├── .prettierrc.yml ├── .nf-core.yml ├── modules ├── nf-core │ ├── xeniumranger │ │ ├── relabel │ │ │ ├── tests │ │ │ │ ├── nextflow.config │ │ │ │ ├── tags.yml │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── main.nf.test │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ ├── resegment │ │ │ ├── tests │ │ │ │ ├── nextflow.config │ │ │ │ ├── tags.yml │ │ │ │ ├── main.nf.test.snap │ │ │ │ └── main.nf.test │ │ │ ├── main.nf │ │ │ └── meta.yml │ │ └── import-segmentation │ │ │ ├── tests │ │ │ ├── nextflow.config │ │ │ ├── tags.yml │ │ │ └── main.nf.test.snap │ │ │ ├── main.nf │ │ │ └── meta.yml │ ├── cellpose │ │ ├── tests │ │ │ ├── tags.yml │ │ │ ├── nextflow_wflows.config │ │ │ ├── main.nf.test │ │ │ └── main.nf.test.snap │ │ ├── meta.yml │ │ └── main.nf │ ├── custom │ │ └── dumpsoftwareversions │ │ │ ├── main.nf │ │ │ ├── meta.yml │ │ │ └── templates │ │ │ └── dumpsoftwareversions.py │ └── multiqc │ │ ├── main.nf │ │ └── meta.yml └── local │ ├── proseg │ ├── tests │ │ ├── tags.yml │ │ └── main.nf.test │ ├── preprocess │ │ └── main.nf │ ├── meta.yml │ └── main.nf │ └── samplesheet_check.nf ├── .gitignore ├── docs ├── images │ ├── spatialxe-metromap.png │ ├── nf-core-spatialxe_logo_dark.png │ └── nf-core-spatialxe_logo_light.png ├── README.md └── output.md ├── lib ├── nfcore_external_java_deps.jar ├── Utils.groovy ├── WorkflowSpatialxe.groovy ├── WorkflowMain.groovy └── NfcoreTemplate.groovy ├── assets ├── nf-core-spatialxe_logo_light.png ├── samplesheet.csv ├── multiqc_config.yml ├── email_template.txt ├── sendmail_template.txt ├── schema_input.json ├── slackreport.json ├── methods_description_template.yml ├── email_template.html └── adaptivecard.json ├── .gitattributes ├── .github ├── .dockstore.yml ├── ISSUE_TEMPLATE │ ├── config.yml │ ├── feature_request.yml │ └── bug_report.yml ├── workflows │ ├── linting_comment.yml │ ├── awstest.yml │ ├── awsfulltest.yml │ ├── ci.yml │ ├── fix-linting.yml │ ├── branch.yml │ └── linting.yml ├── PULL_REQUEST_TEMPLATE.md └── CONTRIBUTING.md ├── .prettierignore ├── pyproject.toml ├── CHANGELOG.md ├── .editorconfig ├── .gitpod.yml ├── LICENSE ├── conf ├── test_full.config ├── test.config ├── modules.config └── base.config ├── .devcontainer └── devcontainer.json ├── subworkflows └── local │ └── input_check.nf ├── CITATION.cff ├── modules.json ├── main.nf ├── CITATIONS.md ├── workflows └── spatialxe.nf ├── README.md ├── nextflow.config ├── CODE_OF_CONDUCT.md ├── bin └── check_samplesheet.py └── nextflow_schema.json /.prettierrc.yml: -------------------------------------------------------------------------------- 1 | printWidth: 120 2 | -------------------------------------------------------------------------------- /.nf-core.yml: -------------------------------------------------------------------------------- 1 | repository_type: pipeline 2 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/relabel/tests/nextflow.config: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/resegment/tests/nextflow.config: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/import-segmentation/tests/nextflow.config: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /modules/local/proseg/tests/tags.yml: -------------------------------------------------------------------------------- 1 | proseg: 2 | - "modules/nf-core/proseg/**" 3 | -------------------------------------------------------------------------------- /modules/nf-core/cellpose/tests/tags.yml: -------------------------------------------------------------------------------- 1 | cellpose: 2 | - "modules/nf-core/cellpose/**" 3 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .nextflow* 2 | work/ 3 | data/ 4 | results/ 5 | .DS_Store 6 | testing/ 7 | testing* 8 | *.pyc 9 | -------------------------------------------------------------------------------- /docs/images/spatialxe-metromap.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/spatialxe/HEAD/docs/images/spatialxe-metromap.png -------------------------------------------------------------------------------- /lib/nfcore_external_java_deps.jar: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/spatialxe/HEAD/lib/nfcore_external_java_deps.jar -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/relabel/tests/tags.yml: -------------------------------------------------------------------------------- 1 | xeniumranger/relabel: 2 | - "modules/nf-core/xeniumranger/relabel/**" 3 | -------------------------------------------------------------------------------- /assets/nf-core-spatialxe_logo_light.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/spatialxe/HEAD/assets/nf-core-spatialxe_logo_light.png -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/resegment/tests/tags.yml: -------------------------------------------------------------------------------- 1 | xeniumranger/resegment: 2 | - "modules/nf-core/xeniumranger/resegment/**" 3 | -------------------------------------------------------------------------------- /docs/images/nf-core-spatialxe_logo_dark.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/spatialxe/HEAD/docs/images/nf-core-spatialxe_logo_dark.png -------------------------------------------------------------------------------- /docs/images/nf-core-spatialxe_logo_light.png: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/nf-core/spatialxe/HEAD/docs/images/nf-core-spatialxe_logo_light.png -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/import-segmentation/tests/tags.yml: -------------------------------------------------------------------------------- 1 | xeniumranger/import-segmentation: 2 | - "modules/nf-core/xeniumranger/import-segmentation/**" 3 | -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- 1 | *.config linguist-language=nextflow 2 | *.nf.test linguist-language=nextflow 3 | modules/nf-core/** linguist-generated 4 | subworkflows/nf-core/** linguist-generated 5 | -------------------------------------------------------------------------------- /.github/.dockstore.yml: -------------------------------------------------------------------------------- 1 | # Dockstore config version, not pipeline version 2 | version: 1.2 3 | workflows: 4 | - subclass: nfl 5 | primaryDescriptorPath: /nextflow.config 6 | publish: True 7 | -------------------------------------------------------------------------------- /.prettierignore: -------------------------------------------------------------------------------- 1 | email_template.html 2 | adaptivecard.json 3 | slackreport.json 4 | .nextflow* 5 | work/ 6 | data/ 7 | results/ 8 | .DS_Store 9 | testing/ 10 | testing* 11 | *.pyc 12 | bin/ 13 | -------------------------------------------------------------------------------- /modules/nf-core/cellpose/tests/nextflow_wflows.config: -------------------------------------------------------------------------------- 1 | process { 2 | withName: "CELLPOSE" { 3 | ext.args = '--pretrained_model nuclei --diameter 9 --channel_axis 0 --no_npy --save_flows' 4 | } 5 | } 6 | -------------------------------------------------------------------------------- /assets/samplesheet.csv: -------------------------------------------------------------------------------- 1 | sample,fastq_1,fastq_2 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 3 | SAMPLE_SINGLE_END,/path/to/fastq/files/AEG588A4_S4_L003_R1_001.fastq.gz, 4 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/config.yml: -------------------------------------------------------------------------------- 1 | contact_links: 2 | - name: Join nf-core 3 | url: https://nf-co.re/join 4 | about: Please join the nf-core community here 5 | - name: "Slack #spatialxe channel" 6 | url: https://nfcore.slack.com/channels/spatialxe 7 | about: Discussion about the nf-core/spatialxe pipeline 8 | -------------------------------------------------------------------------------- /pyproject.toml: -------------------------------------------------------------------------------- 1 | # Config file for Python. Mostly used to configure linting of bin/check_samplesheet.py with Black. 2 | # Should be kept the same as nf-core/tools to avoid fighting with template synchronisation. 3 | [tool.black] 4 | line-length = 120 5 | target_version = ["py37", "py38", "py39", "py310"] 6 | 7 | [tool.isort] 8 | profile = "black" 9 | known_first_party = ["nf_core"] 10 | multi_line_output = 3 11 | -------------------------------------------------------------------------------- /CHANGELOG.md: -------------------------------------------------------------------------------- 1 | # nf-core/spatialxe: Changelog 2 | 3 | The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) 4 | and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). 5 | 6 | ## v1.0dev - [date] 7 | 8 | Initial release of nf-core/spatialxe, created with the [nf-core](https://nf-co.re/) template. 9 | 10 | ### `Added` 11 | 12 | ### `Fixed` 13 | 14 | ### `Dependencies` 15 | 16 | ### `Deprecated` 17 | -------------------------------------------------------------------------------- /docs/README.md: -------------------------------------------------------------------------------- 1 | # nf-core/spatialxe: Documentation 2 | 3 | The nf-core/spatialxe documentation is split into the following pages: 4 | 5 | - [Usage](usage.md) 6 | - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. 7 | - [Output](output.md) 8 | - An overview of the different results produced by the pipeline and how to interpret them. 9 | 10 | You can find a lot more documentation about installing, configuring and running nf-core pipelines on the website: [https://nf-co.re](https://nf-co.re) 11 | -------------------------------------------------------------------------------- /assets/multiqc_config.yml: -------------------------------------------------------------------------------- 1 | report_comment: > 2 | This report has been generated by the nf-core/spatialxe 3 | analysis pipeline. For information about how to interpret these results, please see the 4 | documentation. 5 | report_section_order: 6 | "nf-core-spatialxe-methods-description": 7 | order: -1000 8 | software_versions: 9 | order: -1001 10 | "nf-core-spatialxe-summary": 11 | order: -1002 12 | 13 | export_plots: true 14 | -------------------------------------------------------------------------------- /.editorconfig: -------------------------------------------------------------------------------- 1 | root = true 2 | 3 | [*] 4 | charset = utf-8 5 | end_of_line = lf 6 | insert_final_newline = true 7 | trim_trailing_whitespace = true 8 | indent_size = 4 9 | indent_style = space 10 | 11 | [*.{md,yml,yaml,html,css,scss,js,cff}] 12 | indent_size = 2 13 | 14 | # These files are edited and tested upstream in nf-core/modules 15 | [/modules/nf-core/**] 16 | charset = unset 17 | end_of_line = unset 18 | insert_final_newline = unset 19 | trim_trailing_whitespace = unset 20 | indent_style = unset 21 | indent_size = unset 22 | 23 | [/assets/email*] 24 | indent_size = unset 25 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/feature_request.yml: -------------------------------------------------------------------------------- 1 | name: Feature request 2 | description: Suggest an idea for the nf-core/spatialxe pipeline. Please write in the title as the first word *module* (suggestin a new module for spatialxe) or *implement* for general feature request. 3 | labels: enhancement 4 | body: 5 | - type: textarea 6 | id: description 7 | attributes: 8 | label: Description of feature 9 | description: Please describe your suggestion for a new feature. It might help to describe a problem or use case, plus any alternatives that you have considered. 10 | validations: 11 | required: true 12 | -------------------------------------------------------------------------------- /modules/nf-core/custom/dumpsoftwareversions/main.nf: -------------------------------------------------------------------------------- 1 | process CUSTOM_DUMPSOFTWAREVERSIONS { 2 | label 'process_single' 3 | 4 | // Requires `pyyaml` which does not have a dedicated container but is in the MultiQC container 5 | conda "bioconda::multiqc=1.13" 6 | container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 7 | 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 8 | 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" 9 | 10 | input: 11 | path versions 12 | 13 | output: 14 | path "software_versions.yml" , emit: yml 15 | path "software_versions_mqc.yml", emit: mqc_yml 16 | path "versions.yml" , emit: versions 17 | 18 | when: 19 | task.ext.when == null || task.ext.when 20 | 21 | script: 22 | def args = task.ext.args ?: '' 23 | template 'dumpsoftwareversions.py' 24 | } 25 | -------------------------------------------------------------------------------- /.gitpod.yml: -------------------------------------------------------------------------------- 1 | image: nfcore/gitpod:latest 2 | 3 | vscode: 4 | extensions: # based on nf-core.nf-core-extensionpack 5 | - codezombiech.gitignore # Language support for .gitignore files 6 | # - cssho.vscode-svgviewer # SVG viewer 7 | - esbenp.prettier-vscode # Markdown/CommonMark linting and style checking for Visual Studio Code 8 | - eamodio.gitlens # Quickly glimpse into whom, why, and when a line or code block was changed 9 | - EditorConfig.EditorConfig # override user/workspace settings with settings found in .editorconfig files 10 | - Gruntfuggly.todo-tree # Display TODO and FIXME in a tree view in the activity bar 11 | - mechatroner.rainbow-csv # Highlight columns in csv files in different colors 12 | # - nextflow.nextflow # Nextflow syntax highlighting 13 | - oderwat.indent-rainbow # Highlight indentation level 14 | - streetsidesoftware.code-spell-checker # Spelling checker for source code 15 | -------------------------------------------------------------------------------- /.github/workflows/linting_comment.yml: -------------------------------------------------------------------------------- 1 | name: nf-core linting comment 2 | # This workflow is triggered after the linting action is complete 3 | # It posts an automated comment to the PR, even if the PR is coming from a fork 4 | 5 | on: 6 | workflow_run: 7 | workflows: ["nf-core linting"] 8 | 9 | jobs: 10 | test: 11 | runs-on: ubuntu-latest 12 | steps: 13 | - name: Download lint results 14 | uses: dawidd6/action-download-artifact@v2 15 | with: 16 | workflow: linting.yml 17 | workflow_conclusion: completed 18 | 19 | - name: Get PR number 20 | id: pr_number 21 | run: echo "pr_number=$(cat linting-logs/PR_number.txt)" >> $GITHUB_OUTPUT 22 | 23 | - name: Post PR comment 24 | uses: marocchino/sticky-pull-request-comment@v2 25 | with: 26 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 27 | number: ${{ steps.pr_number.outputs.pr_number }} 28 | path: linting-logs/lint_results.md 29 | -------------------------------------------------------------------------------- /modules/local/samplesheet_check.nf: -------------------------------------------------------------------------------- 1 | process SAMPLESHEET_CHECK { 2 | tag "$samplesheet" 3 | label 'process_single' 4 | 5 | conda "conda-forge::python=3.8.3" 6 | container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 7 | 'https://depot.galaxyproject.org/singularity/python:3.8.3' : 8 | 'quay.io/biocontainers/python:3.8.3' }" 9 | 10 | input: 11 | path samplesheet 12 | 13 | output: 14 | path '*.csv' , emit: csv 15 | path "versions.yml", emit: versions 16 | 17 | when: 18 | task.ext.when == null || task.ext.when 19 | 20 | script: // This script is bundled with the pipeline, in nf-core/spatialxe/bin/ 21 | """ 22 | check_samplesheet.py \\ 23 | $samplesheet \\ 24 | samplesheet.valid.csv 25 | 26 | cat <<-END_VERSIONS > versions.yml 27 | "${task.process}": 28 | python: \$(python --version | sed 's/Python //g') 29 | END_VERSIONS 30 | """ 31 | } 32 | -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- 1 | MIT License 2 | 3 | Copyright (c) Florian Heyl 4 | 5 | Permission is hereby granted, free of charge, to any person obtaining a copy 6 | of this software and associated documentation files (the "Software"), to deal 7 | in the Software without restriction, including without limitation the rights 8 | to use, copy, modify, merge, publish, distribute, sublicense, and/or sell 9 | copies of the Software, and to permit persons to whom the Software is 10 | furnished to do so, subject to the following conditions: 11 | 12 | The above copyright notice and this permission notice shall be included in all 13 | copies or substantial portions of the Software. 14 | 15 | THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR 16 | IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, 17 | FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE 18 | AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER 19 | LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, 20 | OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE 21 | SOFTWARE. 22 | -------------------------------------------------------------------------------- /modules/nf-core/custom/dumpsoftwareversions/meta.yml: -------------------------------------------------------------------------------- 1 | name: custom_dumpsoftwareversions 2 | description: Custom module used to dump software versions within the nf-core pipeline template 3 | keywords: 4 | - custom 5 | - version 6 | tools: 7 | - custom: 8 | description: Custom module used to dump software versions within the nf-core pipeline template 9 | homepage: https://github.com/nf-core/tools 10 | documentation: https://github.com/nf-core/tools 11 | licence: ["MIT"] 12 | input: 13 | - versions: 14 | type: file 15 | description: YML file containing software versions 16 | pattern: "*.yml" 17 | 18 | output: 19 | - yml: 20 | type: file 21 | description: Standard YML file containing software versions 22 | pattern: "software_versions.yml" 23 | - mqc_yml: 24 | type: file 25 | description: MultiQC custom content YML file containing software versions 26 | pattern: "software_versions_mqc.yml" 27 | - versions: 28 | type: file 29 | description: File containing software versions 30 | pattern: "versions.yml" 31 | 32 | authors: 33 | - "@drpatelh" 34 | - "@grst" 35 | -------------------------------------------------------------------------------- /.github/workflows/awstest.yml: -------------------------------------------------------------------------------- 1 | name: nf-core AWS test 2 | # This workflow can be triggered manually with the GitHub actions workflow dispatch button. 3 | # It runs the -profile 'test' on AWS batch 4 | 5 | on: 6 | workflow_dispatch: 7 | jobs: 8 | run-tower: 9 | name: Run AWS tests 10 | if: github.repository == 'nf-core/spatialxe' 11 | runs-on: ubuntu-latest 12 | steps: 13 | # Launch workflow using Tower CLI tool action 14 | - name: Launch workflow via tower 15 | uses: nf-core/tower-action@v3 16 | with: 17 | workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} 18 | access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} 19 | compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} 20 | workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/spatialxe/work-${{ github.sha }} 21 | parameters: | 22 | { 23 | "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/spatialxe/results-test-${{ github.sha }}" 24 | } 25 | profiles: test,aws_tower 26 | - uses: actions/upload-artifact@v3 27 | with: 28 | name: Tower debug log file 29 | path: tower_action_*.log 30 | -------------------------------------------------------------------------------- /conf/test_full.config: -------------------------------------------------------------------------------- 1 | /* 2 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 | Nextflow config file for running full-size tests 4 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 | Defines input files and everything required to run a full size pipeline test. 6 | 7 | Use as follows: 8 | nextflow run nf-core/spatialxe -profile test_full, --outdir 9 | 10 | ---------------------------------------------------------------------------------------- 11 | */ 12 | 13 | params { 14 | config_profile_name = 'Full test profile' 15 | config_profile_description = 'Full test dataset to check pipeline function' 16 | 17 | // Input data for full size test 18 | // TODO nf-core: Specify the paths to your full test data ( on nf-core/test-datasets or directly in repositories, e.g. SRA) 19 | // TODO nf-core: Give any required params for the test so that command line flags are not needed 20 | input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_full_illumina_amplicon.csv' 21 | 22 | // Genome references 23 | genome = 'R64-1-1' 24 | } 25 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/resegment/tests/main.nf.test.snap: -------------------------------------------------------------------------------- 1 | { 2 | "xeniumranger resegment stub": { 3 | "content": [ 4 | { 5 | "0": [ 6 | [ 7 | { 8 | "id": "test_xeniumranger_resegment" 9 | }, 10 | "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" 11 | ] 12 | ], 13 | "1": [ 14 | "versions.yml:md5,4671141281357e0ce26d9cb35fed23a8" 15 | ], 16 | "outs": [ 17 | [ 18 | { 19 | "id": "test_xeniumranger_resegment" 20 | }, 21 | "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" 22 | ] 23 | ], 24 | "versions": [ 25 | "versions.yml:md5,4671141281357e0ce26d9cb35fed23a8" 26 | ] 27 | } 28 | ], 29 | "meta": { 30 | "nf-test": "0.9.0", 31 | "nextflow": "24.04.4" 32 | }, 33 | "timestamp": "2024-10-30T23:22:35.438329" 34 | } 35 | } -------------------------------------------------------------------------------- /conf/test.config: -------------------------------------------------------------------------------- 1 | /* 2 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 | Nextflow config file for running minimal tests 4 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 | Defines input files and everything required to run a fast and simple pipeline test. 6 | 7 | Use as follows: 8 | nextflow run nf-core/spatialxe -profile test, --outdir 9 | 10 | ---------------------------------------------------------------------------------------- 11 | */ 12 | 13 | params { 14 | config_profile_name = 'Test profile' 15 | config_profile_description = 'Minimal test dataset to check pipeline function' 16 | 17 | // Limit resources so that this can run on GitHub Actions 18 | max_cpus = 2 19 | max_memory = '6.GB' 20 | max_time = '6.h' 21 | 22 | // Input data 23 | // TODO nf-core: Specify the paths to your test data on nf-core/test-datasets 24 | // TODO nf-core: Give any required params for the test so that command line flags are not needed 25 | input = 'https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv' 26 | 27 | // Genome references 28 | genome = 'R64-1-1' 29 | } 30 | -------------------------------------------------------------------------------- /.devcontainer/devcontainer.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "nfcore", 3 | "image": "nfcore/gitpod:latest", 4 | "remoteUser": "gitpod", 5 | 6 | // Configure tool-specific properties. 7 | "customizations": { 8 | // Configure properties specific to VS Code. 9 | "vscode": { 10 | // Set *default* container specific settings.json values on container create. 11 | "settings": { 12 | "python.defaultInterpreterPath": "/opt/conda/bin/python", 13 | "python.linting.enabled": true, 14 | "python.linting.pylintEnabled": true, 15 | "python.formatting.autopep8Path": "/opt/conda/bin/autopep8", 16 | "python.formatting.yapfPath": "/opt/conda/bin/yapf", 17 | "python.linting.flake8Path": "/opt/conda/bin/flake8", 18 | "python.linting.pycodestylePath": "/opt/conda/bin/pycodestyle", 19 | "python.linting.pydocstylePath": "/opt/conda/bin/pydocstyle", 20 | "python.linting.pylintPath": "/opt/conda/bin/pylint" 21 | }, 22 | 23 | // Add the IDs of extensions you want installed when the container is created. 24 | "extensions": ["ms-python.python", "ms-python.vscode-pylance", "nf-core.nf-core-extensionpack"] 25 | } 26 | } 27 | } 28 | -------------------------------------------------------------------------------- /assets/email_template.txt: -------------------------------------------------------------------------------- 1 | ---------------------------------------------------- 2 | ,--./,-. 3 | ___ __ __ __ ___ /,-._.--~\\ 4 | |\\ | |__ __ / ` / \\ |__) |__ } { 5 | | \\| | \\__, \\__/ | \\ |___ \\`-._,-`-, 6 | `._,._,' 7 | nf-core/spatialxe v${version} 8 | ---------------------------------------------------- 9 | Run Name: $runName 10 | 11 | <% if (success){ 12 | out << "## nf-core/spatialxe execution completed successfully! ##" 13 | } else { 14 | out << """#################################################### 15 | ## nf-core/spatialxe execution completed unsuccessfully! ## 16 | #################################################### 17 | The exit status of the task that caused the workflow execution to fail was: $exitStatus. 18 | The full error message was: 19 | 20 | ${errorReport} 21 | """ 22 | } %> 23 | 24 | 25 | The workflow was completed at $dateComplete (duration: $duration) 26 | 27 | The command used to launch the workflow was as follows: 28 | 29 | $commandLine 30 | 31 | 32 | 33 | Pipeline Configuration: 34 | ----------------------- 35 | <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> 36 | 37 | -- 38 | nf-core/spatialxe 39 | https://github.com/nf-core/spatialxe 40 | -------------------------------------------------------------------------------- /assets/sendmail_template.txt: -------------------------------------------------------------------------------- 1 | To: $email 2 | Subject: $subject 3 | Mime-Version: 1.0 4 | Content-Type: multipart/related;boundary="nfcoremimeboundary" 5 | 6 | --nfcoremimeboundary 7 | Content-Type: text/html; charset=utf-8 8 | 9 | $email_html 10 | 11 | --nfcoremimeboundary 12 | Content-Type: image/png;name="nf-core-spatialxe_logo.png" 13 | Content-Transfer-Encoding: base64 14 | Content-ID: 15 | Content-Disposition: inline; filename="nf-core-spatialxe_logo_light.png" 16 | 17 | <% out << new File("$projectDir/assets/nf-core-spatialxe_logo_light.png"). 18 | bytes. 19 | encodeBase64(). 20 | toString(). 21 | tokenize( '\n' )*. 22 | toList()*. 23 | collate( 76 )*. 24 | collect { it.join() }. 25 | flatten(). 26 | join( '\n' ) %> 27 | 28 | <% 29 | if (mqcFile){ 30 | def mqcFileObj = new File("$mqcFile") 31 | if (mqcFileObj.length() < mqcMaxSize){ 32 | out << """ 33 | --nfcoremimeboundary 34 | Content-Type: text/html; name=\"multiqc_report\" 35 | Content-Transfer-Encoding: base64 36 | Content-ID: 37 | Content-Disposition: attachment; filename=\"${mqcFileObj.getName()}\" 38 | 39 | ${mqcFileObj. 40 | bytes. 41 | encodeBase64(). 42 | toString(). 43 | tokenize( '\n' )*. 44 | toList()*. 45 | collate( 76 )*. 46 | collect { it.join() }. 47 | flatten(). 48 | join( '\n' )} 49 | """ 50 | }} 51 | %> 52 | 53 | --nfcoremimeboundary-- 54 | -------------------------------------------------------------------------------- /.github/PULL_REQUEST_TEMPLATE.md: -------------------------------------------------------------------------------- 1 | 13 | 14 | ## PR checklist 15 | 16 | - [ ] This comment contains a description of changes (with reason). 17 | - [ ] If you've fixed a bug or added code that should be tested, add tests! 18 | - [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/nf-core/spatialxe/tree/master/.github/CONTRIBUTING.md)- [ ] If necessary, also make a PR on the nf-core/spatialxe _branch_ on the [nf-core/test-datasets](https://github.com/nf-core/test-datasets) repository. 19 | - [ ] Make sure your code lints (`nf-core lint`). 20 | - [ ] Ensure the test suite passes (`nextflow run . -profile test,docker --outdir `). 21 | - [ ] Usage Documentation in `docs/usage.md` is updated. 22 | - [ ] Output Documentation in `docs/output.md` is updated. 23 | - [ ] `CHANGELOG.md` is updated. 24 | - [ ] `README.md` is updated (including new tool citations and authors/contributors). 25 | -------------------------------------------------------------------------------- /.github/workflows/awsfulltest.yml: -------------------------------------------------------------------------------- 1 | name: nf-core AWS full size tests 2 | # This workflow is triggered on published releases. 3 | # It can be additionally triggered manually with GitHub actions workflow dispatch button. 4 | # It runs the -profile 'test_full' on AWS batch 5 | 6 | on: 7 | release: 8 | types: [published] 9 | workflow_dispatch: 10 | jobs: 11 | run-tower: 12 | name: Run AWS full tests 13 | if: github.repository == 'nf-core/spatialxe' 14 | runs-on: ubuntu-latest 15 | steps: 16 | - name: Launch workflow via tower 17 | uses: nf-core/tower-action@v3 18 | # TODO nf-core: You can customise AWS full pipeline tests as required 19 | # Add full size test data (but still relatively small datasets for few samples) 20 | # on the `test_full.config` test runs with only one set of parameters 21 | with: 22 | workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} 23 | access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} 24 | compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} 25 | workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/spatialxe/work-${{ github.sha }} 26 | parameters: | 27 | { 28 | "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/spatialxe/results-${{ github.sha }}" 29 | } 30 | profiles: test_full,aws_tower 31 | - uses: actions/upload-artifact@v3 32 | with: 33 | name: Tower debug log file 34 | path: tower_action_*.log 35 | -------------------------------------------------------------------------------- /.github/workflows/ci.yml: -------------------------------------------------------------------------------- 1 | name: nf-core CI 2 | # This workflow runs the pipeline with the minimal test dataset to check that it completes without any syntax errors 3 | on: 4 | push: 5 | branches: 6 | - dev 7 | pull_request: 8 | release: 9 | types: [published] 10 | 11 | env: 12 | NXF_ANSI_LOG: false 13 | 14 | concurrency: 15 | group: "${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}" 16 | cancel-in-progress: true 17 | 18 | jobs: 19 | test: 20 | name: Run pipeline with test data 21 | # Only run on push if this is the nf-core dev branch (merged PRs) 22 | if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'nf-core/spatialxe') }}" 23 | runs-on: ubuntu-latest 24 | strategy: 25 | matrix: 26 | NXF_VER: 27 | - "22.10.1" 28 | - "latest-everything" 29 | steps: 30 | - name: Check out pipeline code 31 | uses: actions/checkout@v3 32 | 33 | - name: Install Nextflow 34 | uses: nf-core/setup-nextflow@v1 35 | with: 36 | version: "${{ matrix.NXF_VER }}" 37 | 38 | - name: Run pipeline with test data 39 | # TODO nf-core: You can customise CI pipeline run tests as required 40 | # For example: adding multiple test runs with different parameters 41 | # Remember that you can parallelise this by using strategy.matrix 42 | run: | 43 | nextflow run ${GITHUB_WORKSPACE} -profile test,docker --outdir ./results 44 | -------------------------------------------------------------------------------- /assets/schema_input.json: -------------------------------------------------------------------------------- 1 | { 2 | "$schema": "http://json-schema.org/draft-07/schema", 3 | "$id": "https://raw.githubusercontent.com/nf-core/spatialxe/master/assets/schema_input.json", 4 | "title": "nf-core/spatialxe pipeline - params.input schema", 5 | "description": "Schema for the file provided with params.input", 6 | "type": "array", 7 | "items": { 8 | "type": "object", 9 | "properties": { 10 | "sample": { 11 | "type": "string", 12 | "pattern": "^\\S+$", 13 | "errorMessage": "Sample name must be provided and cannot contain spaces" 14 | }, 15 | "fastq_1": { 16 | "type": "string", 17 | "pattern": "^\\S+\\.f(ast)?q\\.gz$", 18 | "errorMessage": "FastQ file for reads 1 must be provided, cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'" 19 | }, 20 | "fastq_2": { 21 | "errorMessage": "FastQ file for reads 2 cannot contain spaces and must have extension '.fq.gz' or '.fastq.gz'", 22 | "anyOf": [ 23 | { 24 | "type": "string", 25 | "pattern": "^\\S+\\.f(ast)?q\\.gz$" 26 | }, 27 | { 28 | "type": "string", 29 | "maxLength": 0 30 | } 31 | ] 32 | } 33 | }, 34 | "required": ["sample", "fastq_1"] 35 | } 36 | } 37 | -------------------------------------------------------------------------------- /subworkflows/local/input_check.nf: -------------------------------------------------------------------------------- 1 | // 2 | // Check input samplesheet and get read channels 3 | // 4 | 5 | include { SAMPLESHEET_CHECK } from '../../modules/local/samplesheet_check' 6 | 7 | workflow INPUT_CHECK { 8 | take: 9 | samplesheet // file: /path/to/samplesheet.csv 10 | 11 | main: 12 | SAMPLESHEET_CHECK ( samplesheet ) 13 | .csv 14 | .splitCsv ( header:true, sep:',' ) 15 | .map { create_fastq_channel(it) } 16 | .set { reads } 17 | 18 | emit: 19 | reads // channel: [ val(meta), [ reads ] ] 20 | versions = SAMPLESHEET_CHECK.out.versions // channel: [ versions.yml ] 21 | } 22 | 23 | // Function to get list of [ meta, [ fastq_1, fastq_2 ] ] 24 | def create_fastq_channel(LinkedHashMap row) { 25 | // create meta map 26 | def meta = [:] 27 | meta.id = row.sample 28 | meta.single_end = row.single_end.toBoolean() 29 | 30 | // add path(s) of the fastq file(s) to the meta map 31 | def fastq_meta = [] 32 | if (!file(row.fastq_1).exists()) { 33 | exit 1, "ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!\n${row.fastq_1}" 34 | } 35 | if (meta.single_end) { 36 | fastq_meta = [ meta, [ file(row.fastq_1) ] ] 37 | } else { 38 | if (!file(row.fastq_2).exists()) { 39 | exit 1, "ERROR: Please check input samplesheet -> Read 2 FastQ file does not exist!\n${row.fastq_2}" 40 | } 41 | fastq_meta = [ meta, [ file(row.fastq_1), file(row.fastq_2) ] ] 42 | } 43 | return fastq_meta 44 | } 45 | -------------------------------------------------------------------------------- /conf/modules.config: -------------------------------------------------------------------------------- 1 | /* 2 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 | Config file for defining DSL2 per module options and publishing paths 4 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 | Available keys to override module options: 6 | ext.args = Additional arguments appended to command in module. 7 | ext.args2 = Second set of arguments appended to command in module (multi-tool modules). 8 | ext.args3 = Third set of arguments appended to command in module (multi-tool modules). 9 | ext.prefix = File name prefix for output files. 10 | ---------------------------------------------------------------------------------------- 11 | */ 12 | 13 | process { 14 | 15 | publishDir = [ 16 | path: { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }, 17 | mode: params.publish_dir_mode, 18 | saveAs: { filename -> filename.equals('versions.yml') ? null : filename } 19 | ] 20 | 21 | withName: SAMPLESHEET_CHECK { 22 | publishDir = [ 23 | path: { "${params.outdir}/pipeline_info" }, 24 | mode: params.publish_dir_mode, 25 | saveAs: { filename -> filename.equals('versions.yml') ? null : filename } 26 | ] 27 | } 28 | 29 | withName: FASTQC { 30 | ext.args = '--quiet' 31 | } 32 | 33 | withName: CUSTOM_DUMPSOFTWAREVERSIONS { 34 | publishDir = [ 35 | path: { "${params.outdir}/pipeline_info" }, 36 | mode: params.publish_dir_mode, 37 | pattern: '*_versions.yml' 38 | ] 39 | } 40 | 41 | } 42 | -------------------------------------------------------------------------------- /modules/nf-core/multiqc/main.nf: -------------------------------------------------------------------------------- 1 | process MULTIQC { 2 | label 'process_single' 3 | 4 | conda "bioconda::multiqc=1.13" 5 | container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 6 | 'https://depot.galaxyproject.org/singularity/multiqc:1.13--pyhdfd78af_0' : 7 | 'quay.io/biocontainers/multiqc:1.13--pyhdfd78af_0' }" 8 | 9 | input: 10 | path multiqc_files, stageAs: "?/*" 11 | path(multiqc_config) 12 | path(extra_multiqc_config) 13 | path(multiqc_logo) 14 | 15 | output: 16 | path "*multiqc_report.html", emit: report 17 | path "*_data" , emit: data 18 | path "*_plots" , optional:true, emit: plots 19 | path "versions.yml" , emit: versions 20 | 21 | when: 22 | task.ext.when == null || task.ext.when 23 | 24 | script: 25 | def args = task.ext.args ?: '' 26 | def config = multiqc_config ? "--config $multiqc_config" : '' 27 | def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : '' 28 | """ 29 | multiqc \\ 30 | --force \\ 31 | $args \\ 32 | $config \\ 33 | $extra_config \\ 34 | . 35 | 36 | cat <<-END_VERSIONS > versions.yml 37 | "${task.process}": 38 | multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) 39 | END_VERSIONS 40 | """ 41 | 42 | stub: 43 | """ 44 | touch multiqc_data 45 | touch multiqc_plots 46 | touch multiqc_report.html 47 | 48 | cat <<-END_VERSIONS > versions.yml 49 | "${task.process}": 50 | multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" ) 51 | END_VERSIONS 52 | """ 53 | } 54 | -------------------------------------------------------------------------------- /CITATION.cff: -------------------------------------------------------------------------------- 1 | cff-version: 1.2.0 2 | message: "If you use `nf-core tools` in your work, please cite the `nf-core` publication" 3 | authors: 4 | - family-names: Ewels 5 | given-names: Philip 6 | - family-names: Peltzer 7 | given-names: Alexander 8 | - family-names: Fillinger 9 | given-names: Sven 10 | - family-names: Patel 11 | given-names: Harshil 12 | - family-names: Alneberg 13 | given-names: Johannes 14 | - family-names: Wilm 15 | given-names: Andreas 16 | - family-names: Garcia 17 | given-names: Maxime Ulysse 18 | - family-names: Di Tommaso 19 | given-names: Paolo 20 | - family-names: Nahnsen 21 | given-names: Sven 22 | title: "The nf-core framework for community-curated bioinformatics pipelines." 23 | version: 2.4.1 24 | doi: 10.1038/s41587-020-0439-x 25 | date-released: 2022-05-16 26 | url: https://github.com/nf-core/tools 27 | prefered-citation: 28 | type: article 29 | authors: 30 | - family-names: Ewels 31 | given-names: Philip 32 | - family-names: Peltzer 33 | given-names: Alexander 34 | - family-names: Fillinger 35 | given-names: Sven 36 | - family-names: Patel 37 | given-names: Harshil 38 | - family-names: Alneberg 39 | given-names: Johannes 40 | - family-names: Wilm 41 | given-names: Andreas 42 | - family-names: Garcia 43 | given-names: Maxime Ulysse 44 | - family-names: Di Tommaso 45 | given-names: Paolo 46 | - family-names: Nahnsen 47 | given-names: Sven 48 | doi: 10.1038/s41587-020-0439-x 49 | journal: nature biotechnology 50 | start: 276 51 | end: 278 52 | title: "The nf-core framework for community-curated bioinformatics pipelines." 53 | issue: 3 54 | volume: 38 55 | year: 2020 56 | url: https://dx.doi.org/10.1038/s41587-020-0439-x 57 | -------------------------------------------------------------------------------- /modules/local/proseg/preprocess/main.nf: -------------------------------------------------------------------------------- 1 | process PROSEG2BAYSOR { 2 | tag "$meta.id" 3 | label 'process_high' 4 | 5 | container "nf-core/proseg:1.1.8" 6 | 7 | input: 8 | path(transcript_metadata) 9 | path(cell_polygons) 10 | 11 | output: 12 | path("xr-transcript-metadata.csv"), emit: xr_metadata 13 | path("xr-cell-polygons.geojson"), emit: xr_polygons 14 | 15 | script: 16 | // Exit if running this module with -profile conda / -profile mamba 17 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 18 | error "PROSEG2BAYSOR (preprocess) module does not support Conda. Please use Docker / Singularity / Podman instead." 19 | } 20 | 21 | """ 22 | proseg-to-baysor \ 23 | ${transcript_metadata} \ 24 | ${cell_polygons} \ 25 | --output-transcript-metadata xr-transcript-metadata.csv \ 26 | --output-cell-polygons xr-cell-polygons.geojson 27 | 28 | cat <<-END_VERSIONS > versions.yml 29 | "${task.process}": 30 | proseg: \$(proseg --version | sed 's/proseg //') 31 | END_VERSIONS 32 | 33 | """ 34 | 35 | stub: 36 | // Exit if running this module with -profile conda / -profile mamba 37 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 38 | error "PROSEG module does not support Conda. Please use Docker / Singularity / Podman instead." 39 | } 40 | def args = task.ext.args ?: '' 41 | def prefix = task.ext.prefix ?: "${meta.id}" 42 | 43 | """ 44 | touch xr-transcript-metadata.csv 45 | touch xr-cell-polygons.geojson 46 | 47 | cat <<-END_VERSIONS > versions.yml 48 | "${task.process}": 49 | proseg: \$(proseg --version | sed 's/proseg //') 50 | END_VERSIONS 51 | """ 52 | } 53 | 54 | -------------------------------------------------------------------------------- /modules/nf-core/cellpose/tests/main.nf.test: -------------------------------------------------------------------------------- 1 | nextflow_process { 2 | 3 | name "Test Process CELLPOSE" 4 | script "../main.nf" 5 | process "CELLPOSE" 6 | 7 | tag "modules" 8 | tag "modules_nfcore" 9 | tag "cellpose" 10 | 11 | test("cellpose - with flows, no model") { 12 | 13 | when { 14 | config "./nextflow_wflows.config" 15 | process { 16 | """ 17 | input[0] = [ 18 | [ id:'test' ], 19 | file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) 20 | ] 21 | input[1] = [] 22 | """ 23 | } 24 | } 25 | 26 | then { 27 | assertAll ( 28 | { assert process.success }, 29 | { assert snapshot(process.out.mask).match("mask") }, 30 | { assert snapshot(process.out.flows).match("flows") }, 31 | { assert snapshot(process.out.versions).match("versions") } 32 | ) 33 | } 34 | 35 | } 36 | 37 | 38 | test("cellpose - stub") { 39 | 40 | options "-stub" 41 | 42 | when { 43 | process { 44 | """ 45 | input[0] = [ 46 | [ id:'test' ], 47 | file(params.modules_testdata_base_path + 'imaging/segmentation/cycif_tonsil_registered.ome.tif', checkIfExists: true) 48 | ] 49 | input[1] = [] 50 | """ 51 | } 52 | } 53 | 54 | then { 55 | assertAll( 56 | { assert process.success }, 57 | { assert snapshot(process.out).match() } 58 | ) 59 | } 60 | 61 | } 62 | 63 | } 64 | -------------------------------------------------------------------------------- /modules/nf-core/multiqc/meta.yml: -------------------------------------------------------------------------------- 1 | name: MultiQC 2 | description: Aggregate results from bioinformatics analyses across many samples into a single report 3 | keywords: 4 | - QC 5 | - bioinformatics tools 6 | - Beautiful stand-alone HTML report 7 | tools: 8 | - multiqc: 9 | description: | 10 | MultiQC searches a given directory for analysis logs and compiles a HTML report. 11 | It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. 12 | homepage: https://multiqc.info/ 13 | documentation: https://multiqc.info/docs/ 14 | licence: ["GPL-3.0-or-later"] 15 | 16 | input: 17 | - multiqc_files: 18 | type: file 19 | description: | 20 | List of reports / files recognised by MultiQC, for example the html and zip output of FastQC 21 | - multiqc_config: 22 | type: file 23 | description: Optional config yml for MultiQC 24 | pattern: "*.{yml,yaml}" 25 | - extra_multiqc_config: 26 | type: file 27 | description: Second optional config yml for MultiQC. Will override common sections in multiqc_config. 28 | pattern: "*.{yml,yaml}" 29 | - multiqc_logo: 30 | type: file 31 | description: Optional logo file for MultiQC 32 | pattern: "*.{png}" 33 | 34 | output: 35 | - report: 36 | type: file 37 | description: MultiQC report file 38 | pattern: "multiqc_report.html" 39 | - data: 40 | type: dir 41 | description: MultiQC data dir 42 | pattern: "multiqc_data" 43 | - plots: 44 | type: file 45 | description: Plots created by MultiQC 46 | pattern: "*_data" 47 | - versions: 48 | type: file 49 | description: File containing software versions 50 | pattern: "versions.yml" 51 | authors: 52 | - "@abhi18av" 53 | - "@bunop" 54 | - "@drpatelh" 55 | - "@jfy133" 56 | -------------------------------------------------------------------------------- /modules.json: -------------------------------------------------------------------------------- 1 | { 2 | "name": "nf-core/spatialxe", 3 | "homePage": "https://github.com/nf-core/spatialxe", 4 | "repos": { 5 | "https://github.com/nf-core/modules.git": { 6 | "modules": { 7 | "nf-core": { 8 | "cellpose": { 9 | "branch": "master", 10 | "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1", 11 | "installed_by": ["modules"] 12 | }, 13 | "custom/dumpsoftwareversions": { 14 | "branch": "master", 15 | "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", 16 | "installed_by": ["modules"] 17 | }, 18 | "multiqc": { 19 | "branch": "master", 20 | "git_sha": "c8e35eb2055c099720a75538d1b8adb3fb5a464c", 21 | "installed_by": ["modules"] 22 | }, 23 | "xeniumranger/import-segmentation": { 24 | "branch": "master", 25 | "git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a", 26 | "installed_by": ["modules"] 27 | }, 28 | "xeniumranger/relabel": { 29 | "branch": "master", 30 | "git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a", 31 | "installed_by": ["modules"] 32 | }, 33 | "xeniumranger/resegment": { 34 | "branch": "master", 35 | "git_sha": "b5e1891a88491d8731b5e68e22bd907726caec4a", 36 | "installed_by": ["modules"] 37 | } 38 | } 39 | } 40 | } 41 | } 42 | } 43 | -------------------------------------------------------------------------------- /assets/slackreport.json: -------------------------------------------------------------------------------- 1 | { 2 | "attachments": [ 3 | { 4 | "fallback": "Plain-text summary of the attachment.", 5 | "color": "<% if (success) { %>good<% } else { %>danger<%} %>", 6 | "author_name": "sanger-tol/readmapping v${version} - ${runName}", 7 | "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", 8 | "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", 9 | "fields": [ 10 | { 11 | "title": "Command used to launch the workflow", 12 | "value": "```${commandLine}```", 13 | "short": false 14 | } 15 | <% 16 | if (!success) { %> 17 | , 18 | { 19 | "title": "Full error message", 20 | "value": "```${errorReport}```", 21 | "short": false 22 | }, 23 | { 24 | "title": "Pipeline configuration", 25 | "value": "<% out << summary.collect{ k,v -> k == "hook_url" ? "_${k}_: (_hidden_)" : ( ( v.class.toString().contains('Path') || ( v.class.toString().contains('String') && v.contains('/') ) ) ? "_${k}_: `${v}`" : (v.class.toString().contains('DateTime') ? ("_${k}_: " + v.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM))) : "_${k}_: ${v}") ) }.join(",\n") %>", 26 | "short": false 27 | } 28 | <% } 29 | %> 30 | ], 31 | "footer": "Completed at <% out << dateComplete.format(java.time.format.DateTimeFormatter.ofLocalizedDateTime(java.time.format.FormatStyle.MEDIUM)) %> (duration: ${duration})" 32 | } 33 | ] 34 | } 35 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/relabel/main.nf: -------------------------------------------------------------------------------- 1 | process XENIUMRANGER_RELABEL { 2 | tag "$meta.id" 3 | label 'process_high' 4 | 5 | container "nf-core/xeniumranger:3.0.1" 6 | 7 | input: 8 | tuple val(meta), path(xenium_bundle) 9 | path(gene_panel) 10 | 11 | output: 12 | tuple val(meta), path("**/outs/**"), emit: outs 13 | path "versions.yml", emit: versions 14 | 15 | when: 16 | task.ext.when == null || task.ext.when 17 | 18 | script: 19 | // Exit if running this module with -profile conda / -profile mamba 20 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 21 | error "XENIUMRANGER_RELABEL module does not support Conda. Please use Docker / Singularity / Podman instead." 22 | } 23 | def args = task.ext.args ?: '' 24 | def prefix = task.ext.prefix ?: "${meta.id}" 25 | 26 | """ 27 | xeniumranger relabel \\ 28 | --id="${prefix}" \\ 29 | --xenium-bundle="${xenium_bundle}" \\ 30 | --panel="${gene_panel}" \\ 31 | --localcores=${task.cpus} \\ 32 | --localmem=${task.memory.toGiga()} \\ 33 | ${args} 34 | 35 | cat <<-END_VERSIONS > versions.yml 36 | "${task.process}": 37 | xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g") 38 | END_VERSIONS 39 | """ 40 | 41 | stub: 42 | // Exit if running this module with -profile conda / -profile mamba 43 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 44 | error "XENIUMRANGER_RELABEL module does not support Conda. Please use Docker / Singularity / Podman instead." 45 | } 46 | def prefix = task.ext.prefix ?: "${meta.id}" 47 | """ 48 | mkdir -p "${prefix}/outs/" 49 | touch "${prefix}/outs/fake_file.txt" 50 | 51 | cat <<-END_VERSIONS > versions.yml 52 | "${task.process}": 53 | xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g") 54 | END_VERSIONS 55 | """ 56 | } 57 | -------------------------------------------------------------------------------- /.github/ISSUE_TEMPLATE/bug_report.yml: -------------------------------------------------------------------------------- 1 | name: Bug report 2 | description: Report something that is broken or incorrect 3 | labels: bug 4 | body: 5 | - type: markdown 6 | attributes: 7 | value: | 8 | Before you post this issue, please check the documentation: 9 | 10 | - [nf-core website: troubleshooting](https://nf-co.re/usage/troubleshooting) 11 | - [nf-core/spatialxe pipeline documentation](https://nf-co.re/spatialxe/usage) 12 | 13 | - type: textarea 14 | id: description 15 | attributes: 16 | label: Description of the bug 17 | description: A clear and concise description of what the bug is. 18 | validations: 19 | required: true 20 | 21 | - type: textarea 22 | id: command_used 23 | attributes: 24 | label: Command used and terminal output 25 | description: Steps to reproduce the behaviour. Please paste the command you used to launch the pipeline and the output from your terminal. 26 | render: console 27 | placeholder: | 28 | $ nextflow run ... 29 | 30 | Some output where something broke 31 | 32 | - type: textarea 33 | id: files 34 | attributes: 35 | label: Relevant files 36 | description: | 37 | Please drag and drop the relevant files here. Create a `.zip` archive if the extension is not allowed. 38 | Your verbose log file `.nextflow.log` is often useful _(this is a hidden file in the directory where you launched the pipeline)_ as well as custom Nextflow configuration files. 39 | 40 | - type: textarea 41 | id: system 42 | attributes: 43 | label: System information 44 | description: | 45 | * Nextflow version _(eg. 22.10.1)_ 46 | * Hardware _(eg. HPC, Desktop, Cloud)_ 47 | * Executor _(eg. slurm, local, awsbatch)_ 48 | * Container engine: _(e.g. Docker, Singularity, Conda, Podman, Shifter or Charliecloud)_ 49 | * OS _(eg. CentOS Linux, macOS, Linux Mint)_ 50 | * Version of nf-core/spatialxe _(eg. 1.1, 1.5, 1.8.2)_ 51 | -------------------------------------------------------------------------------- /.github/workflows/fix-linting.yml: -------------------------------------------------------------------------------- 1 | name: Fix linting from a comment 2 | on: 3 | issue_comment: 4 | types: [created] 5 | 6 | jobs: 7 | deploy: 8 | # Only run if comment is on a PR with the main repo, and if it contains the magic keywords 9 | if: > 10 | contains(github.event.comment.html_url, '/pull/') && 11 | contains(github.event.comment.body, '@nf-core-bot fix linting') && 12 | github.repository == 'nf-core/spatialxe' 13 | runs-on: ubuntu-latest 14 | steps: 15 | # Use the @nf-core-bot token to check out so we can push later 16 | - uses: actions/checkout@v3 17 | with: 18 | token: ${{ secrets.nf_core_bot_auth_token }} 19 | 20 | # Action runs on the issue comment, so we don't get the PR by default 21 | # Use the gh cli to check out the PR 22 | - name: Checkout Pull Request 23 | run: gh pr checkout ${{ github.event.issue.number }} 24 | env: 25 | GITHUB_TOKEN: ${{ secrets.nf_core_bot_auth_token }} 26 | 27 | - uses: actions/setup-node@v3 28 | 29 | - name: Install Prettier 30 | run: npm install -g prettier @prettier/plugin-php 31 | 32 | # Check that we actually need to fix something 33 | - name: Run 'prettier --check' 34 | id: prettier_status 35 | run: | 36 | if prettier --check ${GITHUB_WORKSPACE}; then 37 | echo "result=pass" >> $GITHUB_OUTPUT 38 | else 39 | echo "result=fail" >> $GITHUB_OUTPUT 40 | fi 41 | 42 | - name: Run 'prettier --write' 43 | if: steps.prettier_status.outputs.result == 'fail' 44 | run: prettier --write ${GITHUB_WORKSPACE} 45 | 46 | - name: Commit & push changes 47 | if: steps.prettier_status.outputs.result == 'fail' 48 | run: | 49 | git config user.email "core@nf-co.re" 50 | git config user.name "nf-core-bot" 51 | git config push.default upstream 52 | git add . 53 | git status 54 | git commit -m "[automated] Fix linting with Prettier" 55 | git push 56 | -------------------------------------------------------------------------------- /modules/nf-core/cellpose/meta.yml: -------------------------------------------------------------------------------- 1 | name: "cellpose" 2 | description: cellpose segments cells in images 3 | keywords: 4 | - segmentation 5 | - image 6 | - cellpose 7 | tools: 8 | - "cellpose": 9 | description: "cellpose is an anatomical segmentation algorithm written in Python 10 | 3 by Carsen Stringer and Marius Pachitariu" 11 | homepage: "https://github.com/MouseLand/cellpose" 12 | documentation: "https://cellpose.readthedocs.io/en/latest/command.html" 13 | tool_dev_url: "https://github.com/MouseLand/cellpose" 14 | doi: 10.1038/s41592-022-01663-4 15 | licence: ["BSD 3-Clause"] 16 | identifier: biotools:cellpose 17 | input: 18 | - - meta: 19 | type: map 20 | description: | 21 | Groovy Map containing sample information 22 | (sample id) 23 | - image: 24 | type: file 25 | description: tif file for ready for segmentation 26 | pattern: "*.{tif,tiff}" 27 | - - model: 28 | type: file 29 | description: Optional input file. Cellpose 2 model trained by user using human-in-the-loop 30 | approach. 31 | output: 32 | - mask: 33 | - meta: 34 | type: map 35 | description: | 36 | Groovy Map containing sample information 37 | [sample id] 38 | - "*masks.tif": 39 | type: file 40 | description: labelled mask output from cellpose in tif format 41 | pattern: "*.{tif, tiff}" 42 | - flows: 43 | - meta: 44 | type: map 45 | description: | 46 | Groovy Map containing sample information 47 | [sample id] 48 | - "*flows.tif": 49 | type: file 50 | description: cell flow output from cellpose 51 | pattern: "*.{tif}" 52 | - versions: 53 | - versions.yml: 54 | type: file 55 | description: File containing software versions 56 | pattern: "versions.yml" 57 | authors: 58 | - "@josenimo" 59 | - "@FloWuenne" 60 | maintainers: 61 | - "@josenimo" 62 | - "@FloWuenne" 63 | - "@kbestak" 64 | -------------------------------------------------------------------------------- /assets/methods_description_template.yml: -------------------------------------------------------------------------------- 1 | id: "nf-core-spatialxe-methods-description" 2 | description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." 3 | section_name: "nf-core/spatialxe Methods Description" 4 | section_href: "https://github.com/nf-core/spatialxe" 5 | plot_type: "html" 6 | ## TODO nf-core: Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline 7 | ## You inject any metadata in the Nextflow '${workflow}' object 8 | data: | 9 |

Methods

10 |

Data was processed using nf-core/spatialxe v${workflow.manifest.version} ${doi_text} of the nf-core collection of workflows (Ewels et al., 2020).

11 |

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

12 | 
${workflow.commandLine}
13 |

References

14 |
    15 |
  • Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature Biotechnology, 35(4), 316-319. https://doi.org/10.1038/nbt.3820
    • 16 |
  • Ewels, P. A., Peltzer, A., Fillinger, S., Patel, H., Alneberg, J., Wilm, A., Garcia, M. U., Di Tommaso, P., & Nahnsen, S. (2020). The nf-core framework for community-curated bioinformatics pipelines. Nature Biotechnology, 38(3), 276-278. https://doi.org/10.1038/s41587-020-0439-x
    • 17 |
18 |
19 |
Notes:
20 |
    21 | ${nodoi_text} 22 |
  • The command above does not include parameters contained in any configs or profiles that may have been used. Ensure the config file is also uploaded with your publication!
    • 23 |
  • You should also cite all software used within this run. Check the "Software Versions" of this report to get version information.
    • 24 |
25 |
26 | -------------------------------------------------------------------------------- /modules/nf-core/cellpose/main.nf: -------------------------------------------------------------------------------- 1 | process CELLPOSE { 2 | tag "$meta.id" 3 | label 'process_medium' 4 | 5 | container "docker.io/biocontainers/cellpose:3.0.1_cv1" 6 | 7 | input: 8 | tuple val(meta), path(image) 9 | path(model) 10 | 11 | output: 12 | tuple val(meta), path("*masks.tif") , emit: mask 13 | tuple val(meta), path("*flows.tif") , emit: flows, optional: true 14 | path "versions.yml" , emit: versions 15 | 16 | when: 17 | task.ext.when == null || task.ext.when 18 | 19 | script: 20 | // Exit if running this module with -profile conda / -profile mamba 21 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 22 | error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead." 23 | } 24 | def args = task.ext.args ?: '' 25 | def prefix = task.ext.prefix ?: "${meta.id}" 26 | def model_command = model ? "--pretrained_model $model" : "" 27 | def VERSION = '3.0.1' 28 | """ 29 | cellpose \\ 30 | --image_path $image \\ 31 | --save_tif \\ 32 | $model_command \\ 33 | $args 34 | 35 | cat <<-END_VERSIONS > versions.yml 36 | "${task.process}": 37 | cellpose: $VERSION 38 | END_VERSIONS 39 | """ 40 | stub: 41 | // Exit if running this module with -profile conda / -profile mamba 42 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 43 | error "I did not manage to create a cellpose module in Conda that works in all OSes. Please use Docker / Singularity / Podman instead." 44 | } 45 | def prefix = task.ext.prefix ?: "${meta.id}" 46 | def VERSION = "3.0.1" // WARN: Version information not provided by tool on CLI. Please update this string when bumping container versions. 47 | def name = image.name 48 | def base = name.lastIndexOf('.') != -1 ? name[0..name.lastIndexOf('.') - 1] : name 49 | """ 50 | touch ${base}_cp_masks.tif 51 | 52 | cat <<-END_VERSIONS > versions.yml 53 | "${task.process}": 54 | cellpose: $VERSION 55 | END_VERSIONS 56 | """ 57 | 58 | } 59 | -------------------------------------------------------------------------------- /lib/Utils.groovy: -------------------------------------------------------------------------------- 1 | // 2 | // This file holds several Groovy functions that could be useful for any Nextflow pipeline 3 | // 4 | 5 | import org.yaml.snakeyaml.Yaml 6 | 7 | class Utils { 8 | 9 | // 10 | // When running with -profile conda, warn if channels have not been set-up appropriately 11 | // 12 | public static void checkCondaChannels(log) { 13 | Yaml parser = new Yaml() 14 | def channels = [] 15 | try { 16 | def config = parser.load("conda config --show channels".execute().text) 17 | channels = config.channels 18 | } catch(NullPointerException | IOException e) { 19 | log.warn "Could not verify conda channel configuration." 20 | return 21 | } 22 | 23 | // Check that all channels are present 24 | // This channel list is ordered by required channel priority. 25 | def required_channels_in_order = ['conda-forge', 'bioconda', 'defaults'] 26 | def channels_missing = ((required_channels_in_order as Set) - (channels as Set)) as Boolean 27 | 28 | // Check that they are in the right order 29 | def channel_priority_violation = false 30 | def n = required_channels_in_order.size() 31 | for (int i = 0; i < n - 1; i++) { 32 | channel_priority_violation |= !(channels.indexOf(required_channels_in_order[i]) < channels.indexOf(required_channels_in_order[i+1])) 33 | } 34 | 35 | if (channels_missing | channel_priority_violation) { 36 | log.warn "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + 37 | " There is a problem with your Conda configuration!\n\n" + 38 | " You will need to set-up the conda-forge and bioconda channels correctly.\n" + 39 | " Please refer to https://bioconda.github.io/\n" + 40 | " The observed channel order is \n" + 41 | " ${channels}\n" + 42 | " but the following channel order is required:\n" + 43 | " ${required_channels_in_order}\n" + 44 | "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" 45 | } 46 | } 47 | } 48 | -------------------------------------------------------------------------------- /main.nf: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env nextflow 2 | /* 3 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 4 | nf-core/spatialxe 5 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 6 | Github : https://github.com/nf-core/spatialxe 7 | 8 | Website: https://nf-co.re/spatialxe 9 | Slack : https://nfcore.slack.com/channels/spatialxe 10 | ---------------------------------------------------------------------------------------- 11 | */ 12 | 13 | nextflow.enable.dsl = 2 14 | 15 | /* 16 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 17 | GENOME PARAMETER VALUES 18 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 19 | */ 20 | 21 | params.fasta = WorkflowMain.getGenomeAttribute(params, 'fasta') 22 | 23 | /* 24 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 25 | VALIDATE & PRINT PARAMETER SUMMARY 26 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 27 | */ 28 | 29 | WorkflowMain.initialise(workflow, params, log) 30 | 31 | /* 32 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 | NAMED WORKFLOW FOR PIPELINE 34 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 35 | */ 36 | 37 | include { SPATIALXE } from './workflows/spatialxe' 38 | 39 | // 40 | // WORKFLOW: Run main nf-core/spatialxe analysis pipeline 41 | // 42 | workflow NFCORE_SPATIALXE { 43 | SPATIALXE () 44 | } 45 | 46 | /* 47 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 48 | RUN ALL WORKFLOWS 49 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 50 | */ 51 | 52 | // 53 | // WORKFLOW: Execute a single named workflow for the pipeline 54 | // See: https://github.com/nf-core/rnaseq/issues/619 55 | // 56 | workflow { 57 | NFCORE_SPATIALXE () 58 | } 59 | 60 | /* 61 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 | THE END 63 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 | */ 65 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/relabel/meta.yml: -------------------------------------------------------------------------------- 1 | name: xeniumranger_relabel 2 | description: The xeniumranger relabel module allows you to change the gene labels 3 | applied to decoded transcripts. 4 | keywords: 5 | - spatial 6 | - relabel 7 | - gene labels 8 | - transcripts 9 | - xeniumranger 10 | tools: 11 | - xeniumranger: 12 | description: | 13 | Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells. 14 | homepage: "https://www.10xgenomics.com/support/software/xenium-ranger/latest" 15 | documentation: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started" 16 | tool_dev_url: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis" 17 | licence: 18 | - 10x Genomics EULA 19 | identifier: "" 20 | input: 21 | - - meta: 22 | type: map 23 | description: | 24 | Groovy Map containing run information 25 | e.g. [id:'xenium_bundle_path'] 26 | - xenium_bundle: 27 | type: directory 28 | description: Path to the xenium output bundle generated by the Xenium Onboard 29 | Analysis pipeline 30 | - - gene_panel: 31 | type: file 32 | description: Gene panel JSON file to use for relabeling decoded transcripts 33 | output: 34 | - outs: 35 | - meta: 36 | type: file 37 | description: Files containing the outputs of Cell Ranger, see official 10X Genomics 38 | documentation for a complete list 39 | pattern: "${meta.id}/outs/*" 40 | - "**/outs/**": 41 | type: file 42 | description: Files containing the outputs of xenium ranger, see official 10X 43 | Genomics documentation for a complete list of outputs 44 | pattern: "${meta.id}/outs/*" 45 | - versions: 46 | - versions.yml: 47 | type: file 48 | description: File containing software versions 49 | pattern: "versions.yml" 50 | authors: 51 | - "@khersameesh24" 52 | maintainers: 53 | - "@khersameesh24" 54 | -------------------------------------------------------------------------------- /.github/workflows/branch.yml: -------------------------------------------------------------------------------- 1 | name: nf-core branch protection 2 | # This workflow is triggered on PRs to master branch on the repository 3 | # It fails when someone tries to make a PR against the nf-core `master` branch instead of `dev` 4 | on: 5 | pull_request_target: 6 | branches: [master] 7 | 8 | jobs: 9 | test: 10 | runs-on: ubuntu-latest 11 | steps: 12 | # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches 13 | - name: Check PRs 14 | if: github.repository == 'nf-core/spatialxe' 15 | run: | 16 | { [[ ${{github.event.pull_request.head.repo.full_name }} == nf-core/spatialxe ]] && [[ $GITHUB_HEAD_REF = "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] 17 | 18 | # If the above check failed, post a comment on the PR explaining the failure 19 | # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets 20 | - name: Post PR comment 21 | if: failure() 22 | uses: mshick/add-pr-comment@v1 23 | with: 24 | message: | 25 | ## This PR is against the `master` branch :x: 26 | 27 | * Do not close this PR 28 | * Click _Edit_ and change the `base` to `dev` 29 | * This CI test will remain failed until you push a new commit 30 | 31 | --- 32 | 33 | Hi @${{ github.event.pull_request.user.login }}, 34 | 35 | It looks like this pull-request is has been made against the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `master` branch. 36 | The `master` branch on nf-core repositories should always contain code from the latest release. 37 | Because of this, PRs to `master` are only allowed if they come from the [${{github.event.pull_request.head.repo.full_name }}](https://github.com/${{github.event.pull_request.head.repo.full_name }}) `dev` branch. 38 | 39 | You do not need to close this PR, you can change the target branch to `dev` by clicking the _"Edit"_ button at the top of this page. 40 | Note that even after this, the test will continue to show as failing until you push a new commit. 41 | 42 | Thanks again for your contribution! 43 | repo-token: ${{ secrets.GITHUB_TOKEN }} 44 | allow-repeats: false 45 | -------------------------------------------------------------------------------- /CITATIONS.md: -------------------------------------------------------------------------------- 1 | # nf-core/spatialxe: Citations 2 | 3 | ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) 4 | 5 | > Ewels PA, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, Garcia MU, Di Tommaso P, Nahnsen S. The nf-core framework for community-curated bioinformatics pipelines. Nat Biotechnol. 2020 Mar;38(3):276-278. doi: 10.1038/s41587-020-0439-x. PubMed PMID: 32055031. 6 | 7 | ## [Nextflow](https://pubmed.ncbi.nlm.nih.gov/28398311/) 8 | 9 | > Di Tommaso P, Chatzou M, Floden EW, Barja PP, Palumbo E, Notredame C. Nextflow enables reproducible computational workflows. Nat Biotechnol. 2017 Apr 11;35(4):316-319. doi: 10.1038/nbt.3820. PubMed PMID: 28398311. 10 | 11 | ## Pipeline tools 12 | 13 | - [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/) 14 | 15 | - [MultiQC](https://pubmed.ncbi.nlm.nih.gov/27312411/) 16 | > 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. 17 | 18 | ## Software packaging/containerisation tools 19 | 20 | - [Anaconda](https://anaconda.com) 21 | 22 | > Anaconda Software Distribution. Computer software. Vers. 2-2.4.0. Anaconda, Nov. 2016. Web. 23 | 24 | - [Bioconda](https://pubmed.ncbi.nlm.nih.gov/29967506/) 25 | 26 | > Grüning B, Dale R, Sjödin A, Chapman BA, Rowe J, Tomkins-Tinch CH, Valieris R, Köster J; Bioconda Team. Bioconda: sustainable and comprehensive software distribution for the life sciences. Nat Methods. 2018 Jul;15(7):475-476. doi: 10.1038/s41592-018-0046-7. PubMed PMID: 29967506. 27 | 28 | - [BioContainers](https://pubmed.ncbi.nlm.nih.gov/28379341/) 29 | 30 | > da Veiga Leprevost F, Grüning B, Aflitos SA, Röst HL, Uszkoreit J, Barsnes H, Vaudel M, Moreno P, Gatto L, Weber J, Bai M, Jimenez RC, Sachsenberg T, Pfeuffer J, Alvarez RV, Griss J, Nesvizhskii AI, Perez-Riverol Y. BioContainers: an open-source and community-driven framework for software standardization. Bioinformatics. 2017 Aug 15;33(16):2580-2582. doi: 10.1093/bioinformatics/btx192. PubMed PMID: 28379341; PubMed Central PMCID: PMC5870671. 31 | 32 | - [Docker](https://dl.acm.org/doi/10.5555/2600239.2600241) 33 | 34 | - [Singularity](https://pubmed.ncbi.nlm.nih.gov/28494014/) 35 | > Kurtzer GM, Sochat V, Bauer MW. Singularity: Scientific containers for mobility of compute. PLoS One. 2017 May 11;12(5):e0177459. doi: 10.1371/journal.pone.0177459. eCollection 2017. PubMed PMID: 28494014; PubMed Central PMCID: PMC5426675. 36 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/resegment/main.nf: -------------------------------------------------------------------------------- 1 | process XENIUMRANGER_RESEGMENT { 2 | tag "$meta.id" 3 | label 'process_high' 4 | 5 | container "nf-core/xeniumranger:3.0.1" 6 | 7 | input: 8 | tuple val(meta), path(xenium_bundle) 9 | val(expansion_distance) 10 | val(dapi_filter) 11 | val(boundary_stain) 12 | val(interior_stain) 13 | 14 | output: 15 | tuple val(meta), path("**/outs/**"), emit: outs 16 | path "versions.yml", emit: versions 17 | 18 | when: 19 | task.ext.when == null || task.ext.when 20 | 21 | script: 22 | // Exit if running this module with -profile conda / -profile mamba 23 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 24 | error "XENIUMRANGER_RESEGMENT module does not support Conda. Please use Docker / Singularity / Podman instead." 25 | } 26 | def args = task.ext.args ?: "" 27 | def prefix = task.ext.prefix ?: "${meta.id}" 28 | 29 | def expansion_distance = expansion_distance ? "--expansion-distance=\"${expansion_distance}\"": "" 30 | def dapi_filter = dapi_filter ? "--dapi-filter=\"${dapi_filter}\"": "" 31 | 32 | // Do not use boundary stain in analysis, but keep default interior stain and DAPI 33 | def boundary_stain = boundary_stain ? "--boundary-stain=disable": "" 34 | // Do not use interior stain in analysis, but keep default boundary stain and DAPI 35 | def interior_stain = interior_stain ? "--interior-stain=disable": "" 36 | 37 | """ 38 | xeniumranger resegment \\ 39 | --id="${prefix}" \\ 40 | --xenium-bundle="${xenium_bundle}" \\ 41 | ${expansion_distance} \\ 42 | ${dapi_filter} \\ 43 | ${boundary_stain} \\ 44 | ${interior_stain} \\ 45 | --localcores=${task.cpus} \\ 46 | --localmem=${task.memory.toGiga()} \\ 47 | ${args} 48 | 49 | cat <<-END_VERSIONS > versions.yml 50 | "${task.process}": 51 | xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g") 52 | END_VERSIONS 53 | """ 54 | 55 | stub: 56 | // Exit if running this module with -profile conda / -profile mamba 57 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 58 | error "XENIUMRANGER_RESEGMENT module does not support Conda. Please use Docker / Singularity / Podman instead." 59 | } 60 | def prefix = task.ext.prefix ?: "${meta.id}" 61 | """ 62 | mkdir -p "${prefix}/outs/" 63 | touch "${prefix}/outs/fake_file.txt" 64 | 65 | cat <<-END_VERSIONS > versions.yml 66 | "${task.process}": 67 | xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g") 68 | END_VERSIONS 69 | """ 70 | } 71 | -------------------------------------------------------------------------------- /assets/email_template.html: -------------------------------------------------------------------------------- 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | nf-core/spatialxe Pipeline Report 9 | 10 | 11 |
12 | 13 | 14 | 15 |

nf-core/spatialxe v${version}

16 |

Run Name: $runName

17 | 18 | <% if (!success){ 19 | out << """ 20 |
21 |

nf-core/spatialxe execution completed unsuccessfully!

22 |

The exit status of the task that caused the workflow execution to fail was: $exitStatus.

23 |

The full error message was:

24 | 
${errorReport}
25 |
26 | """ 27 | } else { 28 | out << """ 29 |
30 | nf-core/spatialxe execution completed successfully! 31 |
32 | """ 33 | } 34 | %> 35 | 36 |

The workflow was completed at $dateComplete (duration: $duration)

37 |

The command used to launch the workflow was as follows:

38 | 
$commandLine
39 | 40 |

Pipeline Configuration:

41 | 42 | 43 | <% out << summary.collect{ k,v -> "" }.join("\n") %> 44 | 45 |
$k
$v
46 | 47 |

nf-core/spatialxe

48 |

https://github.com/nf-core/spatialxe

49 | 50 |
51 | 52 | 53 | 54 | -------------------------------------------------------------------------------- /modules/nf-core/cellpose/tests/main.nf.test.snap: -------------------------------------------------------------------------------- 1 | { 2 | "flows": { 3 | "content": [ 4 | [ 5 | [ 6 | { 7 | "id": "test" 8 | }, 9 | "cycif_tonsil_registered.ome_flows.tif:md5,de79a792d4bebd2f9753ceb47a0de5f7" 10 | ] 11 | ] 12 | ], 13 | "meta": { 14 | "nf-test": "0.8.4", 15 | "nextflow": "23.10.1" 16 | }, 17 | "timestamp": "2024-03-18T14:22:16.855256249" 18 | }, 19 | "versions": { 20 | "content": [ 21 | [ 22 | "versions.yml:md5,ce42208b574084f390cf58b4c19b5717" 23 | ] 24 | ], 25 | "meta": { 26 | "nf-test": "0.8.4", 27 | "nextflow": "23.10.1" 28 | }, 29 | "timestamp": "2024-03-18T14:22:16.875087557" 30 | }, 31 | "cellpose - stub": { 32 | "content": [ 33 | { 34 | "0": [ 35 | [ 36 | { 37 | "id": "test" 38 | }, 39 | "cycif_tonsil_registered.ome_cp_masks.tif:md5,d41d8cd98f00b204e9800998ecf8427e" 40 | ] 41 | ], 42 | "1": [ 43 | 44 | ], 45 | "2": [ 46 | "versions.yml:md5,ce42208b574084f390cf58b4c19b5717" 47 | ], 48 | "flows": [ 49 | 50 | ], 51 | "mask": [ 52 | [ 53 | { 54 | "id": "test" 55 | }, 56 | "cycif_tonsil_registered.ome_cp_masks.tif:md5,d41d8cd98f00b204e9800998ecf8427e" 57 | ] 58 | ], 59 | "versions": [ 60 | "versions.yml:md5,ce42208b574084f390cf58b4c19b5717" 61 | ] 62 | } 63 | ], 64 | "meta": { 65 | "nf-test": "0.8.4", 66 | "nextflow": "23.10.1" 67 | }, 68 | "timestamp": "2024-03-18T14:22:39.339792992" 69 | }, 70 | "mask": { 71 | "content": [ 72 | [ 73 | [ 74 | { 75 | "id": "test" 76 | }, 77 | "cycif_tonsil_registered.ome_cp_masks.tif:md5,001ad312413f18bc2615741bd3ad12cf" 78 | ] 79 | ] 80 | ], 81 | "meta": { 82 | "nf-test": "0.8.4", 83 | "nextflow": "23.10.1" 84 | }, 85 | "timestamp": "2024-03-18T14:22:16.8369758" 86 | } 87 | } -------------------------------------------------------------------------------- /modules/local/proseg/meta.yml: -------------------------------------------------------------------------------- 1 | name: "proseg" 2 | description: Probabilistic cell segmentation for in situ spatial transcriptomics 3 | keywords: 4 | - segmentation 5 | - cell segmentation 6 | - spatialomics 7 | - probabilistic segmentation 8 | - in situ spatial transcriptomics 9 | tools: 10 | - "proseg": 11 | description: "Proseg (probabilistic segmentation) is a cell segmentation method for in situ spatial transcriptomics. Xenium, CosMx, and MERSCOPE platforms are currently supported." 12 | homepage: "https://github.com/dcjones/proseg/tree/main" 13 | documentation: "https://github.com/dcjones/proseg/blob/main/README.md" 14 | tool_dev_url: "https://github.com/dcjones/proseg" 15 | doi: "" 16 | licence: ["GNU Public License"] 17 | 18 | input: 19 | - - meta: 20 | type: map 21 | description: | 22 | Groovy Map containing run information 23 | e.g. `[ id:'run_id']` 24 | - transcripts: 25 | type: file 26 | description: | 27 | File containing the transcript position 28 | pattern: "transcripts.csv.gz" 29 | 30 | output: 31 | - - meta: 32 | type: map 33 | description: | 34 | Groovy Map containing run information 35 | e.g. `[ id:'run_id']` 36 | - cell_polygons: 37 | type: file 38 | description: 2D polygons for each cell in GeoJSON format. These are flattened from 3D 39 | pattern: "cell-polygons.geojson.gz" 40 | - - expected_counts: 41 | type: file 42 | description: cell-by-gene count matrix 43 | pattern: "expected-counts.csv.gz" 44 | - - cell_metadata: 45 | type: file 46 | description: Cell centroids, volume, and other information 47 | pattern: "cell-metadata.csv.gz" 48 | - - transcript_metadata: 49 | type: file 50 | description: Transcript ids, genes, revised positions, assignment probability 51 | pattern: "transcript-metadata.csv.gz" 52 | - - gene_metadata: 53 | type: file 54 | description: Per-gene summary statistics 55 | pattern: "gene-metadata.csv.gz" 56 | - - rates: 57 | type: file 58 | description: Cell-by-gene Poisson rate parameters 59 | pattern: "rates.csv.gz" 60 | - - cell_polygon_layers: 61 | type: file 62 | description: A separate, non-overlapping cell polygon for each z-layer, preserving 3D segmentation 63 | pattern: "cell-polygons-layers.geojson.gz" 64 | - - cell_hulls: 65 | type: file 66 | description: Convex hulls around assigned transcripts 67 | pattern: "cell-hulls.geojson.gz" 68 | - - versions: 69 | type: file 70 | description: File containing software versions 71 | pattern: "versions.yml" 72 | 73 | authors: 74 | - "@khersameesh24" 75 | maintainers: 76 | - "@khersameesh24" 77 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/relabel/tests/main.nf.test.snap: -------------------------------------------------------------------------------- 1 | { 2 | "xeniumranger relabel": { 3 | "content": [ 4 | [ 5 | "versions.yml:md5,ab2584177544560d5a9e9c36f7d24354" 6 | ], 7 | [ 8 | "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4", 9 | "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00", 10 | "cell_boundaries.csv.gz:md5,8b4f2aa455a6fb14b2669a42db32ea7e", 11 | "cell_boundaries.parquet:md5,e55d6a7fbec336103994baad8c8e4a9a", 12 | "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6", 13 | "barcodes.tsv.gz:md5,04ea06796d6b28517c288904ca043582", 14 | "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e", 15 | "matrix.mtx.gz:md5,489f86fbd8d65d6b973bb9cc7c5a76f1", 16 | "cells.csv.gz:md5,3cef2d7cc8cfba1d47bdb7c65c3d5d5f", 17 | "cells.parquet:md5,9b30b35ab961d2d243a1426e8dc980fe", 18 | "cells.zarr.zip:md5,556e47d5b14150239b10b2f801defa2b", 19 | "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde", 20 | "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b", 21 | "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98", 22 | "nucleus_boundaries.csv.gz:md5,e417b6e293298870956d42c7106cbd0c", 23 | "nucleus_boundaries.parquet:md5,bacbfc3c2e956d899e1d8ccba5dd7c5e", 24 | "transcripts.parquet:md5,c0f40d5c61b87404bc9efb84ff0563a8" 25 | ] 26 | ], 27 | "meta": { 28 | "nf-test": "0.9.0", 29 | "nextflow": "24.04.4" 30 | }, 31 | "timestamp": "2024-10-29T21:06:09.082129" 32 | }, 33 | "xeniumranger relabel stub": { 34 | "content": [ 35 | { 36 | "0": [ 37 | [ 38 | { 39 | "id": "test_xeniumranger_relabel" 40 | }, 41 | "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" 42 | ] 43 | ], 44 | "1": [ 45 | "versions.yml:md5,ab2584177544560d5a9e9c36f7d24354" 46 | ], 47 | "outs": [ 48 | [ 49 | { 50 | "id": "test_xeniumranger_relabel" 51 | }, 52 | "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" 53 | ] 54 | ], 55 | "versions": [ 56 | "versions.yml:md5,ab2584177544560d5a9e9c36f7d24354" 57 | ] 58 | } 59 | ], 60 | "meta": { 61 | "nf-test": "0.9.0", 62 | "nextflow": "24.04.4" 63 | }, 64 | "timestamp": "2024-10-22T15:22:34.353444" 65 | } 66 | } -------------------------------------------------------------------------------- /assets/adaptivecard.json: -------------------------------------------------------------------------------- 1 | { 2 | "type": "message", 3 | "attachments": [ 4 | { 5 | "contentType": "application/vnd.microsoft.card.adaptive", 6 | "contentUrl": null, 7 | "content": { 8 | "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", 9 | "msteams": { 10 | "width": "Full" 11 | }, 12 | "type": "AdaptiveCard", 13 | "version": "1.2", 14 | "body": [ 15 | { 16 | "type": "TextBlock", 17 | "size": "Large", 18 | "weight": "Bolder", 19 | "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", 20 | "text": "nf-core/spatialxe v${version} - ${runName}", 21 | "wrap": true 22 | }, 23 | { 24 | "type": "TextBlock", 25 | "spacing": "None", 26 | "text": "Completed at ${dateComplete} (duration: ${duration})", 27 | "isSubtle": true, 28 | "wrap": true 29 | }, 30 | { 31 | "type": "TextBlock", 32 | "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors. The full error message was: ${errorReport}.<% } %>", 33 | "wrap": true 34 | }, 35 | { 36 | "type": "TextBlock", 37 | "text": "The command used to launch the workflow was as follows:", 38 | "wrap": true 39 | }, 40 | { 41 | "type": "TextBlock", 42 | "text": "${commandLine}", 43 | "isSubtle": true, 44 | "wrap": true 45 | } 46 | ], 47 | "actions": [ 48 | { 49 | "type": "Action.ShowCard", 50 | "title": "Pipeline Configuration", 51 | "card": { 52 | "type": "AdaptiveCard", 53 | "\$schema": "http://adaptivecards.io/schemas/adaptive-card.json", 54 | "body": [ 55 | { 56 | "type": "FactSet", 57 | "facts": [<% out << summary.collect{ k,v -> "{\"title\": \"$k\", \"value\" : \"$v\"}"}.join(",\n") %> 58 | ] 59 | } 60 | ] 61 | } 62 | } 63 | ] 64 | } 65 | } 66 | ] 67 | } 68 | -------------------------------------------------------------------------------- /modules/local/proseg/tests/main.nf.test: -------------------------------------------------------------------------------- 1 | nextflow_process { 2 | 3 | name "Test Process PROSEG" 4 | script "../main.nf" 5 | process "PROSEG" 6 | 7 | tag "modules" 8 | tag "modules_nfcore" 9 | tag "proseg" 10 | tag "segmentation" 11 | tag "cell_segmentation" 12 | 13 | 14 | setup { 15 | run("UNZIP") { 16 | script "modules/nf-core/unzip/main.nf" 17 | process { 18 | """ 19 | input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)] 20 | """ 21 | } 22 | } 23 | } 24 | 25 | test("proseg - transcripts.csv") { 26 | 27 | when { 28 | process { 29 | """ 30 | input[0] = Channel.of([ 31 | [id: "test_run_proseg"], 32 | ]).combine(UNZIP.out.unzipped_archive.map { it[1] } + "/transcripts.csv") 33 | """ 34 | } 35 | } 36 | 37 | then { 38 | assertAll( 39 | { assert process.success }, 40 | { assert snapshot(process.out).match() }, 41 | { assert file(process.out.expected_counts.get(0).get(1).find { file(it).name == 'expected-counts.csv.gz' }).exists() }, 42 | { assert file(process.out.cell_metadata.get(0).get(1).find { file(it).name == 'cell-metadata.csv.gz' }).exists() }, 43 | { assert file(process.out.transcript_metadata.get(0).get(1).find { file(it).name == 'transcript-metadata.csv.gz' }).exists() }, 44 | { assert file(process.out.gene_metadata.get(0).get(1).find { file(it).name == 'gene-metadata.csv.gz' }).exists() }, 45 | { assert file(process.out.rates.get(0).get(1).find { file(it).name == 'rates.csv.gz' }).exists() }, 46 | { assert file(process.out.cell_polygons.get(0).get(1).find { file(it).name == 'cell-polygons.geojson.gz' }).exists() }, 47 | { assert file(process.out.cell_polygons_layers.get(0).get(1).find { file(it).name == 'cell-polygons-layers.geojson.gz' }).exists() }, 48 | { assert file(process.out.cell-hulls.get(0).get(1).find { file(it).name == 'cell-hulls.geojson.gz' }).exists() }, 49 | ) 50 | } 51 | 52 | } 53 | 54 | test("proseg stub") { 55 | 56 | options "-stub" 57 | 58 | when { 59 | process { 60 | """ 61 | input[0] = Channel.of([ 62 | [id: "test_run_proseg"], 63 | ]).combine(UNZIP.out.unzipped_archive.map { it[1] } + "/transcripts.csv") 64 | """ 65 | } 66 | } 67 | 68 | then { 69 | assertAll( 70 | { assert process.success }, 71 | { assert snapshot(process.out).match() } 72 | ) 73 | } 74 | 75 | } 76 | 77 | } 78 | -------------------------------------------------------------------------------- /conf/base.config: -------------------------------------------------------------------------------- 1 | /* 2 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 | nf-core/spatialxe Nextflow base config file 4 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 | A 'blank slate' config file, appropriate for general use on most high performance 6 | compute environments. Assumes that all software is installed and available on 7 | the PATH. Runs in `local` mode - all jobs will be run on the logged in environment. 8 | ---------------------------------------------------------------------------------------- 9 | */ 10 | 11 | process { 12 | 13 | // TODO nf-core: Check the defaults for all processes 14 | cpus = { check_max( 1 * task.attempt, 'cpus' ) } 15 | memory = { check_max( 6.GB * task.attempt, 'memory' ) } 16 | time = { check_max( 4.h * task.attempt, 'time' ) } 17 | 18 | errorStrategy = { task.exitStatus in [143,137,104,134,139] ? 'retry' : 'finish' } 19 | maxRetries = 1 20 | maxErrors = '-1' 21 | 22 | // Process-specific resource requirements 23 | // NOTE - Please try and re-use the labels below as much as possible. 24 | // These labels are used and recognised by default in DSL2 files hosted on nf-core/modules. 25 | // If possible, it would be nice to keep the same label naming convention when 26 | // adding in your local modules too. 27 | // TODO nf-core: Customise requirements for specific processes. 28 | // See https://www.nextflow.io/docs/latest/config.html#config-process-selectors 29 | withLabel:process_single { 30 | cpus = { check_max( 1 , 'cpus' ) } 31 | memory = { check_max( 6.GB * task.attempt, 'memory' ) } 32 | time = { check_max( 4.h * task.attempt, 'time' ) } 33 | } 34 | withLabel:process_low { 35 | cpus = { check_max( 2 * task.attempt, 'cpus' ) } 36 | memory = { check_max( 12.GB * task.attempt, 'memory' ) } 37 | time = { check_max( 4.h * task.attempt, 'time' ) } 38 | } 39 | withLabel:process_medium { 40 | cpus = { check_max( 6 * task.attempt, 'cpus' ) } 41 | memory = { check_max( 36.GB * task.attempt, 'memory' ) } 42 | time = { check_max( 8.h * task.attempt, 'time' ) } 43 | } 44 | withLabel:process_high { 45 | cpus = { check_max( 12 * task.attempt, 'cpus' ) } 46 | memory = { check_max( 72.GB * task.attempt, 'memory' ) } 47 | time = { check_max( 16.h * task.attempt, 'time' ) } 48 | } 49 | withLabel:process_long { 50 | time = { check_max( 20.h * task.attempt, 'time' ) } 51 | } 52 | withLabel:process_high_memory { 53 | memory = { check_max( 200.GB * task.attempt, 'memory' ) } 54 | } 55 | withLabel:error_ignore { 56 | errorStrategy = 'ignore' 57 | } 58 | withLabel:error_retry { 59 | errorStrategy = 'retry' 60 | maxRetries = 2 61 | } 62 | withName:CUSTOM_DUMPSOFTWAREVERSIONS { 63 | cache = false 64 | } 65 | } 66 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/resegment/meta.yml: -------------------------------------------------------------------------------- 1 | name: xeniumranger_resegment 2 | description: The xeniumranger resegment module allows you to generate a new segmentation of the morphology image space by rerunning the Xenium Onboard Analysis (XOA) segmentation algorithms with modified parameters. 3 | keywords: 4 | - spatial 5 | - resegment 6 | - morphology 7 | - segmentation 8 | - xeniumranger 9 | tools: 10 | - xeniumranger: 11 | description: | 12 | Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells. 13 | homepage: "https://www.10xgenomics.com/support/software/xenium-ranger/latest" 14 | documentation: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started" 15 | tool_dev_url: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis" 16 | licence: 17 | - "10x Genomics EULA" 18 | identifier: "" 19 | input: 20 | - - meta: 21 | type: map 22 | description: | 23 | Groovy Map containing run information 24 | e.g. [ id:'xenium_experiment' ] 25 | - xenium_bundle: 26 | type: directory 27 | description: Path to the xenium output bundle generated by the Xenium Onboard Analysis pipeline 28 | - - expansion_distance: 29 | type: integer 30 | description: Nuclei boundary expansion distance in µm. Only for use when nucleus segmentation provided as input. Default-5 (accepted range 0 - 100) 31 | - - dapi_filter: 32 | type: integer 33 | description: Minimum intensity in photoelectrons to filter nuclei default-100 range of values is 0 to 99th percentile of image stack or 1000, whichever is larger 34 | - - boundary_stain: 35 | type: string 36 | description: Specify the name of the boundary stain to use or disable possible options are default-ATP1A1/CD45/E-Cadherin or disable 37 | - - interior_stain: 38 | type: string 39 | description: Specify the name of the interior stain to use or disable possible options are default-18S or disable 40 | output: 41 | - outs: 42 | - meta: 43 | type: file 44 | description: Files containing the outputs of Cell Ranger, see official 10X Genomics documentation for a complete list 45 | pattern: "${meta.id}/outs/*" 46 | - "**/outs/**": 47 | type: file 48 | description: Files containing the outputs of xenium ranger, see official 10X Genomics documentation for a complete list of outputs 49 | pattern: "${meta.id}/outs/*" 50 | - versions: 51 | - versions.yml: 52 | type: file 53 | description: File containing software versions 54 | pattern: "versions.yml" 55 | authors: 56 | - "@khersameesh24" 57 | maintainers: 58 | - "@khersameesh24" 59 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/import-segmentation/main.nf: -------------------------------------------------------------------------------- 1 | process XENIUMRANGER_IMPORT_SEGMENTATION { 2 | tag "$meta.id" 3 | label 'process_high' 4 | 5 | container "nf-core/xeniumranger:3.0.1" 6 | 7 | input: 8 | tuple val(meta), path(xenium_bundle) 9 | val(expansion_distance) 10 | path(coordinate_transform) 11 | path(nuclei) 12 | path(cells) 13 | path(transcript_assignment) 14 | path(viz_polygons) 15 | 16 | output: 17 | tuple val(meta), path("**/outs/**"), emit: outs 18 | path "versions.yml", emit: versions 19 | 20 | when: 21 | task.ext.when == null || task.ext.when 22 | 23 | script: 24 | // Exit if running this module with -profile conda / -profile mamba 25 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 26 | error "XENIUMRANGER_IMPORT-SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead." 27 | } 28 | def args = task.ext.args ?: '' 29 | def prefix = task.ext.prefix ?: "${meta.id}" 30 | 31 | // image based segmentation options 32 | def expansion_distance = expansion_distance ? "--expansion-distance=\"${expansion_distance}\"": "" // expansion distance (default - 5, range - 0 - 100) 33 | def coordinate_transform = coordinate_transform ? "--coordinate-transform=\"${coordinate_transform}\"": "" 34 | 35 | def nuclei_detection = nuclei ? "--nuclei=\"${nuclei}\"": "" 36 | def cells = cells ? "--cells=\"${cells}\"": "" 37 | 38 | // transcript based segmentation 39 | def transcript_assignment = transcript_assignment ? "--transcript-assignment=\"${transcript_assignment}\"": "" 40 | def viz_polygons = viz_polygons ? "--viz-polygons=\"${viz_polygons}\"":"" 41 | 42 | // shared argument 43 | def units = coordinate_transform ? "--units=microns": "--units=pixels" 44 | 45 | """ 46 | xeniumranger import-segmentation \\ 47 | --id="${prefix}" \\ 48 | --xenium-bundle="${xenium_bundle}" \\ 49 | --localcores=${task.cpus} \\ 50 | --localmem=${task.memory.toGiga()} \\ 51 | ${coordinate_transform} \\ 52 | ${nuclei_detection} \\ 53 | ${cells} \\ 54 | ${expansion_distance} \\ 55 | ${transcript_assignment} \\ 56 | ${viz_polygons} \\ 57 | ${units} \\ 58 | ${args} 59 | 60 | cat <<-END_VERSIONS > versions.yml 61 | "${task.process}": 62 | xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g") 63 | END_VERSIONS 64 | """ 65 | 66 | stub: 67 | // Exit if running this module with -profile conda / -profile mamba 68 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 69 | error "XENIUMRANGER_IMPORT-SEGMENTATION module does not support Conda. Please use Docker / Singularity / Podman instead." 70 | } 71 | def prefix = task.ext.prefix ?: "${meta.id}" 72 | """ 73 | mkdir -p "${prefix}/outs/" 74 | touch "${prefix}/outs/fake_file.txt" 75 | 76 | cat <<-END_VERSIONS > versions.yml 77 | "${task.process}": 78 | xeniumranger: \$(xeniumranger -V | sed -e "s/xeniumranger-/- /g") 79 | END_VERSIONS 80 | """ 81 | } 82 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/resegment/tests/main.nf.test: -------------------------------------------------------------------------------- 1 | nextflow_process { 2 | 3 | name "Test Process XENIUMRANGER_RESEGMENT" 4 | script "../main.nf" 5 | process "XENIUMRANGER_RESEGMENT" 6 | config "./nextflow.config" 7 | 8 | tag "modules" 9 | tag "modules_nfcore" 10 | tag "xeniumranger" 11 | tag "xeniumranger/resegment" 12 | tag "unzip" 13 | 14 | setup { 15 | run("UNZIP") { 16 | script "modules/nf-core/unzip/main.nf" 17 | process { 18 | """ 19 | input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)] 20 | """ 21 | } 22 | } 23 | } 24 | 25 | test("xeniumranger resegment") { 26 | when { 27 | process { 28 | """ 29 | input[0] = Channel.of([ 30 | [id: "test_xeniumranger_resegment"], 31 | ]).combine(UNZIP.out.unzipped_archive.map { it[1] }) 32 | input[1] = [] 33 | input[2] = [] 34 | input[3] = [] 35 | input[4] = [] 36 | """ 37 | } 38 | } 39 | then { 40 | assertAll( 41 | { assert process.success }, 42 | { assert process.out.outs != null }, 43 | { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() }, 44 | { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.csv.gz' }).exists() }, 45 | { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.parquet' }).exists() }, 46 | { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'cells.zarr.zip' }).exists() }, 47 | { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.parquet' }).exists() }, 48 | { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.zarr.zip' }).exists() }, 49 | { assert file(process.out.outs.get(0).get(1).find { file(it).name == 'analysis.zarr.zip' }).exists() }, 50 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'cell_feature_matrix.zarr.zip' }).exists() } 51 | ) 52 | } 53 | } 54 | 55 | test("xeniumranger resegment stub") { 56 | options "-stub" 57 | when { 58 | process { 59 | """ 60 | input[0] = Channel.of([ 61 | [id: "test_xeniumranger_resegment"], 62 | ]).combine(UNZIP.out.unzipped_archive.map { it[1] }) 63 | input[1] = [] 64 | input[2] = [] 65 | input[3] = [] 66 | input[4] = [] 67 | """ 68 | } 69 | } 70 | then { 71 | assertAll( 72 | { assert process.success }, 73 | { assert snapshot(process.out).match() } 74 | ) 75 | } 76 | } 77 | } -------------------------------------------------------------------------------- /modules/local/proseg/main.nf: -------------------------------------------------------------------------------- 1 | process PROSEG { 2 | tag "$meta.id" 3 | label 'process_high' 4 | 5 | container "nf-core/proseg:1.1.8" 6 | 7 | input: 8 | tuple val(meta), path(transcripts) 9 | 10 | output: 11 | tuple val(meta), path("cell-polygons.geojson.gz"), emit: cell_polygons_2d 12 | path("expected-counts.csv.gz"), emit: expected_counts 13 | path("cell-metadata.csv.gz"), emit: cell_metadata 14 | path("transcript-metadata.csv.gz"), emit: transcript_metadata 15 | path("gene-metadata.csv.gz"), emit: gene_metadata 16 | path("rates.csv.gz"), emit: rates 17 | path("cell-polygons-layers.geojson.gz"), emit: cell_polygons_layers 18 | path("cell-hulls.geojson.gz"), emit: cell_hulls 19 | path("versions.yml"), emit: versions 20 | 21 | when: 22 | task.ext.when == null || task.ext.when 23 | 24 | script: 25 | // Exit if running this module with -profile conda / -profile mamba 26 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 27 | error "PROSEG module does not support Conda. Please use Docker / Singularity / Podman instead." 28 | } 29 | def args = task.ext.args ?: '' 30 | def prefix = task.ext.prefix ?: "${meta.id}" 31 | def platform = preset ? "${params.preset}" : "" 32 | 33 | // check for preset values 34 | if (!(platform in ['xenium', 'cosmx', 'merscope'])) { 35 | error "${platform} is an invalid platform (preset) type. Please specify xenium, cosmx, or merscope" 36 | } 37 | 38 | """ 39 | proseg \\ 40 | --${preset} \\ 41 | ${transcripts} \\ 42 | --nthreads ${task.cpus} \\ 43 | --output-expected-counts expected-counts.csv.gz \\ 44 | --output-cell-metadata cell-metadata.csv.gz \\ 45 | --output-transcript-metadata transcript-metadata.csv.gz \\ 46 | --output-gene-metadata gene-metadata.csv.gz \\ 47 | --output-rates rates.csv.gz \\ 48 | --output-cell-polygons cell-polygons.geojson.gz \\ 49 | --output-cell-polygon-layers cell-polygons-layers.geojson.gz \\ 50 | --output-cell-hulls cell-hulls.geojson.gz \\ 51 | ${args} 52 | 53 | cat <<-END_VERSIONS > versions.yml 54 | "${task.process}": 55 | proseg: \$(proseg --version | sed 's/proseg //') 56 | END_VERSIONS 57 | """ 58 | 59 | stub: 60 | // Exit if running this module with -profile conda / -profile mamba 61 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 62 | error "PROSEG module does not support Conda. Please use Docker / Singularity / Podman instead." 63 | } 64 | def args = task.ext.args ?: '' 65 | def prefix = task.ext.prefix ?: "${meta.id}" 66 | 67 | """ 68 | touch expected-counts.csv.gz 69 | touch cell-metadata.csv.gz 70 | touch transcript-metadata.csv.gz 71 | touch gene-metadata.csv.gz 72 | touch rates.csv.gz 73 | touch cell-polygons.geojson.gz 74 | touch cell-polygons-layers.geojson.gz 75 | touch cell-hulls.geojson.gz 76 | 77 | cat <<-END_VERSIONS > versions.yml 78 | "${task.process}": 79 | proseg: \$(proseg --version | sed 's/proseg //') 80 | END_VERSIONS 81 | """ 82 | } 83 | -------------------------------------------------------------------------------- /lib/WorkflowSpatialxe.groovy: -------------------------------------------------------------------------------- 1 | // 2 | // This file holds several functions specific to the workflow/spatialxe.nf in the nf-core/spatialxe pipeline 3 | // 4 | 5 | import groovy.text.SimpleTemplateEngine 6 | 7 | class WorkflowSpatialxe { 8 | 9 | // 10 | // Check and validate parameters 11 | // 12 | public static void initialise(params, log) { 13 | genomeExistsError(params, log) 14 | 15 | 16 | if (!params.fasta) { 17 | log.error "Genome fasta file not specified with e.g. '--fasta genome.fa' or via a detectable config file." 18 | System.exit(1) 19 | } 20 | } 21 | 22 | // 23 | // Get workflow summary for MultiQC 24 | // 25 | public static String paramsSummaryMultiqc(workflow, summary) { 26 | String summary_section = '' 27 | for (group in summary.keySet()) { 28 | def group_params = summary.get(group) // This gets the parameters of that particular group 29 | if (group_params) { 30 | summary_section += "

$group

\n" 31 | summary_section += "
\n" 32 | for (param in group_params.keySet()) { 33 | summary_section += "
$param
${group_params.get(param) ?: 'N/A'}
\n" 34 | } 35 | summary_section += "
\n" 36 | } 37 | } 38 | 39 | String yaml_file_text = "id: '${workflow.manifest.name.replace('/','-')}-summary'\n" 40 | yaml_file_text += "description: ' - this information is collected when the pipeline is started.'\n" 41 | yaml_file_text += "section_name: '${workflow.manifest.name} Workflow Summary'\n" 42 | yaml_file_text += "section_href: 'https://github.com/${workflow.manifest.name}'\n" 43 | yaml_file_text += "plot_type: 'html'\n" 44 | yaml_file_text += "data: |\n" 45 | yaml_file_text += "${summary_section}" 46 | return yaml_file_text 47 | } 48 | 49 | public static String methodsDescriptionText(run_workflow, mqc_methods_yaml) { 50 | // Convert to a named map so can be used as with familar NXF ${workflow} variable syntax in the MultiQC YML file 51 | def meta = [:] 52 | meta.workflow = run_workflow.toMap() 53 | meta["manifest_map"] = run_workflow.manifest.toMap() 54 | 55 | meta["doi_text"] = meta.manifest_map.doi ? "(doi: ${meta.manifest_map.doi})" : "" 56 | meta["nodoi_text"] = meta.manifest_map.doi ? "": "
  • If available, make sure to update the text to include the Zenodo DOI of version of the pipeline used.
    • " 57 | 58 | def methods_text = mqc_methods_yaml.text 59 | 60 | def engine = new SimpleTemplateEngine() 61 | def description_html = engine.createTemplate(methods_text).make(meta) 62 | 63 | return description_html 64 | }// 65 | // Exit pipeline if incorrect --genome key provided 66 | // 67 | private static void genomeExistsError(params, log) { 68 | if (params.genomes && params.genome && !params.genomes.containsKey(params.genome)) { 69 | log.error "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n" + 70 | " Genome '${params.genome}' not found in any config files provided to the pipeline.\n" + 71 | " Currently, the available genome keys are:\n" + 72 | " ${params.genomes.keySet().join(", ")}\n" + 73 | "~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~" 74 | System.exit(1) 75 | } 76 | } 77 | } 78 | -------------------------------------------------------------------------------- /.github/workflows/linting.yml: -------------------------------------------------------------------------------- 1 | name: nf-core linting 2 | # This workflow is triggered on pushes and PRs to the repository. 3 | # It runs the `nf-core lint` and markdown lint tests to ensure 4 | # that the code meets the nf-core guidelines. 5 | on: 6 | push: 7 | branches: 8 | - dev 9 | pull_request: 10 | release: 11 | types: [published] 12 | 13 | jobs: 14 | EditorConfig: 15 | runs-on: ubuntu-latest 16 | steps: 17 | - uses: actions/checkout@v3 18 | 19 | - uses: actions/setup-node@v3 20 | 21 | - name: Install editorconfig-checker 22 | run: npm install -g editorconfig-checker 23 | 24 | - name: Run ECLint check 25 | run: editorconfig-checker -exclude README.md $(find .* -type f | grep -v '.git\|.py\|.md\|json\|yml\|yaml\|html\|css\|work\|.nextflow\|build\|nf_core.egg-info\|log.txt\|Makefile') 26 | 27 | Prettier: 28 | runs-on: ubuntu-latest 29 | steps: 30 | - uses: actions/checkout@v3 31 | 32 | - uses: actions/setup-node@v3 33 | 34 | - name: Install Prettier 35 | run: npm install -g prettier 36 | 37 | - name: Run Prettier --check 38 | run: prettier --check ${GITHUB_WORKSPACE} 39 | 40 | PythonBlack: 41 | runs-on: ubuntu-latest 42 | steps: 43 | - uses: actions/checkout@v3 44 | 45 | - name: Check code lints with Black 46 | uses: psf/black@stable 47 | 48 | # If the above check failed, post a comment on the PR explaining the failure 49 | - name: Post PR comment 50 | if: failure() 51 | uses: mshick/add-pr-comment@v1 52 | with: 53 | message: | 54 | ## Python linting (`black`) is failing 55 | 56 | To keep the code consistent with lots of contributors, we run automated code consistency checks. 57 | To fix this CI test, please run: 58 | 59 | * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` 60 | * Fix formatting errors in your pipeline: `black .` 61 | 62 | Once you push these changes the test should pass, and you can hide this comment :+1: 63 | 64 | We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! 65 | 66 | Thanks again for your contribution! 67 | repo-token: ${{ secrets.GITHUB_TOKEN }} 68 | allow-repeats: false 69 | 70 | nf-core: 71 | runs-on: ubuntu-latest 72 | steps: 73 | - name: Check out pipeline code 74 | uses: actions/checkout@v3 75 | 76 | - name: Install Nextflow 77 | uses: nf-core/setup-nextflow@v1 78 | 79 | - uses: actions/setup-python@v4 80 | with: 81 | python-version: "3.7" 82 | architecture: "x64" 83 | 84 | - name: Install dependencies 85 | run: | 86 | python -m pip install --upgrade pip 87 | pip install nf-core 88 | 89 | - name: Run nf-core lint 90 | env: 91 | GITHUB_COMMENTS_URL: ${{ github.event.pull_request.comments_url }} 92 | GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} 93 | GITHUB_PR_COMMIT: ${{ github.event.pull_request.head.sha }} 94 | run: nf-core -l lint_log.txt lint --dir ${GITHUB_WORKSPACE} --markdown lint_results.md 95 | 96 | - name: Save PR number 97 | if: ${{ always() }} 98 | run: echo ${{ github.event.pull_request.number }} > PR_number.txt 99 | 100 | - name: Upload linting log file artifact 101 | if: ${{ always() }} 102 | uses: actions/upload-artifact@v3 103 | with: 104 | name: linting-logs 105 | path: | 106 | lint_log.txt 107 | lint_results.md 108 | PR_number.txt 109 | -------------------------------------------------------------------------------- /modules/nf-core/custom/dumpsoftwareversions/templates/dumpsoftwareversions.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | 4 | """Provide functions to merge multiple versions.yml files.""" 5 | 6 | 7 | import platform 8 | from textwrap import dedent 9 | 10 | import yaml 11 | 12 | 13 | def _make_versions_html(versions): 14 | """Generate a tabular HTML output of all versions for MultiQC.""" 15 | html = [ 16 | dedent( 17 | """\\ 18 | 23 | 24 | 25 | 26 | 27 | 28 | 29 | 30 | 31 | """ 32 | ) 33 | ] 34 | for process, tmp_versions in sorted(versions.items()): 35 | html.append("") 36 | for i, (tool, version) in enumerate(sorted(tmp_versions.items())): 37 | html.append( 38 | dedent( 39 | f"""\\ 40 | 41 | 42 | 43 | 44 | 45 | """ 46 | ) 47 | ) 48 | html.append("") 49 | html.append("
    Process Name Software Version
    {process if (i == 0) else ''}{tool}{version}
    ") 50 | return "\\n".join(html) 51 | 52 | 53 | def main(): 54 | """Load all version files and generate merged output.""" 55 | versions_this_module = {} 56 | versions_this_module["${task.process}"] = { 57 | "python": platform.python_version(), 58 | "yaml": yaml.__version__, 59 | } 60 | 61 | with open("$versions") as f: 62 | versions_by_process = yaml.load(f, Loader=yaml.BaseLoader) | versions_this_module 63 | 64 | # aggregate versions by the module name (derived from fully-qualified process name) 65 | versions_by_module = {} 66 | for process, process_versions in versions_by_process.items(): 67 | module = process.split(":")[-1] 68 | try: 69 | if versions_by_module[module] != process_versions: 70 | raise AssertionError( 71 | "We assume that software versions are the same between all modules. " 72 | "If you see this error-message it means you discovered an edge-case " 73 | "and should open an issue in nf-core/tools. " 74 | ) 75 | except KeyError: 76 | versions_by_module[module] = process_versions 77 | 78 | versions_by_module["Workflow"] = { 79 | "Nextflow": "$workflow.nextflow.version", 80 | "$workflow.manifest.name": "$workflow.manifest.version", 81 | } 82 | 83 | versions_mqc = { 84 | "id": "software_versions", 85 | "section_name": "${workflow.manifest.name} Software Versions", 86 | "section_href": "https://github.com/${workflow.manifest.name}", 87 | "plot_type": "html", 88 | "description": "are collected at run time from the software output.", 89 | "data": _make_versions_html(versions_by_module), 90 | } 91 | 92 | with open("software_versions.yml", "w") as f: 93 | yaml.dump(versions_by_module, f, default_flow_style=False) 94 | with open("software_versions_mqc.yml", "w") as f: 95 | yaml.dump(versions_mqc, f, default_flow_style=False) 96 | 97 | with open("versions.yml", "w") as f: 98 | yaml.dump(versions_this_module, f, default_flow_style=False) 99 | 100 | 101 | if __name__ == "__main__": 102 | main() 103 | -------------------------------------------------------------------------------- /docs/output.md: -------------------------------------------------------------------------------- 1 | # nf-core/spatialxe: Output 2 | 3 | ## Introduction 4 | 5 | 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. 6 | 7 | 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. 8 | 9 | 10 | 11 | ## Pipeline overview 12 | 13 | The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes data using the following steps: 14 | 15 | - [FastQC](#fastqc) - Raw read QC 16 | - [MultiQC](#multiqc) - Aggregate report describing results and QC from the whole pipeline 17 | - [Pipeline information](#pipeline-information) - Report metrics generated during the workflow execution 18 | 19 | ### FastQC 20 | 21 |
    22 | Output files 23 | 24 | - `fastqc/` 25 | - `*_fastqc.html`: FastQC report containing quality metrics. 26 | - `*_fastqc.zip`: Zip archive containing the FastQC report, tab-delimited data file and plot images. 27 | 28 |
    29 | 30 | [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/). 31 | 32 | ![MultiQC - FastQC sequence counts plot](images/mqc_fastqc_counts.png) 33 | 34 | ![MultiQC - FastQC mean quality scores plot](images/mqc_fastqc_quality.png) 35 | 36 | ![MultiQC - FastQC adapter content plot](images/mqc_fastqc_adapter.png) 37 | 38 | > **NB:** The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They may contain adapter sequence and potentially regions with low quality. 39 | 40 | ### MultiQC 41 | 42 |
    43 | Output files 44 | 45 | - `multiqc/` 46 | - `multiqc_report.html`: a standalone HTML file that can be viewed in your web browser. 47 | - `multiqc_data/`: directory containing parsed statistics from the different tools used in the pipeline. 48 | - `multiqc_plots/`: directory containing static images from the report in various formats. 49 | 50 |
    51 | 52 | [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. 53 | 54 | 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 . 55 | 56 | ### Pipeline information 57 | 58 |
    59 | Output files 60 | 61 | - `pipeline_info/` 62 | - Reports generated by Nextflow: `execution_report.html`, `execution_timeline.html`, `execution_trace.txt` and `pipeline_dag.dot`/`pipeline_dag.svg`. 63 | - 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. 64 | - Reformatted samplesheet files used as input to the pipeline: `samplesheet.valid.csv`. 65 | 66 |
    67 | 68 | [Nextflow](https://www.nextflow.io/docs/latest/tracing.html) provides excellent functionality for generating various reports relevant to the running and execution of the pipeline. This will allow you to troubleshoot errors with the running of the pipeline, and also provide you with other information such as launch commands, run times and resource usage. 69 | -------------------------------------------------------------------------------- /lib/WorkflowMain.groovy: -------------------------------------------------------------------------------- 1 | // 2 | // This file holds several functions specific to the main.nf workflow in the nf-core/spatialxe pipeline 3 | // 4 | 5 | class WorkflowMain { 6 | 7 | // 8 | // Citation string for pipeline 9 | // 10 | public static String citation(workflow) { 11 | return "If you use ${workflow.manifest.name} for your analysis please cite:\n\n" + 12 | // TODO nf-core: Add Zenodo DOI for pipeline after first release 13 | //"* The pipeline\n" + 14 | //" https://doi.org/10.5281/zenodo.XXXXXXX\n\n" + 15 | "* The nf-core framework\n" + 16 | " https://doi.org/10.1038/s41587-020-0439-x\n\n" + 17 | "* Software dependencies\n" + 18 | " https://github.com/${workflow.manifest.name}/blob/master/CITATIONS.md" 19 | } 20 | 21 | // 22 | // Generate help string 23 | // 24 | public static String help(workflow, params, log) { 25 | def command = "nextflow run ${workflow.manifest.name} --input samplesheet.csv --genome GRCh37 -profile docker" 26 | def help_string = '' 27 | help_string += NfcoreTemplate.logo(workflow, params.monochrome_logs) 28 | help_string += NfcoreSchema.paramsHelp(workflow, params, command) 29 | help_string += '\n' + citation(workflow) + '\n' 30 | help_string += NfcoreTemplate.dashedLine(params.monochrome_logs) 31 | return help_string 32 | } 33 | 34 | // 35 | // Generate parameter summary log string 36 | // 37 | public static String paramsSummaryLog(workflow, params, log) { 38 | def summary_log = '' 39 | summary_log += NfcoreTemplate.logo(workflow, params.monochrome_logs) 40 | summary_log += NfcoreSchema.paramsSummaryLog(workflow, params) 41 | summary_log += '\n' + citation(workflow) + '\n' 42 | summary_log += NfcoreTemplate.dashedLine(params.monochrome_logs) 43 | return summary_log 44 | } 45 | 46 | // 47 | // Validate parameters and print summary to screen 48 | // 49 | public static void initialise(workflow, params, log) { 50 | // Print help to screen if required 51 | if (params.help) { 52 | log.info help(workflow, params, log) 53 | System.exit(0) 54 | } 55 | 56 | // Print workflow version and exit on --version 57 | if (params.version) { 58 | String workflow_version = NfcoreTemplate.version(workflow) 59 | log.info "${workflow.manifest.name} ${workflow_version}" 60 | System.exit(0) 61 | } 62 | 63 | // Print parameter summary log to screen 64 | log.info paramsSummaryLog(workflow, params, log) 65 | 66 | // Validate workflow parameters via the JSON schema 67 | if (params.validate_params) { 68 | NfcoreSchema.validateParameters(workflow, params, log) 69 | } 70 | 71 | // Check that a -profile or Nextflow config has been provided to run the pipeline 72 | NfcoreTemplate.checkConfigProvided(workflow, log) 73 | 74 | // Check that conda channels are set-up correctly 75 | if (workflow.profile.tokenize(',').intersect(['conda', 'mamba']).size() >= 1) { 76 | Utils.checkCondaChannels(log) 77 | } 78 | 79 | // Check AWS batch settings 80 | NfcoreTemplate.awsBatch(workflow, params) 81 | 82 | // Check input has been provided 83 | if (!params.input) { 84 | log.error "Please provide an input samplesheet to the pipeline e.g. '--input samplesheet.csv'" 85 | System.exit(1) 86 | } 87 | } 88 | // 89 | // Get attribute from genome config file e.g. fasta 90 | // 91 | public static Object getGenomeAttribute(params, attribute) { 92 | if (params.genomes && params.genome && params.genomes.containsKey(params.genome)) { 93 | if (params.genomes[ params.genome ].containsKey(attribute)) { 94 | return params.genomes[ params.genome ][ attribute ] 95 | } 96 | } 97 | return null 98 | } 99 | } 100 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/import-segmentation/meta.yml: -------------------------------------------------------------------------------- 1 | name: xeniumranger_import_segmentation 2 | description: The xeniumranger import-segmentation module allows you to specify 2D 3 | nuclei and/or cell segmentation results for assigning transcripts to cells and recalculate 4 | all Xenium Onboard Analysis (XOA) outputs that depend on segmentation. Segmentation 5 | results can be generated by community-developed tools or prior Xenium segmentation 6 | result. 7 | keywords: 8 | - spatial 9 | - segmentation 10 | - import segmentation 11 | - nuclear segmentation 12 | - cell segmentation 13 | - xeniumranger 14 | - imaging 15 | tools: 16 | - xeniumranger: 17 | description: | 18 | Xenium Ranger is a set of analysis pipelines that process Xenium In Situ Gene Expression data to relabel, resegment, or import new segmentation results from community-developed tools. Xenium Ranger provides flexible off-instrument reanalysis of Xenium In Situ data. Relabel transcripts, resegment cells with the latest 10x segmentation algorithms, or import your own segmentation data to assign transcripts to cells. 19 | homepage: "https://www.10xgenomics.com/support/software/xenium-ranger/latest" 20 | documentation: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/getting-started" 21 | tool_dev_url: "https://www.10xgenomics.com/support/software/xenium-ranger/latest/analysis" 22 | licence: 23 | - "10x Genomics EULA" 24 | identifier: "" 25 | 26 | input: 27 | - - meta: 28 | type: map 29 | description: | 30 | Groovy Map containing run information 31 | e.g. [id:'xenium_bundle_path'] 32 | - xenium_bundle: 33 | type: directory 34 | description: Path to the xenium output bundle generated by the Xenium Onboard 35 | Analysis pipeline 36 | - - expansion_distance: 37 | type: integer 38 | description: Nuclei boundary expansion distance in µm. Only for use when nucleus 39 | segmentation provided as input. Default-5 (accepted range 0 - 100) 40 | - - coordinate_transform: 41 | type: file 42 | description: Image alignment file containing similarity transform matrix e.g., 43 | the _imagealignment.csv file exported from Xenium Explorer 44 | - - nuclei: 45 | type: file 46 | description: | 47 | Label mask (TIFF or NPY), polygons of nucleus segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the nucleus masks as input). 48 | --nuclei will use nucleusGeometry polygon if it exists in the GeoJSON (i.e., for QuPath-like GeoJSON files), 49 | or geometry if it does not. Error if --transcript-assignment argument is used. 50 | - - cells: 51 | type: file 52 | description: | 53 | Label mask (TIFF or NPY), polygons of cell segmentations (GeoJSON FeatureCollection), or Xenium Onboard Analysis cells.zarr.zip (the cell masks as input). 54 | Features with a non-cell objectType will be ignored. Error if --transcript-assignment argument is used. 55 | In Xenium Ranger v2.0, --nuclei no longer needs to be used with --cells. 56 | - - transcript_assignment: 57 | type: file 58 | description: | 59 | Transcript CSV with cell assignment from Baysor v0.6. Error if --cells or --nuclei arguments are used. 60 | - - viz_polygons: 61 | type: file 62 | description: | 63 | Cell boundary polygons (GeoJSON) for visualization from Baysor v0.6. Required if --transcript-assignment argument used. Error if --cells or --nuclei arguments used. 64 | output: 65 | - outs: 66 | - meta: 67 | type: file 68 | description: Files containing the outputs of Cell Ranger, see official 10X Genomics 69 | documentation for a complete list 70 | pattern: "${meta.id}/outs/*" 71 | - "**/outs/**": 72 | type: file 73 | description: Files containing the outputs of xenium ranger, see official 10X 74 | Genomics documentation for a complete list of outputs 75 | pattern: "${meta.id}/outs/*" 76 | - versions: 77 | - versions.yml: 78 | type: file 79 | description: File containing software versions 80 | pattern: "versions.yml" 81 | authors: 82 | - "@khersameesh24" 83 | maintainers: 84 | - "@khersameesh24" 85 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/relabel/tests/main.nf.test: -------------------------------------------------------------------------------- 1 | nextflow_process { 2 | 3 | name "Test Process XENIUMRANGER_RELABEL" 4 | script "../main.nf" 5 | process "XENIUMRANGER_RELABEL" 6 | config "./nextflow.config" 7 | 8 | tag "modules" 9 | tag "modules_nfcore" 10 | tag "xeniumranger" 11 | tag "xeniumranger/relabel" 12 | tag "unzip" 13 | 14 | setup { 15 | run("UNZIP") { 16 | script "modules/nf-core/unzip/main.nf" 17 | process { 18 | """ 19 | input[0] = [[], file('https://raw.githubusercontent.com/nf-core/test-datasets/spatialxe/Xenium_Prime_Mouse_Ileum_tiny_outs.zip', checkIfExists: true)] 20 | """ 21 | } 22 | } 23 | } 24 | 25 | test("xeniumranger relabel") { 26 | when { 27 | process { 28 | """ 29 | input[0] = Channel.of([ 30 | [id: "test_xeniumranger_relabel"], 31 | ]).combine(UNZIP.out.unzipped_archive.map { it[1] }) 32 | input[1] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json" 33 | """ 34 | } 35 | } 36 | then { 37 | assertAll( 38 | { assert process.success }, 39 | { assert process.out.outs != null }, 40 | { 41 | assert snapshot( 42 | process.out.versions, 43 | process.out.outs.get(0).get(1).findAll { file(it).name !in [ 44 | "analysis.zarr.zip", 45 | "experiment.xenium", 46 | "transcripts.zarr.zip", 47 | "analysis_summary.html", 48 | "cell_feature_matrix.zarr.zip", 49 | "differential_expression.csv", 50 | "components.csv", 51 | "projection.csv", 52 | "variance.csv", 53 | "metrics_summary.csv", 54 | "clusters.csv" 55 | ]} 56 | ).match() 57 | }, 58 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() }, 59 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'analysis.zarr.zip' }).exists() }, 60 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'experiment.xenium' }).exists() }, 61 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'transcripts.zarr.zip' }).exists() }, 62 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'analysis_summary.html' }).exists() }, 63 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'cell_feature_matrix.zarr.zip' }).exists() }, 64 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'differential_expression.csv' }).exists() }, 65 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'components.csv' }).exists() }, 66 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'projection.csv' }).exists() }, 67 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'variance.csv' }).exists() }, 68 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'metrics_summary.csv' }).exists() }, 69 | { assert path(process.out.outs.get(0).get(1).find { file(it).name == 'clusters.csv' }).exists() }, 70 | ) 71 | } 72 | } 73 | 74 | test("xeniumranger relabel stub") { 75 | options "-stub" 76 | when { 77 | process { 78 | """ 79 | input[0] = Channel.of([ 80 | [id: "test_xeniumranger_relabel"], 81 | ]).combine(UNZIP.out.unzipped_archive.map { it[1] }) 82 | input[1] = UNZIP.out.unzipped_archive.map { it[1] } + "/gene_panel.json" 83 | """ 84 | } 85 | } 86 | then { 87 | assertAll( 88 | { assert process.success }, 89 | { assert snapshot(process.out).match() } 90 | ) 91 | } 92 | } 93 | } -------------------------------------------------------------------------------- /workflows/spatialxe.nf: -------------------------------------------------------------------------------- 1 | /* 2 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 | VALIDATE INPUTS 4 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 | */ 6 | 7 | def summary_params = NfcoreSchema.paramsSummaryMap(workflow, params) 8 | 9 | // Validate input parameters 10 | WorkflowSpatialxe.initialise(params, log) 11 | 12 | // TODO nf-core: Add all file path parameters for the pipeline to the list below 13 | // Check input path parameters to see if they exist 14 | def checkPathParamList = [ params.input, params.multiqc_config, params.fasta ] 15 | for (param in checkPathParamList) { if (param) { file(param, checkIfExists: true) } } 16 | 17 | // Check mandatory parameters 18 | if (params.input) { ch_input = file(params.input) } else { exit 1, 'Input samplesheet not specified!' } 19 | 20 | /* 21 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 22 | CONFIG FILES 23 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 24 | */ 25 | 26 | ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true) 27 | ch_multiqc_custom_config = params.multiqc_config ? Channel.fromPath( params.multiqc_config, checkIfExists: true ) : Channel.empty() 28 | ch_multiqc_logo = params.multiqc_logo ? Channel.fromPath( params.multiqc_logo, checkIfExists: true ) : Channel.empty() 29 | 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) 30 | 31 | /* 32 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 | IMPORT LOCAL MODULES/SUBWORKFLOWS 34 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 35 | */ 36 | 37 | // 38 | // SUBWORKFLOW: Consisting of a mix of local and nf-core/modules 39 | // 40 | include { INPUT_CHECK } from '../subworkflows/local/input_check' 41 | 42 | /* 43 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 44 | IMPORT NF-CORE MODULES/SUBWORKFLOWS 45 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 46 | */ 47 | 48 | // 49 | // MODULE: Installed directly from nf-core/modules 50 | // 51 | include { FASTQC } from '../modules/nf-core/fastqc/main' 52 | include { MULTIQC } from '../modules/nf-core/multiqc/main' 53 | include { CUSTOM_DUMPSOFTWAREVERSIONS } from '../modules/nf-core/custom/dumpsoftwareversions/main' 54 | 55 | /* 56 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 57 | RUN MAIN WORKFLOW 58 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 59 | */ 60 | 61 | // Info required for completion email and summary 62 | def multiqc_report = [] 63 | 64 | workflow SPATIALXE { 65 | 66 | ch_versions = Channel.empty() 67 | 68 | // 69 | // SUBWORKFLOW: Read in samplesheet, validate and stage input files 70 | // 71 | INPUT_CHECK ( 72 | ch_input 73 | ) 74 | ch_versions = ch_versions.mix(INPUT_CHECK.out.versions) 75 | 76 | // 77 | // MODULE: Run FastQC 78 | // 79 | FASTQC ( 80 | INPUT_CHECK.out.reads 81 | ) 82 | ch_versions = ch_versions.mix(FASTQC.out.versions.first()) 83 | 84 | CUSTOM_DUMPSOFTWAREVERSIONS ( 85 | ch_versions.unique().collectFile(name: 'collated_versions.yml') 86 | ) 87 | 88 | // 89 | // MODULE: MultiQC 90 | // 91 | workflow_summary = WorkflowSpatialxe.paramsSummaryMultiqc(workflow, summary_params) 92 | ch_workflow_summary = Channel.value(workflow_summary) 93 | 94 | methods_description = WorkflowSpatialxe.methodsDescriptionText(workflow, ch_multiqc_custom_methods_description) 95 | ch_methods_description = Channel.value(methods_description) 96 | 97 | ch_multiqc_files = Channel.empty() 98 | ch_multiqc_files = ch_multiqc_files.mix(ch_workflow_summary.collectFile(name: 'workflow_summary_mqc.yaml')) 99 | ch_multiqc_files = ch_multiqc_files.mix(ch_methods_description.collectFile(name: 'methods_description_mqc.yaml')) 100 | ch_multiqc_files = ch_multiqc_files.mix(CUSTOM_DUMPSOFTWAREVERSIONS.out.mqc_yml.collect()) 101 | ch_multiqc_files = ch_multiqc_files.mix(FASTQC.out.zip.collect{it[1]}.ifEmpty([])) 102 | 103 | MULTIQC ( 104 | ch_multiqc_files.collect(), 105 | ch_multiqc_config.toList(), 106 | ch_multiqc_custom_config.toList(), 107 | ch_multiqc_logo.toList() 108 | ) 109 | multiqc_report = MULTIQC.out.report.toList() 110 | } 111 | 112 | /* 113 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 114 | COMPLETION EMAIL AND SUMMARY 115 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 116 | */ 117 | 118 | workflow.onComplete { 119 | if (params.email || params.email_on_fail) { 120 | NfcoreTemplate.email(workflow, params, summary_params, projectDir, log, multiqc_report) 121 | } 122 | NfcoreTemplate.summary(workflow, params, log) 123 | if (params.hook_url) { 124 | NfcoreTemplate.IM_notification(workflow, params, summary_params, projectDir, log) 125 | } 126 | } 127 | 128 | /* 129 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 130 | THE END 131 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 132 | */ 133 | -------------------------------------------------------------------------------- /modules/nf-core/xeniumranger/import-segmentation/tests/main.nf.test.snap: -------------------------------------------------------------------------------- 1 | { 2 | "xeniumranger import-segmentation": { 3 | "content": [ 4 | [ 5 | "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63" 6 | ], 7 | [ 8 | "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4", 9 | "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00", 10 | "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6", 11 | "barcodes.tsv.gz:md5,04ea06796d6b28517c288904ca043582", 12 | "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e", 13 | "matrix.mtx.gz:md5,489f86fbd8d65d6b973bb9cc7c5a76f1", 14 | "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde", 15 | "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b", 16 | "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98" 17 | ] 18 | ], 19 | "meta": { 20 | "nf-test": "0.9.0", 21 | "nextflow": "24.04.4" 22 | }, 23 | "timestamp": "2024-10-30T00:13:13.575888" 24 | }, 25 | "xeniumranger import-segmentation nuclei npy": { 26 | "content": [ 27 | [ 28 | "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63" 29 | ], 30 | [ 31 | "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4", 32 | "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00", 33 | "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6", 34 | "barcodes.tsv.gz:md5,04ea06796d6b28517c288904ca043582", 35 | "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e", 36 | "matrix.mtx.gz:md5,489f86fbd8d65d6b973bb9cc7c5a76f1", 37 | "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde", 38 | "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b", 39 | "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98" 40 | ] 41 | ], 42 | "meta": { 43 | "nf-test": "0.9.0", 44 | "nextflow": "24.04.4" 45 | }, 46 | "timestamp": "2024-10-29T23:03:26.726334" 47 | }, 48 | "xeniumranger import-segmentation segmentation csv": { 49 | "content": [ 50 | [ 51 | "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63" 52 | ], 53 | [ 54 | "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4", 55 | "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00", 56 | "cell_feature_matrix.h5:md5,5d74ea595561e0300b6c3e5ec8d06fff", 57 | "barcodes.tsv.gz:md5,97496a9b448d9380cff0575b8e7a6f57", 58 | "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e", 59 | "matrix.mtx.gz:md5,f93ed82a2a74c154392fc6237642f1d2", 60 | "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde", 61 | "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b", 62 | "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98" 63 | ] 64 | ], 65 | "meta": { 66 | "nf-test": "0.9.0", 67 | "nextflow": "24.04.4" 68 | }, 69 | "timestamp": "2024-10-29T23:22:58.158857" 70 | }, 71 | "xeniumranger import-segmentation stub": { 72 | "content": [ 73 | { 74 | "0": [ 75 | [ 76 | { 77 | "id": "test_xeniumranger_import-segmentation" 78 | }, 79 | "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" 80 | ] 81 | ], 82 | "1": [ 83 | "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63" 84 | ], 85 | "outs": [ 86 | [ 87 | { 88 | "id": "test_xeniumranger_import-segmentation" 89 | }, 90 | "fake_file.txt:md5,d41d8cd98f00b204e9800998ecf8427e" 91 | ] 92 | ], 93 | "versions": [ 94 | "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63" 95 | ] 96 | } 97 | ], 98 | "meta": { 99 | "nf-test": "0.9.0", 100 | "nextflow": "24.04.4" 101 | }, 102 | "timestamp": "2024-10-30T22:49:39.204133" 103 | }, 104 | "xeniumranger import-segmentation nuclei tif": { 105 | "content": [ 106 | [ 107 | "versions.yml:md5,d76e870d71abf94ed9ae972a08b83f63" 108 | ], 109 | [ 110 | "dispersion.csv:md5,e8b1abb880ece8fb730ce34a15f958b4", 111 | "features_selected.csv:md5,c5e32d69f001f938ed316d2108a21e00", 112 | "cell_feature_matrix.h5:md5,96cb400f1b1dd6f8796daea0ad5c74e6", 113 | "barcodes.tsv.gz:md5,04ea06796d6b28517c288904ca043582", 114 | "features.tsv.gz:md5,7862242129681900a9cc4086dc83b62e", 115 | "matrix.mtx.gz:md5,489f86fbd8d65d6b973bb9cc7c5a76f1", 116 | "gene_panel.json:md5,8890dd5fd90706e751554ac3fdfdedde", 117 | "morphology.ome.tif:md5,6b65fff28a38a001b8f25061737fbf9b", 118 | "morphology_focus_0000.ome.tif:md5,90e796ad634d14e62cf2ebcadf2eaf98" 119 | ] 120 | ], 121 | "meta": { 122 | "nf-test": "0.9.0", 123 | "nextflow": "24.04.4" 124 | }, 125 | "timestamp": "2024-10-29T23:11:37.18721" 126 | } 127 | } -------------------------------------------------------------------------------- /.github/CONTRIBUTING.md: -------------------------------------------------------------------------------- 1 | # nf-core/spatialxe: Contributing Guidelines 2 | 3 | Hi there! 4 | Many thanks for taking an interest in improving nf-core/spatialxe. 5 | 6 | We try to manage the required tasks for nf-core/spatialxe using GitHub issues, you probably came to this page when creating one. 7 | Please use the pre-filled template to save time. 8 | 9 | However, don't be put off by this template - other more general issues and suggestions are welcome! 10 | Contributions to the code are even more welcome ;) 11 | 12 | > If you need help using or modifying nf-core/spatialxe then the best place to ask is on the nf-core Slack [#spatialxe](https://nfcore.slack.com/channels/spatialxe) channel ([join our Slack here](https://nf-co.re/join/slack)). 13 | 14 | ## Contribution workflow 15 | 16 | If you'd like to write some code for nf-core/spatialxe, the standard workflow is as follows: 17 | 18 | 1. Check that there isn't already an issue about your idea in the [nf-core/spatialxe issues](https://github.com/nf-core/spatialxe/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this 19 | 2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [nf-core/spatialxe repository](https://github.com/nf-core/spatialxe) to your GitHub account 20 | 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) 21 | 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 22 | 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged 23 | 24 | If you're not used to this workflow with git, you can start with some [docs from GitHub](https://help.github.com/en/github/collaborating-with-issues-and-pull-requests) or even their [excellent `git` resources](https://try.github.io/). 25 | 26 | ## Tests 27 | 28 | When you create a pull request with changes, [GitHub Actions](https://github.com/features/actions) will run automatic tests. 29 | Typically, pull-requests are only fully reviewed when these tests are passing, though of course we can help out before then. 30 | 31 | There are typically two types of tests that run: 32 | 33 | ### Lint tests 34 | 35 | `nf-core` has a [set of guidelines](https://nf-co.re/developers/guidelines) which all pipelines must adhere to. 36 | To enforce these and ensure that all pipelines stay in sync, we have developed a helper tool which runs checks on the pipeline code. This is in the [nf-core/tools repository](https://github.com/nf-core/tools) and once installed can be run locally with the `nf-core lint ` command. 37 | 38 | If any failures or warnings are encountered, please follow the listed URL for more documentation. 39 | 40 | ### Pipeline tests 41 | 42 | Each `nf-core` pipeline should be set up with a minimal set of test-data. 43 | `GitHub Actions` then runs the pipeline on this data to ensure that it exits successfully. 44 | If there are any failures then the automated tests fail. 45 | These tests are run both with the latest available version of `Nextflow` and also the minimum required version that is stated in the pipeline code. 46 | 47 | ## Patch 48 | 49 | :warning: Only in the unlikely and regretful event of a release happening with a bug. 50 | 51 | - On your own fork, make a new branch `patch` based on `upstream/master`. 52 | - Fix the bug, and bump version (X.Y.Z+1). 53 | - A PR should be made on `master` from patch to directly this particular bug. 54 | 55 | ## Getting help 56 | 57 | For further information/help, please consult the [nf-core/spatialxe documentation](https://nf-co.re/spatialxe/usage) and don't hesitate to get in touch on the nf-core Slack [#spatialxe](https://nfcore.slack.com/channels/spatialxe) channel ([join our Slack here](https://nf-co.re/join/slack)). 58 | 59 | ## Pipeline contribution conventions 60 | 61 | To make the nf-core/spatialxe code and processing logic more understandable for new contributors and to ensure quality, we semi-standardise the way the code and other contributions are written. 62 | 63 | ### Adding a new step 64 | 65 | If you wish to contribute a new step, please use the following coding standards: 66 | 67 | 1. Define the corresponding input channel into your new process from the expected previous process channel 68 | 2. Write the process block (see below). 69 | 3. Define the output channel if needed (see below). 70 | 4. Add any new parameters to `nextflow.config` with a default (see below). 71 | 5. Add any new parameters to `nextflow_schema.json` with help text (via the `nf-core schema build` tool). 72 | 6. Add sanity checks and validation for all relevant parameters. 73 | 7. Perform local tests to validate that the new code works as expected. 74 | 8. If applicable, add a new test command in `.github/workflow/ci.yml`. 75 | 9. Update MultiQC config `assets/multiqc_config.yml` so relevant suffixes, file name clean up and module plots are in the appropriate order. If applicable, add a [MultiQC](https://https://multiqc.info/) module. 76 | 10. Add a description of the output files and if relevant any appropriate images from the MultiQC report to `docs/output.md`. 77 | 78 | ### Default values 79 | 80 | Parameters should be initialised / defined with default values in `nextflow.config` under the `params` scope. 81 | 82 | Once there, use `nf-core schema build` to add to `nextflow_schema.json`. 83 | 84 | ### Default processes resource requirements 85 | 86 | Sensible defaults for process resource requirements (CPUs / memory / time) for a process should be defined in `conf/base.config`. These should generally be specified generic with `withLabel:` selectors so they can be shared across multiple processes/steps of the pipeline. A nf-core standard set of labels that should be followed where possible can be seen in the [nf-core pipeline template](https://github.com/nf-core/tools/blob/master/nf_core/pipeline-template/conf/base.config), which has the default process as a single core-process, and then different levels of multi-core configurations for increasingly large memory requirements defined with standardised labels. 87 | 88 | The process resources can be passed on to the tool dynamically within the process with the `${task.cpu}` and `${task.memory}` variables in the `script:` block. 89 | 90 | ### Naming schemes 91 | 92 | Please use the following naming schemes, to make it easy to understand what is going where. 93 | 94 | - initial process channel: `ch_output_from_` 95 | - intermediate and terminal channels: `ch__for_` 96 | 97 | ### Nextflow version bumping 98 | 99 | If you are using a new feature from core Nextflow, you may bump the minimum required version of nextflow in the pipeline with: `nf-core bump-version --nextflow . [min-nf-version]` 100 | 101 | ### Images and figures 102 | 103 | For overview images and other documents we follow the nf-core [style guidelines and examples](https://nf-co.re/developers/design_guidelines). 104 | 105 | ## GitHub Codespaces 106 | 107 | This repo includes a devcontainer configuration which will create a GitHub Codespaces for Nextflow development! This is an online developer environment that runs in your browser, complete with VSCode and a terminal. 108 | 109 | To get started: 110 | 111 | - Open the repo in [Codespaces](https://github.com/nf-core/spatialxe/codespaces) 112 | - Tools installed 113 | - nf-core 114 | - Nextflow 115 | 116 | Devcontainer specs: 117 | 118 | - [DevContainer config](.devcontainer/devcontainer.json) 119 | - [Dockerfile](.devcontainer/Dockerfile) 120 | -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | # ![nf-core/spatialxe](docs/images/nf-core-spatialxe_logo_light.png#gh-light-mode-only) ![nf-core/spatialxe](docs/images/nf-core-spatialxe_logo_dark.png#gh-dark-mode-only) 2 | 3 | [![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/spatialxe/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) 4 | 5 | [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A522.10.1-23aa62.svg)](https://www.nextflow.io/) 6 | [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) 7 | [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) 8 | [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) 9 | [![Launch on Nextflow Tower](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Nextflow%20Tower-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/nf-core/spatialxe) 10 | 11 | [![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23spatialxe-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/spatialxe)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Watch on YouTube](http://img.shields.io/badge/youtube-nf--core-FF0000?labelColor=000000&logo=youtube)](https://www.youtube.com/c/nf-core) 12 | 13 | ## Introduction 14 | 15 | **nf-core/spatialxe** is a bioinformatics best-practice processing and quality control pipeline for Xenium data. **The pipeline is currently under developement and not completed yet!**. The current plan for the pipeline implementation is shown in the metromap below. Please note that the pipeline steps and methods might change as we move forward in the development cycle. 16 | 17 | ![nf-core/spatialxe-metromap](docs/images/spatialxe-metromap.png) 18 | 19 | The pipeline is built using [Nextflow](https://www.nextflow.io), a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The [Nextflow DSL2](https://www.nextflow.io/docs/latest/dsl2.html) implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies. Where possible, these processes have been submitted to and installed from [nf-core/modules](https://github.com/nf-core/modules) in order to make them available to all nf-core pipelines, and to everyone within the Nextflow community! 20 | 21 | 22 | 23 | On release, automated continuous integration tests run the pipeline on a full-sized dataset on the AWS cloud infrastructure. This ensures that the pipeline runs on AWS, has sensible resource allocation defaults set to run on real-world datasets, and permits the persistent storage of results to benchmark between pipeline releases and other analysis sources. The results obtained from the full-sized test can be viewed on the [nf-core website](https://nf-co.re/spatialxe/results). 24 | 25 | ## Pipeline summary 26 | 27 | ## Quick Start 28 | 29 | 1. Install [`Nextflow`](https://www.nextflow.io/docs/latest/getstarted.html#installation) (`>=22.10.1`) 30 | 31 | 2. Install any of [`Docker`](https://docs.docker.com/engine/installation/), [`Singularity`](https://www.sylabs.io/guides/3.0/user-guide/) (you can follow [this tutorial](https://singularity-tutorial.github.io/01-installation/)), [`Podman`](https://podman.io/), [`Shifter`](https://nersc.gitlab.io/development/shifter/how-to-use/) or [`Charliecloud`](https://hpc.github.io/charliecloud/) for full pipeline reproducibility _(you can use [`Conda`](https://conda.io/miniconda.html) both to install Nextflow itself and also to manage software within pipelines. Please only use it within pipelines as a last resort; see [docs](https://nf-co.re/usage/configuration#basic-configuration-profiles))_. 32 | 33 | 3. Download the pipeline and test it on a minimal dataset with a single command: 34 | 35 | ```bash 36 | nextflow run nf-core/spatialxe -profile test,YOURPROFILE --outdir 37 | ``` 38 | 39 | Note that some form of configuration will be needed so that Nextflow knows how to fetch the required software. This is usually done in the form of a config profile (`YOURPROFILE` in the example command above). You can chain multiple config profiles in a comma-separated string. 40 | 41 | > - The pipeline comes with config profiles called `docker`, `singularity`, `podman`, `shifter`, `charliecloud` and `conda` which instruct the pipeline to use the named tool for software management. For example, `-profile test,docker`. 42 | > - Please check [nf-core/configs](https://github.com/nf-core/configs#documentation) to see if a custom config file to run nf-core pipelines already exists for your Institute. If so, you can simply use `-profile ` in your command. This will enable either `docker` or `singularity` and set the appropriate execution settings for your local compute environment. 43 | > - If you are using `singularity`, please use the [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use) command to download images first, before running the pipeline. Setting the [`NXF_SINGULARITY_CACHEDIR` or `singularity.cacheDir`](https://www.nextflow.io/docs/latest/singularity.html?#singularity-docker-hub) Nextflow options enables you to store and re-use the images from a central location for future pipeline runs. 44 | > - If you are using `conda`, it is highly recommended to use the [`NXF_CONDA_CACHEDIR` or `conda.cacheDir`](https://www.nextflow.io/docs/latest/conda.html) settings to store the environments in a central location for future pipeline runs. 45 | 46 | 4. Start running your own analysis! 47 | 48 | 49 | 50 | ```bash 51 | nextflow run nf-core/spatialxe --input samplesheet.csv --outdir --genome GRCh37 -profile 52 | ``` 53 | 54 | ## Documentation 55 | 56 | The nf-core/spatialxe pipeline comes with documentation about the pipeline [usage](https://nf-co.re/spatialxe/usage), [parameters](https://nf-co.re/spatialxe/parameters) and [output](https://nf-co.re/spatialxe/output). 57 | 58 | ## Credits 59 | 60 | nf-core/spatialxe was originally written by Sameesh Kher (khersameesh24) and Florian Heyl (heylf). 61 | 62 | We thank the following people for their extensive assistance in the development of this pipeline: 63 | 64 | - Tobias Krause 65 | - Krešimir Beštak (kbestak) 66 | - Matthias Hörtenhuber (mashehu) 67 | 68 | ## Contributions and Support 69 | 70 | If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). 71 | 72 | For further information or help, don't hesitate to get in touch on the [Slack `#spatialxe` channel](https://nfcore.slack.com/channels/spatialxe) (you can join with [this invite](https://nf-co.re/join/slack)). 73 | 74 | ## Citations 75 | 76 | 77 | 78 | 79 | 80 | 81 | An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. 82 | 83 | You can cite the `nf-core` publication as follows: 84 | 85 | > **The nf-core framework for community-curated bioinformatics pipelines.** 86 | > 87 | > Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. 88 | > 89 | > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). 90 | -------------------------------------------------------------------------------- /nextflow.config: -------------------------------------------------------------------------------- 1 | /* 2 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 3 | nf-core/spatialxe Nextflow config file 4 | ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 5 | Default config options for all compute environments 6 | ---------------------------------------------------------------------------------------- 7 | */ 8 | 9 | // Global default params, used in configs 10 | params { 11 | 12 | // TODO nf-core: Specify your pipeline's command line flags 13 | // Input options 14 | input = null 15 | 16 | 17 | // References 18 | genome = null 19 | igenomes_base = 's3://ngi-igenomes/igenomes' 20 | igenomes_ignore = false 21 | // MultiQC options 22 | multiqc_config = null 23 | multiqc_title = null 24 | multiqc_logo = null 25 | max_multiqc_email_size = '25.MB' 26 | multiqc_methods_description = null 27 | 28 | // Boilerplate options 29 | outdir = null 30 | tracedir = "${params.outdir}/pipeline_info" 31 | publish_dir_mode = 'copy' 32 | email = null 33 | email_on_fail = null 34 | plaintext_email = false 35 | monochrome_logs = false 36 | hook_url = null 37 | help = false 38 | version = false 39 | validate_params = true 40 | show_hidden_params = false 41 | schema_ignore_params = 'genomes' 42 | 43 | 44 | // Config options 45 | custom_config_version = 'master' 46 | custom_config_base = "https://raw.githubusercontent.com/nf-core/configs/${params.custom_config_version}" 47 | config_profile_description = null 48 | config_profile_contact = null 49 | config_profile_url = null 50 | config_profile_name = null 51 | 52 | 53 | // Max resource options 54 | // Defaults only, expecting to be overwritten 55 | max_memory = '128.GB' 56 | max_cpus = 16 57 | max_time = '240.h' 58 | 59 | } 60 | 61 | // Load base.config by default for all pipelines 62 | includeConfig 'conf/base.config' 63 | 64 | // Load nf-core custom profiles from different Institutions 65 | try { 66 | includeConfig "${params.custom_config_base}/nfcore_custom.config" 67 | } catch (Exception e) { 68 | System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") 69 | } 70 | 71 | // Load nf-core/spatialxe custom profiles from different institutions. 72 | // Warning: Uncomment only if a pipeline-specific instititutional config already exists on nf-core/configs! 73 | // try { 74 | // includeConfig "${params.custom_config_base}/pipeline/spatialxe.config" 75 | // } catch (Exception e) { 76 | // System.err.println("WARNING: Could not load nf-core/config/spatialxe profiles: ${params.custom_config_base}/pipeline/spatialxe.config") 77 | // } 78 | 79 | 80 | profiles { 81 | debug { process.beforeScript = 'echo $HOSTNAME' } 82 | conda { 83 | conda.enabled = true 84 | docker.enabled = false 85 | singularity.enabled = false 86 | podman.enabled = false 87 | shifter.enabled = false 88 | charliecloud.enabled = false 89 | } 90 | mamba { 91 | conda.enabled = true 92 | conda.useMamba = true 93 | docker.enabled = false 94 | singularity.enabled = false 95 | podman.enabled = false 96 | shifter.enabled = false 97 | charliecloud.enabled = false 98 | } 99 | docker { 100 | docker.enabled = true 101 | docker.userEmulation = true 102 | singularity.enabled = false 103 | podman.enabled = false 104 | shifter.enabled = false 105 | charliecloud.enabled = false 106 | } 107 | arm { 108 | docker.runOptions = '-u $(id -u):$(id -g) --platform=linux/amd64' 109 | } 110 | singularity { 111 | singularity.enabled = true 112 | singularity.autoMounts = true 113 | docker.enabled = false 114 | podman.enabled = false 115 | shifter.enabled = false 116 | charliecloud.enabled = false 117 | } 118 | podman { 119 | podman.enabled = true 120 | docker.enabled = false 121 | singularity.enabled = false 122 | shifter.enabled = false 123 | charliecloud.enabled = false 124 | } 125 | shifter { 126 | shifter.enabled = true 127 | docker.enabled = false 128 | singularity.enabled = false 129 | podman.enabled = false 130 | charliecloud.enabled = false 131 | } 132 | charliecloud { 133 | charliecloud.enabled = true 134 | docker.enabled = false 135 | singularity.enabled = false 136 | podman.enabled = false 137 | shifter.enabled = false 138 | } 139 | gitpod { 140 | executor.name = 'local' 141 | executor.cpus = 16 142 | executor.memory = 60.GB 143 | } 144 | test { includeConfig 'conf/test.config' } 145 | test_full { includeConfig 'conf/test_full.config' } 146 | } 147 | 148 | 149 | // Load igenomes.config if required 150 | if (!params.igenomes_ignore) { 151 | includeConfig 'conf/igenomes.config' 152 | } else { 153 | params.genomes = [:] 154 | } 155 | 156 | 157 | // Export these variables to prevent local Python/R libraries from conflicting with those in the container 158 | // 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. 159 | // 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. 160 | 161 | env { 162 | PYTHONNOUSERSITE = 1 163 | R_PROFILE_USER = "/.Rprofile" 164 | R_ENVIRON_USER = "/.Renviron" 165 | JULIA_DEPOT_PATH = "/usr/local/share/julia" 166 | } 167 | 168 | // Capture exit codes from upstream processes when piping 169 | process.shell = ['/bin/bash', '-euo', 'pipefail'] 170 | 171 | def trace_timestamp = new java.util.Date().format( 'yyyy-MM-dd_HH-mm-ss') 172 | timeline { 173 | enabled = true 174 | file = "${params.tracedir}/execution_timeline_${trace_timestamp}.html" 175 | } 176 | report { 177 | enabled = true 178 | file = "${params.tracedir}/execution_report_${trace_timestamp}.html" 179 | } 180 | trace { 181 | enabled = true 182 | file = "${params.tracedir}/execution_trace_${trace_timestamp}.txt" 183 | } 184 | dag { 185 | enabled = true 186 | file = "${params.tracedir}/pipeline_dag_${trace_timestamp}.html" 187 | } 188 | 189 | manifest { 190 | name = 'nf-core/spatialxe' 191 | author = """Florian Heyl""" 192 | homePage = 'https://github.com/nf-core/spatialxe' 193 | description = """A pipeline for spatialomics Xenium data.""" 194 | mainScript = 'main.nf' 195 | nextflowVersion = '!>=22.10.1' 196 | version = '1.0dev' 197 | doi = '' 198 | } 199 | 200 | // Load modules.config for DSL2 module specific options 201 | includeConfig 'conf/modules.config' 202 | 203 | // Function to ensure that resource requirements don't go beyond 204 | // a maximum limit 205 | def check_max(obj, type) { 206 | if (type == 'memory') { 207 | try { 208 | if (obj.compareTo(params.max_memory as nextflow.util.MemoryUnit) == 1) 209 | return params.max_memory as nextflow.util.MemoryUnit 210 | else 211 | return obj 212 | } catch (all) { 213 | println " ### ERROR ### Max memory '${params.max_memory}' is not valid! Using default value: $obj" 214 | return obj 215 | } 216 | } else if (type == 'time') { 217 | try { 218 | if (obj.compareTo(params.max_time as nextflow.util.Duration) == 1) 219 | return params.max_time as nextflow.util.Duration 220 | else 221 | return obj 222 | } catch (all) { 223 | println " ### ERROR ### Max time '${params.max_time}' is not valid! Using default value: $obj" 224 | return obj 225 | } 226 | } else if (type == 'cpus') { 227 | try { 228 | return Math.min( obj, params.max_cpus as int ) 229 | } catch (all) { 230 | println " ### ERROR ### Max cpus '${params.max_cpus}' is not valid! Using default value: $obj" 231 | return obj 232 | } 233 | } 234 | } 235 | -------------------------------------------------------------------------------- /CODE_OF_CONDUCT.md: -------------------------------------------------------------------------------- 1 | # Code of Conduct at nf-core (v1.0) 2 | 3 | ## Our Pledge 4 | 5 | In the interest of fostering an open, collaborative, and welcoming environment, we as contributors and maintainers of nf-core, pledge to making participation in our projects and community a harassment-free experience for everyone, regardless of: 6 | 7 | - Age 8 | - Body size 9 | - Familial status 10 | - Gender identity and expression 11 | - Geographical location 12 | - Level of experience 13 | - Nationality and national origins 14 | - Native language 15 | - Physical and neurological ability 16 | - Race or ethnicity 17 | - Religion 18 | - Sexual identity and orientation 19 | - Socioeconomic status 20 | 21 | Please note that the list above is alphabetised and is therefore not ranked in any order of preference or importance. 22 | 23 | ## Preamble 24 | 25 | > Note: This Code of Conduct (CoC) has been drafted by the nf-core Safety Officer and been edited after input from members of the nf-core team and others. "We", in this document, refers to the Safety Officer and members of the nf-core core team, both of whom are deemed to be members of the nf-core community and are therefore required to abide by this Code of Conduct. This document will amended periodically to keep it up-to-date, and in case of any dispute, the most current version will apply. 26 | 27 | An up-to-date list of members of the nf-core core team can be found [here](https://nf-co.re/about). Our current safety officer is Renuka Kudva. 28 | 29 | nf-core is a young and growing community that welcomes contributions from anyone with a shared vision for [Open Science Policies](https://www.fosteropenscience.eu/taxonomy/term/8). Open science policies encompass inclusive behaviours and we strive to build and maintain a safe and inclusive environment for all individuals. 30 | 31 | We have therefore adopted this code of conduct (CoC), which we require all members of our community and attendees in nf-core events to adhere to in all our workspaces at all times. Workspaces include but are not limited to Slack, meetings on Zoom, Jitsi, YouTube live etc. 32 | 33 | Our CoC will be strictly enforced and the nf-core team reserve the right to exclude participants who do not comply with our guidelines from our workspaces and future nf-core activities. 34 | 35 | We ask all members of our community to help maintain a supportive and productive workspace and to avoid behaviours that can make individuals feel unsafe or unwelcome. Please help us maintain and uphold this CoC. 36 | 37 | Questions, concerns or ideas on what we can include? Contact safety [at] nf-co [dot] re 38 | 39 | ## Our Responsibilities 40 | 41 | The safety officer is responsible for clarifying the standards of acceptable behavior and are expected to take appropriate and fair corrective action in response to any instances of unacceptable behaviour. 42 | 43 | The safety officer in consultation with the nf-core core team have the right and responsibility to remove, edit, or reject comments, commits, code, wiki edits, issues, and other contributions that are not aligned to this Code of Conduct, or to ban temporarily or permanently any contributor for other behaviors that they deem inappropriate, threatening, offensive, or harmful. 44 | 45 | Members of the core team or the safety officer who violate the CoC will be required to recuse themselves pending investigation. They will not have access to any reports of the violations and be subject to the same actions as others in violation of the CoC. 46 | 47 | ## When are where does this Code of Conduct apply? 48 | 49 | Participation in the nf-core community is contingent on following these guidelines in all our workspaces and events. This includes but is not limited to the following listed alphabetically and therefore in no order of preference: 50 | 51 | - Communicating with an official project email address. 52 | - Communicating with community members within the nf-core Slack channel. 53 | - Participating in hackathons organised by nf-core (both online and in-person events). 54 | - Participating in collaborative work on GitHub, Google Suite, community calls, mentorship meetings, email correspondence. 55 | - Participating in workshops, training, and seminar series organised by nf-core (both online and in-person events). This applies to events hosted on web-based platforms such as Zoom, Jitsi, YouTube live etc. 56 | - Representing nf-core on social media. This includes both official and personal accounts. 57 | 58 | ## nf-core cares 😊 59 | 60 | nf-core's CoC and expectations of respectful behaviours for all participants (including organisers and the nf-core team) include but are not limited to the following (listed in alphabetical order): 61 | 62 | - Ask for consent before sharing another community member’s personal information (including photographs) on social media. 63 | - Be respectful of differing viewpoints and experiences. We are all here to learn from one another and a difference in opinion can present a good learning opportunity. 64 | - Celebrate your accomplishments at events! (Get creative with your use of emojis 🎉 🥳 💯 🙌 !) 65 | - Demonstrate empathy towards other community members. (We don’t all have the same amount of time to dedicate to nf-core. If tasks are pending, don’t hesitate to gently remind members of your team. If you are leading a task, ask for help if you feel overwhelmed.) 66 | - Engage with and enquire after others. (This is especially important given the geographically remote nature of the nf-core community, so let’s do this the best we can) 67 | - Focus on what is best for the team and the community. (When in doubt, ask) 68 | - Graciously accept constructive criticism, yet be unafraid to question, deliberate, and learn. 69 | - Introduce yourself to members of the community. (We’ve all been outsiders and we know that talking to strangers can be hard for some, but remember we’re interested in getting to know you and your visions for open science!) 70 | - Show appreciation and **provide clear feedback**. (This is especially important because we don’t see each other in person and it can be harder to interpret subtleties. Also remember that not everyone understands a certain language to the same extent as you do, so **be clear in your communications to be kind.**) 71 | - Take breaks when you feel like you need them. 72 | - Using welcoming and inclusive language. (Participants are encouraged to display their chosen pronouns on Zoom or in communication on Slack.) 73 | 74 | ## nf-core frowns on 😕 75 | 76 | The following behaviours from any participants within the nf-core community (including the organisers) will be considered unacceptable under this code of conduct. Engaging or advocating for any of the following could result in expulsion from nf-core workspaces. 77 | 78 | - Deliberate intimidation, stalking or following and sustained disruption of communication among participants of the community. This includes hijacking shared screens through actions such as using the annotate tool in conferencing software such as Zoom. 79 | - “Doxing” i.e. posting (or threatening to post) another person’s personal identifying information online. 80 | - Spamming or trolling of individuals on social media. 81 | - Use of sexual or discriminatory imagery, comments, or jokes and unwelcome sexual attention. 82 | - Verbal and text comments that reinforce social structures of domination related to gender, gender identity and expression, sexual orientation, ability, physical appearance, body size, race, age, religion or work experience. 83 | 84 | ### Online Trolling 85 | 86 | The majority of nf-core interactions and events are held online. Unfortunately, holding events online comes with the added issue of online trolling. This is unacceptable, reports of such behaviour will be taken very seriously, and perpetrators will be excluded from activities immediately. 87 | 88 | All community members are required to ask members of the group they are working within for explicit consent prior to taking screenshots of individuals during video calls. 89 | 90 | ## Procedures for Reporting CoC violations 91 | 92 | If someone makes you feel uncomfortable through their behaviours or actions, report it as soon as possible. 93 | 94 | You can reach out to members of the [nf-core core team](https://nf-co.re/about) and they will forward your concerns to the safety officer(s). 95 | 96 | Issues directly concerning members of the core team will be dealt with by other members of the core team and the safety manager, and possible conflicts of interest will be taken into account. nf-core is also in discussions about having an ombudsperson, and details will be shared in due course. 97 | 98 | All reports will be handled with utmost discretion and confidentially. 99 | 100 | ## Attribution and Acknowledgements 101 | 102 | - The [Contributor Covenant, version 1.4](http://contributor-covenant.org/version/1/4) 103 | - The [OpenCon 2017 Code of Conduct](http://www.opencon2017.org/code_of_conduct) (CC BY 4.0 OpenCon organisers, SPARC and Right to Research Coalition) 104 | - The [eLife innovation sprint 2020 Code of Conduct](https://sprint.elifesciences.org/code-of-conduct/) 105 | - The [Mozilla Community Participation Guidelines v3.1](https://www.mozilla.org/en-US/about/governance/policies/participation/) (version 3.1, CC BY-SA 3.0 Mozilla) 106 | 107 | ## Changelog 108 | 109 | ### v1.0 - March 12th, 2021 110 | 111 | - Complete rewrite from original [Contributor Covenant](http://contributor-covenant.org/) CoC. 112 | -------------------------------------------------------------------------------- /bin/check_samplesheet.py: -------------------------------------------------------------------------------- 1 | #!/usr/bin/env python 2 | 3 | 4 | """Provide a command line tool to validate and transform tabular samplesheets.""" 5 | 6 | 7 | import argparse 8 | import csv 9 | import logging 10 | import sys 11 | from collections import Counter 12 | from pathlib import Path 13 | 14 | logger = logging.getLogger() 15 | 16 | 17 | class RowChecker: 18 | """ 19 | Define a service that can validate and transform each given row. 20 | 21 | Attributes: 22 | modified (list): A list of dicts, where each dict corresponds to a previously 23 | validated and transformed row. The order of rows is maintained. 24 | 25 | """ 26 | 27 | VALID_FORMATS = ( 28 | ".fq.gz", 29 | ".fastq.gz", 30 | ) 31 | 32 | def __init__( 33 | self, 34 | sample_col="sample", 35 | first_col="fastq_1", 36 | second_col="fastq_2", 37 | single_col="single_end", 38 | **kwargs, 39 | ): 40 | """ 41 | Initialize the row checker with the expected column names. 42 | 43 | Args: 44 | sample_col (str): The name of the column that contains the sample name 45 | (default "sample"). 46 | first_col (str): The name of the column that contains the first (or only) 47 | FASTQ file path (default "fastq_1"). 48 | second_col (str): The name of the column that contains the second (if any) 49 | FASTQ file path (default "fastq_2"). 50 | single_col (str): The name of the new column that will be inserted and 51 | records whether the sample contains single- or paired-end sequencing 52 | reads (default "single_end"). 53 | 54 | """ 55 | super().__init__(**kwargs) 56 | self._sample_col = sample_col 57 | self._first_col = first_col 58 | self._second_col = second_col 59 | self._single_col = single_col 60 | self._seen = set() 61 | self.modified = [] 62 | 63 | def validate_and_transform(self, row): 64 | """ 65 | Perform all validations on the given row and insert the read pairing status. 66 | 67 | Args: 68 | row (dict): A mapping from column headers (keys) to elements of that row 69 | (values). 70 | 71 | """ 72 | self._validate_sample(row) 73 | self._validate_first(row) 74 | self._validate_second(row) 75 | self._validate_pair(row) 76 | self._seen.add((row[self._sample_col], row[self._first_col])) 77 | self.modified.append(row) 78 | 79 | def _validate_sample(self, row): 80 | """Assert that the sample name exists and convert spaces to underscores.""" 81 | if len(row[self._sample_col]) <= 0: 82 | raise AssertionError("Sample input is required.") 83 | # Sanitize samples slightly. 84 | row[self._sample_col] = row[self._sample_col].replace(" ", "_") 85 | 86 | def _validate_first(self, row): 87 | """Assert that the first FASTQ entry is non-empty and has the right format.""" 88 | if len(row[self._first_col]) <= 0: 89 | raise AssertionError("At least the first FASTQ file is required.") 90 | self._validate_fastq_format(row[self._first_col]) 91 | 92 | def _validate_second(self, row): 93 | """Assert that the second FASTQ entry has the right format if it exists.""" 94 | if len(row[self._second_col]) > 0: 95 | self._validate_fastq_format(row[self._second_col]) 96 | 97 | def _validate_pair(self, row): 98 | """Assert that read pairs have the same file extension. Report pair status.""" 99 | if row[self._first_col] and row[self._second_col]: 100 | row[self._single_col] = False 101 | first_col_suffix = Path(row[self._first_col]).suffixes[-2:] 102 | second_col_suffix = Path(row[self._second_col]).suffixes[-2:] 103 | if first_col_suffix != second_col_suffix: 104 | raise AssertionError("FASTQ pairs must have the same file extensions.") 105 | else: 106 | row[self._single_col] = True 107 | 108 | def _validate_fastq_format(self, filename): 109 | """Assert that a given filename has one of the expected FASTQ extensions.""" 110 | if not any(filename.endswith(extension) for extension in self.VALID_FORMATS): 111 | raise AssertionError( 112 | f"The FASTQ file has an unrecognized extension: {filename}\n" 113 | f"It should be one of: {', '.join(self.VALID_FORMATS)}" 114 | ) 115 | 116 | def validate_unique_samples(self): 117 | """ 118 | Assert that the combination of sample name and FASTQ filename is unique. 119 | 120 | In addition to the validation, also rename all samples to have a suffix of _T{n}, where n is the 121 | number of times the same sample exist, but with different FASTQ files, e.g., multiple runs per experiment. 122 | 123 | """ 124 | if len(self._seen) != len(self.modified): 125 | raise AssertionError("The pair of sample name and FASTQ must be unique.") 126 | seen = Counter() 127 | for row in self.modified: 128 | sample = row[self._sample_col] 129 | seen[sample] += 1 130 | row[self._sample_col] = f"{sample}_T{seen[sample]}" 131 | 132 | 133 | def read_head(handle, num_lines=10): 134 | """Read the specified number of lines from the current position in the file.""" 135 | lines = [] 136 | for idx, line in enumerate(handle): 137 | if idx == num_lines: 138 | break 139 | lines.append(line) 140 | return "".join(lines) 141 | 142 | 143 | def sniff_format(handle): 144 | """ 145 | Detect the tabular format. 146 | 147 | Args: 148 | handle (text file): A handle to a `text file`_ object. The read position is 149 | expected to be at the beginning (index 0). 150 | 151 | Returns: 152 | csv.Dialect: The detected tabular format. 153 | 154 | .. _text file: 155 | https://docs.python.org/3/glossary.html#term-text-file 156 | 157 | """ 158 | peek = read_head(handle) 159 | handle.seek(0) 160 | sniffer = csv.Sniffer() 161 | if not sniffer.has_header(peek): 162 | logger.critical("The given sample sheet does not appear to contain a header.") 163 | sys.exit(1) 164 | dialect = sniffer.sniff(peek) 165 | return dialect 166 | 167 | 168 | def check_samplesheet(file_in, file_out): 169 | """ 170 | Check that the tabular samplesheet has the structure expected by nf-core pipelines. 171 | 172 | Validate the general shape of the table, expected columns, and each row. Also add 173 | an additional column which records whether one or two FASTQ reads were found. 174 | 175 | Args: 176 | file_in (pathlib.Path): The given tabular samplesheet. The format can be either 177 | CSV, TSV, or any other format automatically recognized by ``csv.Sniffer``. 178 | file_out (pathlib.Path): Where the validated and transformed samplesheet should 179 | be created; always in CSV format. 180 | 181 | Example: 182 | This function checks that the samplesheet follows the following structure, 183 | see also the `viral recon samplesheet`_:: 184 | 185 | sample,fastq_1,fastq_2 186 | SAMPLE_PE,SAMPLE_PE_RUN1_1.fastq.gz,SAMPLE_PE_RUN1_2.fastq.gz 187 | SAMPLE_PE,SAMPLE_PE_RUN2_1.fastq.gz,SAMPLE_PE_RUN2_2.fastq.gz 188 | SAMPLE_SE,SAMPLE_SE_RUN1_1.fastq.gz, 189 | 190 | .. _viral recon samplesheet: 191 | https://raw.githubusercontent.com/nf-core/test-datasets/viralrecon/samplesheet/samplesheet_test_illumina_amplicon.csv 192 | 193 | """ 194 | required_columns = {"sample", "fastq_1", "fastq_2"} 195 | # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. 196 | with file_in.open(newline="") as in_handle: 197 | reader = csv.DictReader(in_handle, dialect=sniff_format(in_handle)) 198 | # Validate the existence of the expected header columns. 199 | if not required_columns.issubset(reader.fieldnames): 200 | req_cols = ", ".join(required_columns) 201 | logger.critical(f"The sample sheet **must** contain these column headers: {req_cols}.") 202 | sys.exit(1) 203 | # Validate each row. 204 | checker = RowChecker() 205 | for i, row in enumerate(reader): 206 | try: 207 | checker.validate_and_transform(row) 208 | except AssertionError as error: 209 | logger.critical(f"{str(error)} On line {i + 2}.") 210 | sys.exit(1) 211 | checker.validate_unique_samples() 212 | header = list(reader.fieldnames) 213 | header.insert(1, "single_end") 214 | # See https://docs.python.org/3.9/library/csv.html#id3 to read up on `newline=""`. 215 | with file_out.open(mode="w", newline="") as out_handle: 216 | writer = csv.DictWriter(out_handle, header, delimiter=",") 217 | writer.writeheader() 218 | for row in checker.modified: 219 | writer.writerow(row) 220 | 221 | 222 | def parse_args(argv=None): 223 | """Define and immediately parse command line arguments.""" 224 | parser = argparse.ArgumentParser( 225 | description="Validate and transform a tabular samplesheet.", 226 | epilog="Example: python check_samplesheet.py samplesheet.csv samplesheet.valid.csv", 227 | ) 228 | parser.add_argument( 229 | "file_in", 230 | metavar="FILE_IN", 231 | type=Path, 232 | help="Tabular input samplesheet in CSV or TSV format.", 233 | ) 234 | parser.add_argument( 235 | "file_out", 236 | metavar="FILE_OUT", 237 | type=Path, 238 | help="Transformed output samplesheet in CSV format.", 239 | ) 240 | parser.add_argument( 241 | "-l", 242 | "--log-level", 243 | help="The desired log level (default WARNING).", 244 | choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"), 245 | default="WARNING", 246 | ) 247 | return parser.parse_args(argv) 248 | 249 | 250 | def main(argv=None): 251 | """Coordinate argument parsing and program execution.""" 252 | args = parse_args(argv) 253 | logging.basicConfig(level=args.log_level, format="[%(levelname)s] %(message)s") 254 | if not args.file_in.is_file(): 255 | logger.error(f"The given input file {args.file_in} was not found!") 256 | sys.exit(2) 257 | args.file_out.parent.mkdir(parents=True, exist_ok=True) 258 | check_samplesheet(args.file_in, args.file_out) 259 | 260 | 261 | if __name__ == "__main__": 262 | sys.exit(main()) 263 | -------------------------------------------------------------------------------- /nextflow_schema.json: -------------------------------------------------------------------------------- 1 | { 2 | "$schema": "http://json-schema.org/draft-07/schema", 3 | "$id": "https://raw.githubusercontent.com/nf-core/spatialxe/master/nextflow_schema.json", 4 | "title": "nf-core/spatialxe pipeline parameters", 5 | "description": "A pipeline for spatialomics Xenium data.", 6 | "type": "object", 7 | "definitions": { 8 | "input_output_options": { 9 | "title": "Input/output options", 10 | "type": "object", 11 | "fa_icon": "fas fa-terminal", 12 | "description": "Define where the pipeline should find input data and save output data.", 13 | "required": ["input", "outdir"], 14 | "properties": { 15 | "input": { 16 | "type": "string", 17 | "format": "file-path", 18 | "mimetype": "text/csv", 19 | "pattern": "^\\S+\\.csv$", 20 | "schema": "assets/schema_input.json", 21 | "description": "Path to comma-separated file containing information about the samples in the experiment.", 22 | "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/spatialxe/usage#samplesheet-input).", 23 | "fa_icon": "fas fa-file-csv" 24 | }, 25 | "outdir": { 26 | "type": "string", 27 | "format": "directory-path", 28 | "description": "The output directory where the results will be saved. You have to use absolute paths to storage on Cloud infrastructure.", 29 | "fa_icon": "fas fa-folder-open" 30 | }, 31 | "email": { 32 | "type": "string", 33 | "description": "Email address for completion summary.", 34 | "fa_icon": "fas fa-envelope", 35 | "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.", 36 | "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$" 37 | }, 38 | "multiqc_title": { 39 | "type": "string", 40 | "description": "MultiQC report title. Printed as page header, used for filename if not otherwise specified.", 41 | "fa_icon": "fas fa-file-signature" 42 | } 43 | } 44 | }, 45 | "reference_genome_options": { 46 | "title": "Reference genome options", 47 | "type": "object", 48 | "fa_icon": "fas fa-dna", 49 | "description": "Reference genome related files and options required for the workflow.", 50 | "properties": { 51 | "genome": { 52 | "type": "string", 53 | "description": "Name of iGenomes reference.", 54 | "fa_icon": "fas fa-book", 55 | "help_text": "If using a reference genome configured in the pipeline using iGenomes, use this parameter to give the ID for the reference. This is then used to build the full paths for all required reference genome files e.g. `--genome GRCh38`. \n\nSee the [nf-core website docs](https://nf-co.re/usage/reference_genomes) for more details." 56 | }, 57 | "fasta": { 58 | "type": "string", 59 | "format": "file-path", 60 | "mimetype": "text/plain", 61 | "pattern": "^\\S+\\.fn?a(sta)?(\\.gz)?$", 62 | "description": "Path to FASTA genome file.", 63 | "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.", 64 | "fa_icon": "far fa-file-code" 65 | }, 66 | "igenomes_base": { 67 | "type": "string", 68 | "format": "directory-path", 69 | "description": "Directory / URL base for iGenomes references.", 70 | "default": "s3://ngi-igenomes/igenomes", 71 | "fa_icon": "fas fa-cloud-download-alt", 72 | "hidden": true 73 | }, 74 | "igenomes_ignore": { 75 | "type": "boolean", 76 | "description": "Do not load the iGenomes reference config.", 77 | "fa_icon": "fas fa-ban", 78 | "hidden": true, 79 | "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`." 80 | } 81 | } 82 | }, 83 | "institutional_config_options": { 84 | "title": "Institutional config options", 85 | "type": "object", 86 | "fa_icon": "fas fa-university", 87 | "description": "Parameters used to describe centralised config profiles. These should not be edited.", 88 | "help_text": "The centralised nf-core configuration profiles use a handful of pipeline parameters to describe themselves. This information is then printed to the Nextflow log when you run a pipeline. You should not need to change these values when you run a pipeline.", 89 | "properties": { 90 | "custom_config_version": { 91 | "type": "string", 92 | "description": "Git commit id for Institutional configs.", 93 | "default": "master", 94 | "hidden": true, 95 | "fa_icon": "fas fa-users-cog" 96 | }, 97 | "custom_config_base": { 98 | "type": "string", 99 | "description": "Base directory for Institutional configs.", 100 | "default": "https://raw.githubusercontent.com/nf-core/configs/master", 101 | "hidden": true, 102 | "help_text": "If you're running offline, Nextflow will not be able to fetch the institutional config files from the internet. If you don't need them, then this is not a problem. If you do need them, you should download the files from the repo and tell Nextflow where to find them with this parameter.", 103 | "fa_icon": "fas fa-users-cog" 104 | }, 105 | "config_profile_name": { 106 | "type": "string", 107 | "description": "Institutional config name.", 108 | "hidden": true, 109 | "fa_icon": "fas fa-users-cog" 110 | }, 111 | "config_profile_description": { 112 | "type": "string", 113 | "description": "Institutional config description.", 114 | "hidden": true, 115 | "fa_icon": "fas fa-users-cog" 116 | }, 117 | "config_profile_contact": { 118 | "type": "string", 119 | "description": "Institutional config contact information.", 120 | "hidden": true, 121 | "fa_icon": "fas fa-users-cog" 122 | }, 123 | "config_profile_url": { 124 | "type": "string", 125 | "description": "Institutional config URL link.", 126 | "hidden": true, 127 | "fa_icon": "fas fa-users-cog" 128 | } 129 | } 130 | }, 131 | "max_job_request_options": { 132 | "title": "Max job request options", 133 | "type": "object", 134 | "fa_icon": "fab fa-acquisitions-incorporated", 135 | "description": "Set the top limit for requested resources for any single job.", 136 | "help_text": "If you are running on a smaller system, a pipeline step requesting more resources than are available may cause the Nextflow to stop the run with an error. These options allow you to cap the maximum resources requested by any single job so that the pipeline will run on your system.\n\nNote that you can not _increase_ the resources requested by any job using these options. For that you will need your own configuration file. See [the nf-core website](https://nf-co.re/usage/configuration) for details.", 137 | "properties": { 138 | "max_cpus": { 139 | "type": "integer", 140 | "description": "Maximum number of CPUs that can be requested for any single job.", 141 | "default": 16, 142 | "fa_icon": "fas fa-microchip", 143 | "hidden": true, 144 | "help_text": "Use to set an upper-limit for the CPU requirement for each process. Should be an integer e.g. `--max_cpus 1`" 145 | }, 146 | "max_memory": { 147 | "type": "string", 148 | "description": "Maximum amount of memory that can be requested for any single job.", 149 | "default": "128.GB", 150 | "fa_icon": "fas fa-memory", 151 | "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", 152 | "hidden": true, 153 | "help_text": "Use to set an upper-limit for the memory requirement for each process. Should be a string in the format integer-unit e.g. `--max_memory '8.GB'`" 154 | }, 155 | "max_time": { 156 | "type": "string", 157 | "description": "Maximum amount of time that can be requested for any single job.", 158 | "default": "240.h", 159 | "fa_icon": "far fa-clock", 160 | "pattern": "^(\\d+\\.?\\s*(s|m|h|day)\\s*)+$", 161 | "hidden": true, 162 | "help_text": "Use to set an upper-limit for the time requirement for each process. Should be a string in the format integer-unit e.g. `--max_time '2.h'`" 163 | } 164 | } 165 | }, 166 | "generic_options": { 167 | "title": "Generic options", 168 | "type": "object", 169 | "fa_icon": "fas fa-file-import", 170 | "description": "Less common options for the pipeline, typically set in a config file.", 171 | "help_text": "These options are common to all nf-core pipelines and allow you to customise some of the core preferences for how the pipeline runs.\n\nTypically these options would be set in a Nextflow config file loaded for all pipeline runs, such as `~/.nextflow/config`.", 172 | "properties": { 173 | "help": { 174 | "type": "boolean", 175 | "description": "Display help text.", 176 | "fa_icon": "fas fa-question-circle", 177 | "hidden": true 178 | }, 179 | "version": { 180 | "type": "boolean", 181 | "description": "Display version and exit.", 182 | "fa_icon": "fas fa-question-circle", 183 | "hidden": true 184 | }, 185 | "publish_dir_mode": { 186 | "type": "string", 187 | "default": "copy", 188 | "description": "Method used to save pipeline results to output directory.", 189 | "help_text": "The Nextflow `publishDir` option specifies which intermediate files should be saved to the output directory. This option tells the pipeline what method should be used to move these files. See [Nextflow docs](https://www.nextflow.io/docs/latest/process.html#publishdir) for details.", 190 | "fa_icon": "fas fa-copy", 191 | "enum": ["symlink", "rellink", "link", "copy", "copyNoFollow", "move"], 192 | "hidden": true 193 | }, 194 | "email_on_fail": { 195 | "type": "string", 196 | "description": "Email address for completion summary, only when pipeline fails.", 197 | "fa_icon": "fas fa-exclamation-triangle", 198 | "pattern": "^([a-zA-Z0-9_\\-\\.]+)@([a-zA-Z0-9_\\-\\.]+)\\.([a-zA-Z]{2,5})$", 199 | "help_text": "An email address to send a summary email to when the pipeline is completed - ONLY sent if the pipeline does not exit successfully.", 200 | "hidden": true 201 | }, 202 | "plaintext_email": { 203 | "type": "boolean", 204 | "description": "Send plain-text email instead of HTML.", 205 | "fa_icon": "fas fa-remove-format", 206 | "hidden": true 207 | }, 208 | "max_multiqc_email_size": { 209 | "type": "string", 210 | "description": "File size limit when attaching MultiQC reports to summary emails.", 211 | "pattern": "^\\d+(\\.\\d+)?\\.?\\s*(K|M|G|T)?B$", 212 | "default": "25.MB", 213 | "fa_icon": "fas fa-file-upload", 214 | "hidden": true 215 | }, 216 | "monochrome_logs": { 217 | "type": "boolean", 218 | "description": "Do not use coloured log outputs.", 219 | "fa_icon": "fas fa-palette", 220 | "hidden": true 221 | }, 222 | "hook_url": { 223 | "type": "string", 224 | "description": "Incoming hook URL for messaging service", 225 | "fa_icon": "fas fa-people-group", 226 | "help_text": "Incoming hook URL for messaging service. Currently, MS Teams and Slack are supported.", 227 | "hidden": true 228 | }, 229 | "multiqc_config": { 230 | "type": "string", 231 | "description": "Custom config file to supply to MultiQC.", 232 | "fa_icon": "fas fa-cog", 233 | "hidden": true 234 | }, 235 | "multiqc_logo": { 236 | "type": "string", 237 | "description": "Custom logo file to supply to MultiQC. File name must also be set in the MultiQC config file", 238 | "fa_icon": "fas fa-image", 239 | "hidden": true 240 | }, 241 | "multiqc_methods_description": { 242 | "type": "string", 243 | "description": "Custom MultiQC yaml file containing HTML including a methods description.", 244 | "fa_icon": "fas fa-cog" 245 | }, 246 | "tracedir": { 247 | "type": "string", 248 | "description": "Directory to keep pipeline Nextflow logs and reports.", 249 | "default": "${params.outdir}/pipeline_info", 250 | "fa_icon": "fas fa-cogs", 251 | "hidden": true 252 | }, 253 | "validate_params": { 254 | "type": "boolean", 255 | "description": "Boolean whether to validate parameters against the schema at runtime", 256 | "default": true, 257 | "fa_icon": "fas fa-check-square", 258 | "hidden": true 259 | }, 260 | "show_hidden_params": { 261 | "type": "boolean", 262 | "fa_icon": "far fa-eye-slash", 263 | "description": "Show all params when using `--help`", 264 | "hidden": true, 265 | "help_text": "By default, parameters set as _hidden_ in the schema are not shown on the command line when a user runs with `--help`. Specifying this option will tell the pipeline to show all parameters." 266 | } 267 | } 268 | } 269 | }, 270 | "allOf": [ 271 | { 272 | "$ref": "#/definitions/input_output_options" 273 | }, 274 | { 275 | "$ref": "#/definitions/reference_genome_options" 276 | }, 277 | { 278 | "$ref": "#/definitions/institutional_config_options" 279 | }, 280 | { 281 | "$ref": "#/definitions/max_job_request_options" 282 | }, 283 | { 284 | "$ref": "#/definitions/generic_options" 285 | } 286 | ] 287 | } 288 | -------------------------------------------------------------------------------- /lib/NfcoreTemplate.groovy: -------------------------------------------------------------------------------- 1 | // 2 | // This file holds several functions used within the nf-core pipeline template. 3 | // 4 | 5 | import org.yaml.snakeyaml.Yaml 6 | 7 | class NfcoreTemplate { 8 | 9 | // 10 | // Check AWS Batch related parameters have been specified correctly 11 | // 12 | public static void awsBatch(workflow, params) { 13 | if (workflow.profile.contains('awsbatch')) { 14 | // Check params.awsqueue and params.awsregion have been set if running on AWSBatch 15 | assert (params.awsqueue && params.awsregion) : "Specify correct --awsqueue and --awsregion parameters on AWSBatch!" 16 | // Check outdir paths to be S3 buckets if running on AWSBatch 17 | assert params.outdir.startsWith('s3:') : "Outdir not on S3 - specify S3 Bucket to run on AWSBatch!" 18 | } 19 | } 20 | 21 | // 22 | // Warn if a -profile or Nextflow config has not been provided to run the pipeline 23 | // 24 | public static void checkConfigProvided(workflow, log) { 25 | if (workflow.profile == 'standard' && workflow.configFiles.size() <= 1) { 26 | log.warn "[$workflow.manifest.name] You are attempting to run the pipeline without any custom configuration!\n\n" + 27 | "This will be dependent on your local compute environment but can be achieved via one or more of the following:\n" + 28 | " (1) Using an existing pipeline profile e.g. `-profile docker` or `-profile singularity`\n" + 29 | " (2) Using an existing nf-core/configs for your Institution e.g. `-profile crick` or `-profile uppmax`\n" + 30 | " (3) Using your own local custom config e.g. `-c /path/to/your/custom.config`\n\n" + 31 | "Please refer to the quick start section and usage docs for the pipeline.\n " 32 | } 33 | } 34 | 35 | // 36 | // Generate version string 37 | // 38 | public static String version(workflow) { 39 | String version_string = "" 40 | 41 | if (workflow.manifest.version) { 42 | def prefix_v = workflow.manifest.version[0] != 'v' ? 'v' : '' 43 | version_string += "${prefix_v}${workflow.manifest.version}" 44 | } 45 | 46 | if (workflow.commitId) { 47 | def git_shortsha = workflow.commitId.substring(0, 7) 48 | version_string += "-g${git_shortsha}" 49 | } 50 | 51 | return version_string 52 | } 53 | 54 | // 55 | // Construct and send completion email 56 | // 57 | public static void email(workflow, params, summary_params, projectDir, log, multiqc_report=[]) { 58 | 59 | // Set up the e-mail variables 60 | def subject = "[$workflow.manifest.name] Successful: $workflow.runName" 61 | if (!workflow.success) { 62 | subject = "[$workflow.manifest.name] FAILED: $workflow.runName" 63 | } 64 | 65 | def summary = [:] 66 | for (group in summary_params.keySet()) { 67 | summary << summary_params[group] 68 | } 69 | 70 | def misc_fields = [:] 71 | misc_fields['Date Started'] = workflow.start 72 | misc_fields['Date Completed'] = workflow.complete 73 | misc_fields['Pipeline script file path'] = workflow.scriptFile 74 | misc_fields['Pipeline script hash ID'] = workflow.scriptId 75 | if (workflow.repository) misc_fields['Pipeline repository Git URL'] = workflow.repository 76 | if (workflow.commitId) misc_fields['Pipeline repository Git Commit'] = workflow.commitId 77 | if (workflow.revision) misc_fields['Pipeline Git branch/tag'] = workflow.revision 78 | misc_fields['Nextflow Version'] = workflow.nextflow.version 79 | misc_fields['Nextflow Build'] = workflow.nextflow.build 80 | misc_fields['Nextflow Compile Timestamp'] = workflow.nextflow.timestamp 81 | 82 | def email_fields = [:] 83 | email_fields['version'] = NfcoreTemplate.version(workflow) 84 | email_fields['runName'] = workflow.runName 85 | email_fields['success'] = workflow.success 86 | email_fields['dateComplete'] = workflow.complete 87 | email_fields['duration'] = workflow.duration 88 | email_fields['exitStatus'] = workflow.exitStatus 89 | email_fields['errorMessage'] = (workflow.errorMessage ?: 'None') 90 | email_fields['errorReport'] = (workflow.errorReport ?: 'None') 91 | email_fields['commandLine'] = workflow.commandLine 92 | email_fields['projectDir'] = workflow.projectDir 93 | email_fields['summary'] = summary << misc_fields 94 | 95 | // On success try attach the multiqc report 96 | def mqc_report = null 97 | try { 98 | if (workflow.success) { 99 | mqc_report = multiqc_report.getVal() 100 | if (mqc_report.getClass() == ArrayList && mqc_report.size() >= 1) { 101 | if (mqc_report.size() > 1) { 102 | log.warn "[$workflow.manifest.name] Found multiple reports from process 'MULTIQC', will use only one" 103 | } 104 | mqc_report = mqc_report[0] 105 | } 106 | } 107 | } catch (all) { 108 | if (multiqc_report) { 109 | log.warn "[$workflow.manifest.name] Could not attach MultiQC report to summary email" 110 | } 111 | } 112 | 113 | // Check if we are only sending emails on failure 114 | def email_address = params.email 115 | if (!params.email && params.email_on_fail && !workflow.success) { 116 | email_address = params.email_on_fail 117 | } 118 | 119 | // Render the TXT template 120 | def engine = new groovy.text.GStringTemplateEngine() 121 | def tf = new File("$projectDir/assets/email_template.txt") 122 | def txt_template = engine.createTemplate(tf).make(email_fields) 123 | def email_txt = txt_template.toString() 124 | 125 | // Render the HTML template 126 | def hf = new File("$projectDir/assets/email_template.html") 127 | def html_template = engine.createTemplate(hf).make(email_fields) 128 | def email_html = html_template.toString() 129 | 130 | // Render the sendmail template 131 | def max_multiqc_email_size = params.max_multiqc_email_size as nextflow.util.MemoryUnit 132 | def smail_fields = [ email: email_address, subject: subject, email_txt: email_txt, email_html: email_html, projectDir: "$projectDir", mqcFile: mqc_report, mqcMaxSize: max_multiqc_email_size.toBytes() ] 133 | def sf = new File("$projectDir/assets/sendmail_template.txt") 134 | def sendmail_template = engine.createTemplate(sf).make(smail_fields) 135 | def sendmail_html = sendmail_template.toString() 136 | 137 | // Send the HTML e-mail 138 | Map colors = logColours(params.monochrome_logs) 139 | if (email_address) { 140 | try { 141 | if (params.plaintext_email) { throw GroovyException('Send plaintext e-mail, not HTML') } 142 | // Try to send HTML e-mail using sendmail 143 | [ 'sendmail', '-t' ].execute() << sendmail_html 144 | log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (sendmail)-" 145 | } catch (all) { 146 | // Catch failures and try with plaintext 147 | def mail_cmd = [ 'mail', '-s', subject, '--content-type=text/html', email_address ] 148 | if ( mqc_report.size() <= max_multiqc_email_size.toBytes() ) { 149 | mail_cmd += [ '-A', mqc_report ] 150 | } 151 | mail_cmd.execute() << email_html 152 | log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Sent summary e-mail to $email_address (mail)-" 153 | } 154 | } 155 | 156 | // Write summary e-mail HTML to a file 157 | def output_d = new File("${params.outdir}/pipeline_info/") 158 | if (!output_d.exists()) { 159 | output_d.mkdirs() 160 | } 161 | def output_hf = new File(output_d, "pipeline_report.html") 162 | output_hf.withWriter { w -> w << email_html } 163 | def output_tf = new File(output_d, "pipeline_report.txt") 164 | output_tf.withWriter { w -> w << email_txt } 165 | } 166 | 167 | // 168 | // Construct and send a notification to a web server as JSON 169 | // e.g. Microsoft Teams and Slack 170 | // 171 | public static void IM_notification(workflow, params, summary_params, projectDir, log) { 172 | def hook_url = params.hook_url 173 | 174 | def summary = [:] 175 | for (group in summary_params.keySet()) { 176 | summary << summary_params[group] 177 | } 178 | 179 | def misc_fields = [:] 180 | misc_fields['start'] = workflow.start 181 | misc_fields['complete'] = workflow.complete 182 | misc_fields['scriptfile'] = workflow.scriptFile 183 | misc_fields['scriptid'] = workflow.scriptId 184 | if (workflow.repository) misc_fields['repository'] = workflow.repository 185 | if (workflow.commitId) misc_fields['commitid'] = workflow.commitId 186 | if (workflow.revision) misc_fields['revision'] = workflow.revision 187 | misc_fields['nxf_version'] = workflow.nextflow.version 188 | misc_fields['nxf_build'] = workflow.nextflow.build 189 | misc_fields['nxf_timestamp'] = workflow.nextflow.timestamp 190 | 191 | def msg_fields = [:] 192 | msg_fields['version'] = NfcoreTemplate.version(workflow) 193 | msg_fields['runName'] = workflow.runName 194 | msg_fields['success'] = workflow.success 195 | msg_fields['dateComplete'] = workflow.complete 196 | msg_fields['duration'] = workflow.duration 197 | msg_fields['exitStatus'] = workflow.exitStatus 198 | msg_fields['errorMessage'] = (workflow.errorMessage ?: 'None') 199 | msg_fields['errorReport'] = (workflow.errorReport ?: 'None') 200 | msg_fields['commandLine'] = workflow.commandLine.replaceFirst(/ +--hook_url +[^ ]+/, "") 201 | msg_fields['projectDir'] = workflow.projectDir 202 | msg_fields['summary'] = summary << misc_fields 203 | 204 | // Render the JSON template 205 | def engine = new groovy.text.GStringTemplateEngine() 206 | // Different JSON depending on the service provider 207 | // Defaults to "Adaptive Cards" (https://adaptivecards.io), except Slack which has its own format 208 | def json_path = hook_url.contains("hooks.slack.com") ? "slackreport.json" : "adaptivecard.json" 209 | def hf = new File("$projectDir/assets/${json_path}") 210 | def json_template = engine.createTemplate(hf).make(msg_fields) 211 | def json_message = json_template.toString() 212 | 213 | // POST 214 | def post = new URL(hook_url).openConnection(); 215 | post.setRequestMethod("POST") 216 | post.setDoOutput(true) 217 | post.setRequestProperty("Content-Type", "application/json") 218 | post.getOutputStream().write(json_message.getBytes("UTF-8")); 219 | def postRC = post.getResponseCode(); 220 | if (! postRC.equals(200)) { 221 | log.warn(post.getErrorStream().getText()); 222 | } 223 | } 224 | 225 | // 226 | // Print pipeline summary on completion 227 | // 228 | public static void summary(workflow, params, log) { 229 | Map colors = logColours(params.monochrome_logs) 230 | if (workflow.success) { 231 | if (workflow.stats.ignoredCount == 0) { 232 | log.info "-${colors.purple}[$workflow.manifest.name]${colors.green} Pipeline completed successfully${colors.reset}-" 233 | } else { 234 | log.info "-${colors.purple}[$workflow.manifest.name]${colors.yellow} Pipeline completed successfully, but with errored process(es) ${colors.reset}-" 235 | } 236 | } else { 237 | log.info "-${colors.purple}[$workflow.manifest.name]${colors.red} Pipeline completed with errors${colors.reset}-" 238 | } 239 | } 240 | 241 | // 242 | // ANSII Colours used for terminal logging 243 | // 244 | public static Map logColours(Boolean monochrome_logs) { 245 | Map colorcodes = [:] 246 | 247 | // Reset / Meta 248 | colorcodes['reset'] = monochrome_logs ? '' : "\033[0m" 249 | colorcodes['bold'] = monochrome_logs ? '' : "\033[1m" 250 | colorcodes['dim'] = monochrome_logs ? '' : "\033[2m" 251 | colorcodes['underlined'] = monochrome_logs ? '' : "\033[4m" 252 | colorcodes['blink'] = monochrome_logs ? '' : "\033[5m" 253 | colorcodes['reverse'] = monochrome_logs ? '' : "\033[7m" 254 | colorcodes['hidden'] = monochrome_logs ? '' : "\033[8m" 255 | 256 | // Regular Colors 257 | colorcodes['black'] = monochrome_logs ? '' : "\033[0;30m" 258 | colorcodes['red'] = monochrome_logs ? '' : "\033[0;31m" 259 | colorcodes['green'] = monochrome_logs ? '' : "\033[0;32m" 260 | colorcodes['yellow'] = monochrome_logs ? '' : "\033[0;33m" 261 | colorcodes['blue'] = monochrome_logs ? '' : "\033[0;34m" 262 | colorcodes['purple'] = monochrome_logs ? '' : "\033[0;35m" 263 | colorcodes['cyan'] = monochrome_logs ? '' : "\033[0;36m" 264 | colorcodes['white'] = monochrome_logs ? '' : "\033[0;37m" 265 | 266 | // Bold 267 | colorcodes['bblack'] = monochrome_logs ? '' : "\033[1;30m" 268 | colorcodes['bred'] = monochrome_logs ? '' : "\033[1;31m" 269 | colorcodes['bgreen'] = monochrome_logs ? '' : "\033[1;32m" 270 | colorcodes['byellow'] = monochrome_logs ? '' : "\033[1;33m" 271 | colorcodes['bblue'] = monochrome_logs ? '' : "\033[1;34m" 272 | colorcodes['bpurple'] = monochrome_logs ? '' : "\033[1;35m" 273 | colorcodes['bcyan'] = monochrome_logs ? '' : "\033[1;36m" 274 | colorcodes['bwhite'] = monochrome_logs ? '' : "\033[1;37m" 275 | 276 | // Underline 277 | colorcodes['ublack'] = monochrome_logs ? '' : "\033[4;30m" 278 | colorcodes['ured'] = monochrome_logs ? '' : "\033[4;31m" 279 | colorcodes['ugreen'] = monochrome_logs ? '' : "\033[4;32m" 280 | colorcodes['uyellow'] = monochrome_logs ? '' : "\033[4;33m" 281 | colorcodes['ublue'] = monochrome_logs ? '' : "\033[4;34m" 282 | colorcodes['upurple'] = monochrome_logs ? '' : "\033[4;35m" 283 | colorcodes['ucyan'] = monochrome_logs ? '' : "\033[4;36m" 284 | colorcodes['uwhite'] = monochrome_logs ? '' : "\033[4;37m" 285 | 286 | // High Intensity 287 | colorcodes['iblack'] = monochrome_logs ? '' : "\033[0;90m" 288 | colorcodes['ired'] = monochrome_logs ? '' : "\033[0;91m" 289 | colorcodes['igreen'] = monochrome_logs ? '' : "\033[0;92m" 290 | colorcodes['iyellow'] = monochrome_logs ? '' : "\033[0;93m" 291 | colorcodes['iblue'] = monochrome_logs ? '' : "\033[0;94m" 292 | colorcodes['ipurple'] = monochrome_logs ? '' : "\033[0;95m" 293 | colorcodes['icyan'] = monochrome_logs ? '' : "\033[0;96m" 294 | colorcodes['iwhite'] = monochrome_logs ? '' : "\033[0;97m" 295 | 296 | // Bold High Intensity 297 | colorcodes['biblack'] = monochrome_logs ? '' : "\033[1;90m" 298 | colorcodes['bired'] = monochrome_logs ? '' : "\033[1;91m" 299 | colorcodes['bigreen'] = monochrome_logs ? '' : "\033[1;92m" 300 | colorcodes['biyellow'] = monochrome_logs ? '' : "\033[1;93m" 301 | colorcodes['biblue'] = monochrome_logs ? '' : "\033[1;94m" 302 | colorcodes['bipurple'] = monochrome_logs ? '' : "\033[1;95m" 303 | colorcodes['bicyan'] = monochrome_logs ? '' : "\033[1;96m" 304 | colorcodes['biwhite'] = monochrome_logs ? '' : "\033[1;97m" 305 | 306 | return colorcodes 307 | } 308 | 309 | // 310 | // Does what is says on the tin 311 | // 312 | public static String dashedLine(monochrome_logs) { 313 | Map colors = logColours(monochrome_logs) 314 | return "-${colors.dim}----------------------------------------------------${colors.reset}-" 315 | } 316 | 317 | // 318 | // nf-core logo 319 | // 320 | public static String logo(workflow, monochrome_logs) { 321 | Map colors = logColours(monochrome_logs) 322 | String workflow_version = NfcoreTemplate.version(workflow) 323 | String.format( 324 | """\n 325 | ${dashedLine(monochrome_logs)} 326 | ${colors.green},--.${colors.black}/${colors.green},-.${colors.reset} 327 | ${colors.blue} ___ __ __ __ ___ ${colors.green}/,-._.--~\'${colors.reset} 328 | ${colors.blue} |\\ | |__ __ / ` / \\ |__) |__ ${colors.yellow}} {${colors.reset} 329 | ${colors.blue} | \\| | \\__, \\__/ | \\ |___ ${colors.green}\\`-._,-`-,${colors.reset} 330 | ${colors.green}`._,._,\'${colors.reset} 331 | ${colors.purple} ${workflow.manifest.name} ${workflow_version}${colors.reset} 332 | ${dashedLine(monochrome_logs)} 333 | """.stripIndent() 334 | ) 335 | } 336 | } 337 | --------------------------------------------------------------------------------