows/pixelator.nf index afb6838b..c7db0457 100644 --- a/workflows/pixelator.nf +++ b/workflows/pixelator.nf @@ -4,37 +4,239 @@ ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { FASTQC } from '../modules/nf-core/fastqc/main' -include { MULTIQC } from '../modules/nf-core/multiqc/main' include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_pixelator_pipeline' + +// Inject the samplesheet SHA-1 into the params object +ch_input = file(params.input) +params.samplesheet_sha = ch_input.bytes.digest('sha-1') + /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - RUN MAIN WORKFLOW + CONFIG FILES ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -workflow PIXELATOR { +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT LOCAL MODULES/SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// SUBWORKFLOW: Consisting of a mix of local and nf-core/modules +// +include { GENERATE_REPORTS } from '../subworkflows/local/generate_reports' + +/* +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ + IMPORT NF-CORE MODULES/SUBWORKFLOWS +~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ +*/ + +// +// MODULE: Installed directly from nf-core/modules +// +include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' +include { CAT_FASTQ } from '../modules/nf-core/cat/fastq/main' +/* +======================================================================================== + IMPORT CUSTOM MODULES/SUBWORKFLOWS +======================================================================================== +*/ + +// +// MODULE: Defined locally +// +include { RENAME_READS } from '../modules/local/rename_reads' +include { PIXELATOR_COLLECT_METADATA } from '../modules/local/pixelator/collect_metadata' +include { PIXELATOR_AMPLICON } from '../modules/local/pixelator/single-cell/amplicon/main' +include { PIXELATOR_QC } from '../modules/local/pixelator/single-cell/qc/main' +include { PIXELATOR_DEMUX } from '../modules/local/pixelator/single-cell/demux/main' +include { PIXELATOR_COLLAPSE } from '../modules/local/pixelator/single-cell/collapse/main' +include { PIXELATOR_GRAPH } from '../modules/local/pixelator/single-cell/graph/main' +include { PIXELATOR_ANALYSIS } from '../modules/local/pixelator/single-cell/analysis/main' +include { PIXELATOR_ANNOTATE } from '../modules/local/pixelator/single-cell/annotate/main' + +/* +======================================================================================== + RUN MAIN WORKFLOW +======================================================================================== +*/ +workflow PIXELATOR { take: - ch_samplesheet // channel: samplesheet read in from --input + ch_samplesheet // channel: [ meta, path(panel_file | []), path(sample_1.fq), path(sample_2.fq) ] main: ch_versions = Channel.empty() - ch_multiqc_files = Channel.empty() // - // MODULE: Run FastQC + // Split the samplesheet channel in reads and panel_files + // + ch_reads = ch_samplesheet.map { [it[0]] + it[2..-1] } + ch_panel_files = ch_samplesheet.map { [it[0], it[1]] } + + ch_fastq_split = ch_reads + .groupTuple() + .branch { + meta, fastq -> + single : fastq.size() == 1 + return [ meta, fastq.flatten() ] + multiple: fastq.size() > 1 + return [ meta, fastq.flatten() ] + } + + // + // MODULE: Dump pixelaor and pipeline information + // + PIXELATOR_COLLECT_METADATA () + ch_versions = ch_versions.mix(PIXELATOR_COLLECT_METADATA.out.versions) + // - FASTQC ( - ch_samplesheet + // MODULE: Concatenate FastQ files from the same sample if required + // + ch_cat_fastq = CAT_FASTQ ( ch_fastq_split.multiple ) + .reads + .mix(ch_fastq_split.single) + + // Check that multi lane samples use the same panel file + ch_checked_panel_files = ch_panel_files + .map { meta, data -> [ meta.id, data] } + .groupTuple() + .map { id, data -> + if (!data) { + return [id, []] + } + def unique_panels = data.unique() + if (unique_panels.size() > 1) { + exit 1, "ERROR: Concatenated samples must use the same panel." + } + return [ id, unique_panels[0] ] + } + + ch_cat_panel_files = ch_cat_fastq + .map { meta, _ -> [meta.id, meta] } + .join(ch_checked_panel_files, failOnMismatch:true, failOnDuplicate:true) + .map { id, meta, panel_files -> [meta, panel_files] } + + ch_versions = ch_versions.mix(CAT_FASTQ.out.versions.first()) + + + // + // MODULE: Rename input reads to match the sample ids from the samplesheet + // + RENAME_READS ( ch_cat_fastq ) + ch_renamed_reads = RENAME_READS.out.reads + ch_versions = ch_versions.mix(RENAME_READS.out.versions.first()) + + // + // MODULE: Run pixelator single-cell amplicon + // + PIXELATOR_AMPLICON ( ch_renamed_reads ) + ch_merged = PIXELATOR_AMPLICON.out.merged + ch_versions = ch_versions.mix(PIXELATOR_AMPLICON.out.versions.first()) + + ch_input_reads = ch_merged + + // + // MODULE: Run pixelator single-cell preqc & pixelator single-cell adapterqc + // + PIXELATOR_QC ( ch_input_reads ) + ch_qc = PIXELATOR_QC.out.processed + ch_versions = ch_versions.mix(PIXELATOR_QC.out.versions.first()) + + ch_fq_and_panel = ch_qc + .join(ch_cat_panel_files, failOnMismatch:true, failOnDuplicate:true) + .map { meta, fq, panel_file -> [meta, fq, panel_file, panel_file ? null : meta.panel ] } + + // + // MODULE: Run pixelator single-cell demux + // + PIXELATOR_DEMUX ( ch_fq_and_panel ) + ch_demuxed = PIXELATOR_DEMUX.out.processed + ch_versions = ch_versions.mix(PIXELATOR_DEMUX.out.versions.first()) + + ch_demuxed_and_panel = ch_demuxed + .join(ch_cat_panel_files, failOnMismatch:true, failOnDuplicate:true) + .map { meta, demuxed, panel_file -> [meta, demuxed, panel_file, panel_file ? null : meta.panel ] } + + // + // MODULE: Run pixelator single-cell collapse + // + PIXELATOR_COLLAPSE ( ch_demuxed_and_panel ) + ch_collapsed = PIXELATOR_COLLAPSE.out.collapsed + ch_versions = ch_versions.mix( PIXELATOR_COLLAPSE.out.versions.first()) + + // + // MODULE: Run pixelator single-cell graph + // + PIXELATOR_GRAPH ( ch_collapsed ) + ch_clustered = PIXELATOR_GRAPH.out.edgelist + ch_versions = ch_versions.mix(PIXELATOR_GRAPH.out.versions.first()) + + ch_clustered_and_panel = ch_clustered + .join(ch_cat_panel_files, failOnMismatch:true, failOnDuplicate:true) + .map { meta, clustered, panel_file -> [meta, clustered, panel_file, panel_file ? null : meta.panel ] } + + // + // MODULE: Run pixelator single-cell annotate + // + PIXELATOR_ANNOTATE ( ch_clustered_and_panel ) + ch_annotated = PIXELATOR_ANNOTATE.out.dataset + ch_versions = ch_versions.mix( PIXELATOR_ANNOTATE.out.versions.first() ) + + // + // MODULE: Run pixelator single-cell analysis + // + PIXELATOR_ANALYSIS ( ch_annotated ) + ch_analysed = PIXELATOR_ANALYSIS.out.dataset + ch_versions = ch_versions.mix(PIXELATOR_ANALYSIS.out.versions.first()) + + + // Prepare all data needed by reporting for each pixelator step + + ch_amplicon_data = PIXELATOR_AMPLICON.out.report_json + .concat(PIXELATOR_AMPLICON.out.metadata) + .groupTuple(size: 2) + + ch_preqc_data = PIXELATOR_QC.out.preqc_report_json + .concat(PIXELATOR_QC.out.preqc_metadata) + .groupTuple(size: 2) + + ch_adapterqc_data = PIXELATOR_QC.out.adapterqc_report_json + .concat(PIXELATOR_QC.out.adapterqc_metadata) + .groupTuple(size: 2) + + ch_demux_data = PIXELATOR_DEMUX.out.report_json + .concat(PIXELATOR_DEMUX.out.metadata) + .groupTuple(size: 2) + + ch_collapse_data = PIXELATOR_COLLAPSE.out.report_json + .concat(PIXELATOR_COLLAPSE.out.metadata) + .groupTuple(size: 2) + + ch_cluster_data = PIXELATOR_GRAPH.out.all_results + ch_annotate_data = PIXELATOR_ANNOTATE.out.all_results + ch_analysis_data = PIXELATOR_ANALYSIS.out.all_results + + GENERATE_REPORTS( + ch_cat_panel_files, + ch_amplicon_data, + ch_preqc_data, + ch_adapterqc_data, + ch_demux_data, + ch_collapse_data, + ch_cluster_data, + ch_annotate_data, + ch_analysis_data ) - ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}) - ch_versions = ch_versions.mix(FASTQC.out.versions.first()) + + ch_versions = ch_versions.mix(GENERATE_REPORTS.out.versions) // // Collate and save software versions @@ -47,47 +249,10 @@ workflow PIXELATOR { newLine: true ).set { ch_collated_versions } - // - // MODULE: MultiQC - // - ch_multiqc_config = Channel.fromPath( - "$projectDir/assets/multiqc_config.yml", checkIfExists: true) - ch_multiqc_custom_config = params.multiqc_config ? - Channel.fromPath(params.multiqc_config, checkIfExists: true) : - Channel.empty() - ch_multiqc_logo = params.multiqc_logo ? - Channel.fromPath(params.multiqc_logo, checkIfExists: true) : - Channel.empty() - - summary_params = paramsSummaryMap( - workflow, parameters_schema: "nextflow_schema.json") - ch_workflow_summary = Channel.value(paramsSummaryMultiqc(summary_params)) - - ch_multiqc_custom_methods_description = params.multiqc_methods_description ? - file(params.multiqc_methods_description, checkIfExists: true) : - file("$projectDir/assets/methods_description_template.yml", checkIfExists: true) - ch_methods_description = Channel.value( - methodsDescriptionText(ch_multiqc_custom_methods_description)) - - ch_multiqc_files = ch_multiqc_files.mix( - ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) - ch_multiqc_files = ch_multiqc_files.mix(ch_collated_versions) - ch_multiqc_files = ch_multiqc_files.mix( - ch_methods_description.collectFile( - name: 'methods_description_mqc.yaml', - sort: true - ) - ) + // TODO: Add MultiQC when plugins are ready - MULTIQC ( - ch_multiqc_files.collect(), - ch_multiqc_config.toList(), - ch_multiqc_custom_config.toList(), - ch_multiqc_logo.toList() - ) emit: - multiqc_report = MULTIQC.out.report.toList() // channel: /path/to/multiqc_report.html versions = ch_versions // channel: [ path(versions.yml) ] }
Process Name \\", + " \\ Software Version
CUSTOM_DUMPSOFTWAREVERSIONSpython3.11.7
yaml5.4.1
TOOL1tool10.11.9
TOOL2tool21.9
WorkflowNextflow
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