diff --git a/.github/CONTRIBUTING.md b/.github/CONTRIBUTING.md index 17fecfa8..e756a668 100644 --- a/.github/CONTRIBUTING.md +++ b/.github/CONTRIBUTING.md @@ -1,9 +1,9 @@ -# genomic-medicine-sweden/skierfe: Contributing Guidelines +# genomic-medicine-sweden/nallo: Contributing Guidelines Hi there! -Many thanks for taking an interest in improving genomic-medicine-sweden/skierfe. +Many thanks for taking an interest in improving genomic-medicine-sweden/nallo. -We try to manage the required tasks for genomic-medicine-sweden/skierfe using GitHub issues, you probably came to this page when creating one. +We try to manage the required tasks for genomic-medicine-sweden/nallo using GitHub issues, you probably came to this page when creating one. Please use the pre-filled template to save time. However, don't be put off by this template - other more general issues and suggestions are welcome! @@ -11,10 +11,10 @@ Contributions to the code are even more welcome ;) ## Contribution workflow -If you'd like to write some code for genomic-medicine-sweden/skierfe, the standard workflow is as follows: +If you'd like to write some code for genomic-medicine-sweden/nallo, the standard workflow is as follows: -1. Check that there isn't already an issue about your idea in the [genomic-medicine-sweden/skierfe issues](https://github.com/genomic-medicine-sweden/skierfe/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this -2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [genomic-medicine-sweden/skierfe repository](https://github.com/genomic-medicine-sweden/skierfe) to your GitHub account +1. Check that there isn't already an issue about your idea in the [genomic-medicine-sweden/nallo issues](https://github.com/genomic-medicine-sweden/nallo/issues) to avoid duplicating work. If there isn't one already, please create one so that others know you're working on this +2. [Fork](https://help.github.com/en/github/getting-started-with-github/fork-a-repo) the [genomic-medicine-sweden/nallo repository](https://github.com/genomic-medicine-sweden/nallo) to your GitHub account 3. Make the necessary changes / additions within your forked repository following [Pipeline conventions](#pipeline-contribution-conventions) 4. Use `nf-core schema build` and add any new parameters to the pipeline JSON schema (requires [nf-core tools](https://github.com/nf-core/tools) >= 1.10). 5. Submit a Pull Request against the `dev` branch and wait for the code to be reviewed and merged @@ -58,7 +58,7 @@ These tests are run both with the latest available version of `Nextflow` and als ## Pipeline contribution conventions -To make the genomic-medicine-sweden/skierfe 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. +To make the genomic-medicine-sweden/nallo 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. ### Adding a new step @@ -108,7 +108,7 @@ This repo includes a devcontainer configuration which will create a GitHub Codes To get started: -- Open the repo in [Codespaces](https://github.com/genomic-medicine-sweden/skierfe/codespaces) +- Open the repo in [Codespaces](https://github.com/genomic-medicine-sweden/nallo/codespaces) - Tools installed - nf-core - Nextflow diff --git a/.github/ISSUE_TEMPLATE/bug_report.yml b/.github/ISSUE_TEMPLATE/bug_report.yml index ee95ed8c..a054825b 100644 --- a/.github/ISSUE_TEMPLATE/bug_report.yml +++ b/.github/ISSUE_TEMPLATE/bug_report.yml @@ -49,6 +49,6 @@ body: * OS _(eg. CentOS Linux, macOS, Linux Mint)_ - * Version of genomic-medicine-sweden/skierfe _(eg. 1.1, 1.5, 1.8.2)_ + * Version of genomic-medicine-sweden/nallo _(eg. 1.1, 1.5, 1.8.2)_ " diff --git a/.github/ISSUE_TEMPLATE/config.yml b/.github/ISSUE_TEMPLATE/config.yml index 5a3b117f..ccc8ca19 100644 --- a/.github/ISSUE_TEMPLATE/config.yml +++ b/.github/ISSUE_TEMPLATE/config.yml @@ -4,4 +4,4 @@ contact_links: about: Please join the nf-core community here - name: "" url: https://google.com - about: Discussion about the nf-core/skierfe pipeline + about: Discussion about the nf-core/nallo pipeline diff --git a/.github/ISSUE_TEMPLATE/feature_request.yml b/.github/ISSUE_TEMPLATE/feature_request.yml index 3330b92a..d412a0cd 100644 --- a/.github/ISSUE_TEMPLATE/feature_request.yml +++ b/.github/ISSUE_TEMPLATE/feature_request.yml @@ -1,5 +1,5 @@ name: Feature request -description: Suggest an idea for the genomic-medicine-sweden/skierfe pipeline +description: Suggest an idea for the genomic-medicine-sweden/nallo pipeline labels: enhancement body: - type: textarea diff --git a/.github/PULL_REQUEST_TEMPLATE.md b/.github/PULL_REQUEST_TEMPLATE.md index 80742015..8546e747 100644 --- a/.github/PULL_REQUEST_TEMPLATE.md +++ b/.github/PULL_REQUEST_TEMPLATE.md @@ -1,21 +1,21 @@ ## PR checklist - [ ] This comment contains a description of changes (with reason). - [ ] If you've fixed a bug or added code that should be tested, add tests! -- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/genomic-medicine-sweden/skierfe/tree/master/.github/CONTRIBUTING.md) +- [ ] If you've added a new tool - have you followed the pipeline conventions in the [contribution docs](https://github.com/genomic-medicine-sweden/nallo/tree/master/.github/CONTRIBUTING.md) - [ ] Make sure your code lints (`nf-core lint`). - [ ] Ensure the test suite passes (`nf-test test main.nf.test -profile test,docker`). - [ ] Check for unexpected warnings in debug mode (`nextflow run . -profile debug,test,docker --outdir `). diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index e0e3e732..81e829fa 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -10,7 +10,7 @@ on: jobs: run-tower: name: Run AWS full tests - if: github.repository == 'fellen31/skierfe' + if: github.repository == 'fellen31/nallo' runs-on: ubuntu-latest steps: - name: Launch workflow via tower @@ -22,10 +22,10 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/skierfe/work-${{ github.sha }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nallo/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/skierfe/results-${{ github.sha }}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nallo/results-${{ github.sha }}" } profiles: test_full,aws_tower - uses: actions/upload-artifact@v3 diff --git a/.github/workflows/awstest.yml b/.github/workflows/awstest.yml index df6ca4b3..69bb6671 100644 --- a/.github/workflows/awstest.yml +++ b/.github/workflows/awstest.yml @@ -7,7 +7,7 @@ on: jobs: run-tower: name: Run AWS tests - if: github.repository == 'fellen31/skierfe' + if: github.repository == 'fellen31/nallo' runs-on: ubuntu-latest steps: # Launch workflow using Tower CLI tool action @@ -17,10 +17,10 @@ jobs: workspace_id: ${{ secrets.TOWER_WORKSPACE_ID }} access_token: ${{ secrets.TOWER_ACCESS_TOKEN }} compute_env: ${{ secrets.TOWER_COMPUTE_ENV }} - workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/skierfe/work-${{ github.sha }} + workdir: s3://${{ secrets.AWS_S3_BUCKET }}/work/nallo/work-${{ github.sha }} parameters: | { - "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/skierfe/results-test-${{ github.sha }}" + "outdir": "s3://${{ secrets.AWS_S3_BUCKET }}/nallo/results-test-${{ github.sha }}" } profiles: test,aws_tower - uses: actions/upload-artifact@v3 diff --git a/.github/workflows/branch.yml b/.github/workflows/branch.yml index fff33cd2..66414ed4 100644 --- a/.github/workflows/branch.yml +++ b/.github/workflows/branch.yml @@ -11,9 +11,9 @@ jobs: steps: # PRs to the nf-core repo master branch are only ok if coming from the nf-core repo `dev` or any `patch` branches - name: Check PRs - if: github.repository == 'genomic-medicine-sweden/skierfe' + if: github.repository == 'genomic-medicine-sweden/nallo' run: | - { [[ ${{github.event.pull_request.head.repo.full_name }} == genomic-medicine-sweden/skierfe ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] + { [[ ${{github.event.pull_request.head.repo.full_name }} == genomic-medicine-sweden/nallo ]] && [[ $GITHUB_HEAD_REF == "dev" ]]; } || [[ $GITHUB_HEAD_REF == "patch" ]] # If the above check failed, post a comment on the PR explaining the failure # NOTE - this doesn't currently work if the PR is coming from a fork, due to limitations in GitHub actions secrets diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml index 080eee2e..37483400 100644 --- a/.github/workflows/ci.yml +++ b/.github/workflows/ci.yml @@ -19,7 +19,7 @@ jobs: test: name: Run pipeline with test data # Only run on push if this is the nf-core dev branch (merged PRs) - if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/skierfe') }}" + if: "${{ github.event_name != 'push' || (github.event_name == 'push' && github.repository == 'genomic-medicine-sweden/nallo') }}" runs-on: ubuntu-latest strategy: matrix: diff --git a/.github/workflows/fix-linting.yml b/.github/workflows/fix-linting.yml index e1c41887..18837ddf 100644 --- a/.github/workflows/fix-linting.yml +++ b/.github/workflows/fix-linting.yml @@ -9,7 +9,7 @@ jobs: if: > contains(github.event.comment.html_url, '/pull/') && contains(github.event.comment.body, '@nf-core-bot fix linting') && - github.repository == 'genomic-medicine-sweden/skierfe' + github.repository == 'genomic-medicine-sweden/nallo' runs-on: ubuntu-latest steps: # Use the @nf-core-bot token to check out so we can push later @@ -85,4 +85,4 @@ jobs: issue-number: ${{ github.event.issue.number }} body: | @${{ github.actor }} I tried to fix the linting errors, but it didn't work. Please fix them manually. - See [CI log](https://github.com/genomic-medicine-sweden/skierfe/actions/runs/${{ github.run_id }}) for more details. + See [CI log](https://github.com/genomic-medicine-sweden/nallo/actions/runs/${{ github.run_id }}) for more details. diff --git a/.nf-core.yml b/.nf-core.yml index 9f1e4e37..1238d24f 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,18 +1,18 @@ lint: files_exist: - CODE_OF_CONDUCT.md - - assets/nf-core-skierfe_logo_light.png - - docs/images/nf-core-skierfe_logo_light.png - - docs/images/nf-core-skierfe_logo_dark.png + - assets/nf-core-nallo_logo_light.png + - docs/images/nf-core-nallo_logo_light.png + - docs/images/nf-core-nallo_logo_dark.png - .github/ISSUE_TEMPLATE/config.yml - .github/workflows/awstest.yml - .github/workflows/awsfulltest.yml - conf/modules.config files_unchanged: - CODE_OF_CONDUCT.md - - assets/nf-core-skierfe_logo_light.png - - docs/images/nf-core-skierfe_logo_light.png - - docs/images/nf-core-skierfe_logo_dark.png + - assets/nf-core-nallo_logo_light.png + - docs/images/nf-core-nallo_logo_light.png + - docs/images/nf-core-nallo_logo_dark.png - .github/ISSUE_TEMPLATE/bug_report.yml - .github/CONTRIBUTING.md multiqc_config: diff --git a/CHANGELOG.md b/CHANGELOG.md index bc5b6a4c..bd141efa 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -1,11 +1,11 @@ -# genomic-medicine-sweden/skierfe: Changelog +# genomic-medicine-sweden/nallo: Changelog The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/) and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html). ## v0.1.0 - [date] -Initial release of genomic-medicine-sweden/skierfe, created with the [nf-core](https://nf-co.re/) template. +Initial release of genomic-medicine-sweden/nallo, created with the [nf-core](https://nf-co.re/) template. ### `Added` diff --git a/CITATIONS.md b/CITATIONS.md index 2307fa64..a6772105 100644 --- a/CITATIONS.md +++ b/CITATIONS.md @@ -1,4 +1,4 @@ -# genomic-medicine-sweden/skierfe: Citations +# genomic-medicine-sweden/nallo: Citations ## [nf-core](https://pubmed.ncbi.nlm.nih.gov/32055031/) diff --git a/README.md b/README.md index 967f0d16..c82aabb6 100644 --- a/README.md +++ b/README.md @@ -1,16 +1,16 @@ -[![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/skierfe/actions/workflows/ci.yml/badge.svg)](https://github.com/genomic-medicine-sweden/skierfe/actions/workflows/ci.yml) -[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/skierfe/actions/workflows/linting.yml/badge.svg)](https://github.com/genomic-medicine-sweden/skierfe/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) +[![GitHub Actions CI Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/ci.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/ci.yml) +[![GitHub Actions Linting Status](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml/badge.svg)](https://github.com/genomic-medicine-sweden/nallo/actions/workflows/linting.yml)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX) [![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com) [![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A523.04.0-23aa62.svg)](https://www.nextflow.io/) [![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/) [![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/) [![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/) -[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/genomic-medicine-sweden/skierfe) +[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://tower.nf/launch?pipeline=https://github.com/genomic-medicine-sweden/nallo) ## Introduction -**genomic-medicine-sweden/skierfe** is a bioinformatics analysis pipeline for long-read rare disease SV/SNV identification using both PacBio and (targeted) ONT-data. Heavily influenced by best-practice pipelines such as [nf-core/nanoseq](https://github.com/nf-core/nanoseq), [nf-core/sarek](https://nf-co.re/sarek), [nf-core/raredisease](https://nf-co.re/raredisease), [PacBio Human WGS Workflow](https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake), [epi2me-labs/wf-human-variation](https://github.com/epi2me-labs/wf-human-variation) and [brentp/rare-disease-wf](https://github.com/brentp/rare-disease-wf). +**genomic-medicine-sweden/nallo** is a bioinformatics analysis pipeline for long-read rare disease SV/SNV identification using both PacBio and (targeted) ONT-data. Heavily influenced by best-practice pipelines such as [nf-core/nanoseq](https://github.com/nf-core/nanoseq), [nf-core/sarek](https://nf-co.re/sarek), [nf-core/raredisease](https://nf-co.re/raredisease), [PacBio Human WGS Workflow](https://github.com/PacificBiosciences/pb-human-wgs-workflow-snakemake), [epi2me-labs/wf-human-variation](https://github.com/epi2me-labs/wf-human-variation) and [brentp/rare-disease-wf](https://github.com/brentp/rare-disease-wf). @@ -70,7 +70,7 @@ HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1 Now, you can run the pipeline using: ```bash -nextflow run genomic-medicine-sweden/skierfe -r dev -profile YOURPROFILE \ +nextflow run genomic-medicine-sweden/nallo -r dev -profile YOURPROFILE \ --input samplesheet.csv \ --preset \ --outdir \ @@ -81,7 +81,7 @@ nextflow run genomic-medicine-sweden/skierfe -r dev -profile YOURPROFILE \ --skip_cnv_calling ``` -For more details and further functionality, please refer to the [usage documentation](https://github.com/genomic-medicine-sweden/skierfe/blob/dev/docs/usage.md). +For more details and further functionality, please refer to the [usage documentation](https://github.com/genomic-medicine-sweden/nallo/blob/dev/docs/usage.md). > [!WARNING] > Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; @@ -90,12 +90,12 @@ For more details and further functionality, please refer to the [usage documenta To run in an offline environment, download the pipeline and singularity images using [`nf-core download`](https://nf-co.re/tools/#downloading-pipelines-for-offline-use): ``` -nf-core download fellen31/skierfe -r dev +nf-core download genomic-medicine-sweden/nallo -r dev ``` ## Credits -genomic-medicine-sweden/skierfe was originally written by Felix Lenner. +genomic-medicine-sweden/nallo was originally written by Felix Lenner. We thank the following people for their extensive assistance in the development of this pipeline: @@ -108,7 +108,7 @@ If you would like to contribute to this pipeline, please see the [contributing g ## Citations - + diff --git a/assets/adaptivecard.json b/assets/adaptivecard.json index 040e3a6f..f24a3292 100644 --- a/assets/adaptivecard.json +++ b/assets/adaptivecard.json @@ -17,7 +17,7 @@ "size": "Large", "weight": "Bolder", "color": "<% if (success) { %>Good<% } else { %>Attention<%} %>", - "text": "genomic-medicine-sweden/skierfe v${version} - ${runName}", + "text": "genomic-medicine-sweden/nallo v${version} - ${runName}", "wrap": true }, { diff --git a/assets/email_template.html b/assets/email_template.html index 96e7eecd..fdcc0a3a 100644 --- a/assets/email_template.html +++ b/assets/email_template.html @@ -4,21 +4,21 @@ - - genomic-medicine-sweden/skierfe Pipeline Report + + genomic-medicine-sweden/nallo Pipeline Report
-

genomic-medicine-sweden/skierfe ${version}

+

genomic-medicine-sweden/nallo ${version}

Run Name: $runName

<% if (!success){ out << """
-

genomic-medicine-sweden/skierfe execution completed unsuccessfully!

+

genomic-medicine-sweden/nallo execution completed unsuccessfully!

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

The full error message was:

${errorReport}
@@ -27,7 +27,7 @@

genomic-medicine-sweden/skierfe execut } else { out << """
- genomic-medicine-sweden/skierfe execution completed successfully! + genomic-medicine-sweden/nallo execution completed successfully!
""" } @@ -44,8 +44,8 @@

Pipeline Configuration:

-

genomic-medicine-sweden/skierfe

-

https://github.com/genomic-medicine-sweden/skierfe

+

genomic-medicine-sweden/nallo

+

https://github.com/genomic-medicine-sweden/nallo

diff --git a/assets/email_template.txt b/assets/email_template.txt index 53fe431b..8cc53769 100644 --- a/assets/email_template.txt +++ b/assets/email_template.txt @@ -1,10 +1,10 @@ Run Name: $runName <% if (success){ - out << "## genomic-medicine-sweden/skierfe execution completed successfully! ##" + out << "## genomic-medicine-sweden/nallo execution completed successfully! ##" } else { out << """#################################################### -## genomic-medicine-sweden/skierfe execution completed unsuccessfully! ## +## genomic-medicine-sweden/nallo execution completed unsuccessfully! ## #################################################### The exit status of the task that caused the workflow execution to fail was: $exitStatus. The full error message was: @@ -27,5 +27,5 @@ Pipeline Configuration: <% out << summary.collect{ k,v -> " - $k: $v" }.join("\n") %> -- -genomic-medicine-sweden/skierfe -https://github.com/genomic-medicine-sweden/skierfe +genomic-medicine-sweden/nallo +https://github.com/genomic-medicine-sweden/nallo diff --git a/assets/methods_description_template.yml b/assets/methods_description_template.yml index 4b407ff8..d5cb2752 100644 --- a/assets/methods_description_template.yml +++ b/assets/methods_description_template.yml @@ -1,13 +1,13 @@ -id: "genomic-medicine-sweden-skierfe-methods-description" +id: "genomic-medicine-sweden-nallo-methods-description" description: "Suggested text and references to use when describing pipeline usage within the methods section of a publication." -section_name: "genomic-medicine-sweden/skierfe Methods Description" -section_href: "https://github.com/genomic-medicine-sweden/skierfe" +section_name: "genomic-medicine-sweden/nallo Methods Description" +section_href: "https://github.com/genomic-medicine-sweden/nallo" plot_type: "html" ## TODO nf-core: Update the HTML below to your preferred methods description, e.g. add publication citation for this pipeline ## You inject any metadata in the Nextflow '${workflow}' object data: |

Methods

-

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

+

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

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

${workflow.commandLine}

${tool_citations}

diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index cb0bb247..0107ed08 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -1,14 +1,12 @@ report_comment: > - This report has been generated by the genomic-medicine-sweden/skierfe + This report has been generated by the genomic-medicine-sweden/nallo analysis pipeline. report_section_order: - "genomic-medicine-sweden-skierfe-methods-description": + "genomic-medicine-sweden-nallo-methods-description": order: -1000 software_versions: order: -1001 - "genomic-medicine-sweden-skierfe-summary": + "genomic-medicine-sweden-nallo-summary": order: -1002 export_plots: true - -disable_version_detection: true diff --git a/assets/nf-core-skierfe_logo_light.png b/assets/nf-core-skierfe_logo_light.png deleted file mode 100644 index 10b4a2e5..00000000 Binary files a/assets/nf-core-skierfe_logo_light.png and /dev/null differ diff --git a/assets/samplesheet.csv b/assets/samplesheet.csv index b8bd10cf..c5109225 100644 --- a/assets/samplesheet.csv +++ b/assets/samplesheet.csv @@ -1,2 +1,2 @@ sample,file,family_id,paternal_id,maternal_id,sex,phenotype -HG002_Revio,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/HG002_PacBio_Revio.fastq.gz,FAM,XXX,YYY,1,1 +HG002_Revio,https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data/HG002_PacBio_Revio.fastq.gz,FAM,XXX,YYY,1,1 diff --git a/assets/samplesheet_multisample_bam.csv b/assets/samplesheet_multisample_bam.csv index 03f8257a..ca6c7a03 100644 --- a/assets/samplesheet_multisample_bam.csv +++ b/assets/samplesheet_multisample_bam.csv @@ -1,3 +1,3 @@ sample,file,family_id,paternal_id,maternal_id,sex,phenotype -HG002_Revio_A,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/HG002_PacBio_Revio.bam,FAM,XXX,YYY,1,1 -HG002_Revio_B,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/HG002_PacBio_Revio.bam,FAM,XXX,YYY,1,1 +HG002_Revio_A,https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data/HG002_PacBio_Revio.bam,FAM,XXX,YYY,1,1 +HG002_Revio_B,https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data/HG002_PacBio_Revio.bam,FAM,XXX,YYY,1,1 diff --git a/assets/schema_gvcfs.json b/assets/schema_gvcfs.json index 905bf382..0ae2d250 100644 --- a/assets/schema_gvcfs.json +++ b/assets/schema_gvcfs.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/fellen31/skierfe/master/assets/schema_gvcfs.json", - "title": "fellen31/skierfe pipeline - params.extra_gvcfs schema", + "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_gvcfs.json", + "title": "genomic-medicine-sweden/nallo pipeline - params.extra_gvcfs schema", "description": "Schema for the file provided with params.extra_gvcfs", "type": "array", "items": { diff --git a/assets/schema_input.json b/assets/schema_input.json index f523bdb4..7730a773 100644 --- a/assets/schema_input.json +++ b/assets/schema_input.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/master/assets/schema_input.json", - "title": "genomic-medicine-sweden/skierfe pipeline - params.input schema", + "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_input.json", + "title": "genomic-medicine-sweden/nallo pipeline - params.input schema", "description": "Schema for the file provided with params.input", "type": "array", "items": { diff --git a/assets/schema_snfs.json b/assets/schema_snfs.json index 77fc416b..59d45232 100644 --- a/assets/schema_snfs.json +++ b/assets/schema_snfs.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/fellen31/skierfe/master/assets/schema_snfs.json", - "title": "fellen31/skierfe pipeline - params.extra_snfs schema", + "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_snfs.json", + "title": "genomic-medicine-sweden/nallo pipeline - params.extra_snfs schema", "description": "Schema for the file provided with params.extra_snfs", "type": "array", "items": { diff --git a/assets/schema_snpdb.json b/assets/schema_snpdb.json index 7e181e99..651ad58a 100644 --- a/assets/schema_snpdb.json +++ b/assets/schema_snpdb.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/fellen31/skierfe/master/assets/schema_gvcfs.json", - "title": "fellen31/skierfe pipeline - params.extra_gvcfs schema", + "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/assets/schema_gvcfs.json", + "title": "genomic-medicine-sweden/nallo pipeline - params.extra_gvcfs schema", "description": "Schema for the file provided with params.extra_gvcfs", "type": "array", "items": { diff --git a/assets/sendmail_template.txt b/assets/sendmail_template.txt index f19b37e9..0811b152 100644 --- a/assets/sendmail_template.txt +++ b/assets/sendmail_template.txt @@ -9,12 +9,12 @@ Content-Type: text/html; charset=utf-8 $email_html --nfcoremimeboundary -Content-Type: image/png;name="genomic-medicine-sweden-skierfe_logo.png" +Content-Type: image/png;name="genomic-medicine-sweden-nallo_logo.png" Content-Transfer-Encoding: base64 Content-ID: -Content-Disposition: inline; filename="genomic-medicine-sweden-skierfe_logo_light.png" +Content-Disposition: inline; filename="genomic-medicine-sweden-nallo_logo_light.png" -<% out << new File("$projectDir/assets/genomic-medicine-sweden-skierfe_logo_light.png"). +<% out << new File("$projectDir/assets/genomic-medicine-sweden-nallo_logo_light.png"). bytes. encodeBase64(). toString(). diff --git a/assets/slackreport.json b/assets/slackreport.json index 812d83e4..01fceeb5 100644 --- a/assets/slackreport.json +++ b/assets/slackreport.json @@ -3,7 +3,7 @@ { "fallback": "Plain-text summary of the attachment.", "color": "<% if (success) { %>good<% } else { %>danger<%} %>", - "author_name": "genomic-medicine-sweden/skierfe ${version} - ${runName}", + "author_name": "genomic-medicine-sweden/nallo ${version} - ${runName}", "author_icon": "https://www.nextflow.io/docs/latest/_static/favicon.ico", "text": "<% if (success) { %>Pipeline completed successfully!<% } else { %>Pipeline completed with errors<% } %>", "fields": [ diff --git a/assets/test_data/snp_dbs.csv b/assets/test_data/snp_dbs.csv index c34e5efa..234c410a 100644 --- a/assets/test_data/snp_dbs.csv +++ b/assets/test_data/snp_dbs.csv @@ -1,3 +1,3 @@ sample,file -cadd,https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/cadd.v1.6.hg38.test_data.zip +cadd,https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data/cadd.v1.6.hg38.test_data.zip diff --git a/conf/base.config b/conf/base.config index 7e48449c..58c512de 100644 --- a/conf/base.config +++ b/conf/base.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - genomic-medicine-sweden/skierfe Nextflow base config file + genomic-medicine-sweden/nallo Nextflow base config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ A 'blank slate' config file, appropriate for general use on most high performance compute environments. Assumes that all software is installed and available on diff --git a/conf/modules/general.config b/conf/modules/general.config index cec8adbb..7594c3c2 100644 --- a/conf/modules/general.config +++ b/conf/modules/general.config @@ -24,7 +24,7 @@ process { ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ - withName: '.*:SKIERFE:FASTQC' { + withName: '.*:NALLO:FASTQC' { ext.args = '--quiet' publishDir = [ path: { "${params.outdir}/qc_raw_reads/fastqc/${meta.id}" }, @@ -33,7 +33,7 @@ process { ] } - withName: '.*:SKIERFE:FQCRS' { + withName: '.*:NALLO:FQCRS' { publishDir = [ path: { "${params.outdir}/qc_raw_reads/fqcrs/${meta.id}" }, mode: params.publish_dir_mode, @@ -41,7 +41,7 @@ process { ] } - withName: '.*:SKIERFE:SPLIT_BED_CHUNKS' { + withName: '.*:NALLO:SPLIT_BED_CHUNKS' { publishDir = [ enabled: false ] diff --git a/conf/test.config b/conf/test.config index b0e9d543..5b8edf5f 100644 --- a/conf/test.config +++ b/conf/test.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a fast and simple pipeline test. Use as follows: - nextflow run genomic-medicine-sweden/skierfe -profile test, --outdir + nextflow run genomic-medicine-sweden/nallo -profile test, --outdir ---------------------------------------------------------------------------------------- */ @@ -23,25 +23,25 @@ params { // Genome references - fasta = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/hg38.test.fa.gz" - input = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/samplesheet.csv" + fasta = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data/hg38.test.fa.gz" + input = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/samplesheet.csv" - bed = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data.bed" + bed = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data.bed" // HiFiCNV - hificnv_xy = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/external/expected_cn.hg38.XY.bed" - hificnv_xx = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/external/expected_cn.hg38.XX.bed" - hificnv_exclude = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/empty.bed" + hificnv_xy = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/external/expected_cn.hg38.XY.bed" + hificnv_xx = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/external/expected_cn.hg38.XX.bed" + hificnv_exclude = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data/empty.bed" // Dipcall - dipcall_par = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/external/hs38.PAR.bed" + dipcall_par = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/external/hs38.PAR.bed" // TRGT - trgt_repeats = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/external/pathogenic_repeats.hg38.bed" + trgt_repeats = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/external/pathogenic_repeats.hg38.bed" // SNV Annotation - vep_cache = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/vep_cache_test_data.tar.gz" - snp_db = "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/dev/assets/test_data/snp_dbs.csv" + vep_cache = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data/vep_cache_test_data.tar.gz" + snp_db = "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/dev/assets/test_data/snp_dbs.csv" parallel_snv = 3 // Create 3 parallel DeepVariant processes preset = "revio" @@ -49,16 +49,16 @@ params { } process { - withName: '.*:SKIERFE:ASSEMBLY:HIFIASM' { + withName: '.*:NALLO:ASSEMBLY:HIFIASM' { ext.args = '-f0' } - withName: '.*:SKIERFE:PHASING:WHATSHAP_PHASE' { + withName: '.*:NALLO:PHASING:WHATSHAP_PHASE' { ext.args = '--ignore-read-groups --indels --distrust-genotypes --include-homozygous' } - withName: '.*:SKIERFE:PREPARE_GENOME:MINIMAP2_INDEX' { + withName: '.*:NALLO:PREPARE_GENOME:MINIMAP2_INDEX' { if(params.preset == 'revio' | params.preset == 'pacbio') { ext.args = "-x map-hifi -I 2G" @@ -67,12 +67,12 @@ process { } } - withName: '.*:SKIERFE:ASSEMBLY_VARIANT_CALLING:MINIMAP2_INDEX_DIPCALL' { + withName: '.*:NALLO:ASSEMBLY_VARIANT_CALLING:MINIMAP2_INDEX_DIPCALL' { ext.args = "-x asm5 -I 2G" } - withName: '.*:SKIERFE:ALIGN_READS:MINIMAP2_ALIGN_UNSPLIT' { + withName: '.*:NALLO:ALIGN_READS:MINIMAP2_ALIGN_UNSPLIT' { if(params.preset == 'revio' | params.preset == 'pacbio') { ext.args = "-y -x map-hifi --secondary=no -Y --split-prefix=tmp" @@ -81,7 +81,7 @@ process { } } - withName: '.*:SKIERFE:ALIGN_READS:MINIMAP2_ALIGN_SPLIT' { + withName: '.*:NALLO:ALIGN_READS:MINIMAP2_ALIGN_SPLIT' { if(params.preset == 'revio' | params.preset == 'pacbio') { ext.args = "-y -x map-hifi --secondary=no -Y --split-prefix=tmp" @@ -90,7 +90,7 @@ process { } } - withName: '.*:SKIERFE:ASSEMBLY_VARIANT_CALLING:DIPCALL' { + withName: '.*:NALLO:ASSEMBLY_VARIANT_CALLING:DIPCALL' { ext.args = '--split-prefix=tmp' diff --git a/conf/test_full.config b/conf/test_full.config index c45de010..5fa1a588 100644 --- a/conf/test_full.config +++ b/conf/test_full.config @@ -5,7 +5,7 @@ Defines input files and everything required to run a full size pipeline test. Use as follows: - nextflow run genomic-medicine-sweden/skierfe -profile test_full, --outdir + nextflow run genomic-medicine-sweden/nallo -profile test_full, --outdir ---------------------------------------------------------------------------------------- */ diff --git a/docs/README.md b/docs/README.md index c07cf445..ca01fef3 100644 --- a/docs/README.md +++ b/docs/README.md @@ -1,6 +1,6 @@ -# genomic-medicine-sweden/skierfe: Documentation +# genomic-medicine-sweden/nallo: Documentation -The genomic-medicine-sweden/skierfe documentation is split into the following pages: +The genomic-medicine-sweden/nallo documentation is split into the following pages: - [Usage](usage.md) - An overview of how the pipeline works, how to run it and a description of all of the different command-line flags. diff --git a/docs/images/skierfe-concept-150523.png b/docs/images/skierfe-concept-150523.png deleted file mode 100644 index 6269e576..00000000 Binary files a/docs/images/skierfe-concept-150523.png and /dev/null differ diff --git a/docs/output.md b/docs/output.md index dee335a1..8f257513 100644 --- a/docs/output.md +++ b/docs/output.md @@ -1,4 +1,4 @@ -# genomic-medicine-sweden/skierfe: Output +# genomic-medicine-sweden/nallo: Output ## Introduction diff --git a/docs/usage.md b/docs/usage.md index 4593a72d..16fa357c 100644 --- a/docs/usage.md +++ b/docs/usage.md @@ -1,23 +1,23 @@ -# genomic-medicine-sweden/skierfe: Usage +# genomic-medicine-sweden/nallo: Usage ## Introduction -genomic-medicine-sweden/skierfe is a bioinformatics analysis pipeline to analyse long-read data. +genomic-medicine-sweden/nallo is a bioinformatics analysis pipeline to analyse long-read data. ## Prerequisites 1. Install Nextflow (>=22.10.1) using the instructions [here.](https://nextflow.io/docs/latest/getstarted.html#installation) 2. Install one of the following technologies for full pipeline reproducibility: Docker, Singularity, Podman, Shifter or Charliecloud. - > Almost all nf-core pipelines give you the option to use conda as well. However, some tools used in the skierfe pipeline do not have a conda package so we do not support conda at the moment. + > Almost all nf-core pipelines give you the option to use conda as well. However, some tools used in the nallo pipeline do not have a conda package so we do not support conda at the moment. -## Run genomic-medicine-sweden/skierfe with test data +## Run genomic-medicine-sweden/nallo with test data Before running the pipeline with your data, we recommend running it with the test dataset available in the `assets/test_data` folder provided with the pipeline. You do not need to download any of the data as part of it came directly with the pipeline and the other part will be fetched automatically for you when you use the test profile. Run the following command, where YOURPROFILE is the package manager you installed on your machine. For example, `-profile test,docker` or `-profile test,singularity`: ``` -nextflow run genomic-medicine-sweden/skierfe \ +nextflow run genomic-medicine-sweden/nallo \ -revision dev -profile test, \ --outdir ``` @@ -35,13 +35,13 @@ work # Directory containing the Nextflow working files ``` > [!NOTE] -> The default cpu and memory configurations used in skierfe are written keeping the test profile (and dataset, which is tiny) in mind. You should override these values in configs to get it to work on larger datasets. Check the section `custom-configuration` below to know more about how to configure resources for your platform. +> The default cpu and memory configurations used in nallo are written keeping the test profile (and dataset, which is tiny) in mind. You should override these values in configs to get it to work on larger datasets. Check the section `custom-configuration` below to know more about how to configure resources for your platform. ### Updating the pipeline The above command downloads the pipeline from GitHub, caches it, and tests it on the test dataset. When you run the command again, it will fetch the pipeline from cache even if a more recent version of the pipeline is available. To make sure that you're running the latest version of the pipeline, update the cached version of the pipeline by including `-latest` in the command. -## Run genomic-medicine-sweden/skierfe with your data +## Run genomic-medicine-sweden/nallo with your data Running the pipeline involves three steps: @@ -85,7 +85,7 @@ An [example samplesheet](../assets/samplesheet.csv) has been provided with the p The typical command for running the pipeline is as follows: ```bash -nextflow run genomic-medicine-sweden/skierfe -r dev -profile docker \ +nextflow run genomic-medicine-sweden/nallo -r dev -profile docker \ --input samplesheet.csv \ --preset \ --outdir \ @@ -116,7 +116,7 @@ Pipeline settings can be provided in a `yaml` or `json` file via `-params-file < > The above pipeline run specified with a params file in yaml format: ```bash -nextflow run fellen31/skierfe -profile docker -params-file params.yaml +nextflow run genomic-medicine-sweden/nallo -profile docker -params-file params.yaml ``` with `params.yaml` containing: @@ -133,7 +133,7 @@ You can also generate such `YAML`/`JSON` files via [nf-core/launch](https://nf-c ## Reference files and parameters -The typical command example above requires no additional files except the reference genome. Skierfe has the ability to skip certrain parts of the pipeline by specifying one or more of the following parameters: +The typical command example above requires no additional files except the reference genome. Nallo has the ability to skip certrain parts of the pipeline by specifying one or more of the following parameters: | Parameter | Description | Type | Default | Required | Hidden | | ---------------------------- | ------------------------------------------ | --------- | ------- | -------- | ------ | @@ -323,7 +323,7 @@ It is a good idea to specify a pipeline version when running the pipeline on you However, there has been no releases of this pipeline. A workaround is to supply a commit ID, e.g. `-revision 6ff95ff`, in order to ensure that the same version of the pipeline is being executed. diff --git a/main.nf b/main.nf index b915334c..93fb25b8 100644 --- a/main.nf +++ b/main.nf @@ -1,9 +1,9 @@ #!/usr/bin/env nextflow /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - genomic-medicine-sweden/skierfe + genomic-medicine-sweden/nallo ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - Github : https://github.com/genomic-medicine-sweden/skierfe + Github : https://github.com/genomic-medicine-sweden/nallo ---------------------------------------------------------------------------------------- */ @@ -15,11 +15,11 @@ nextflow.enable.dsl = 2 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -include { SKIERFE } from './workflows/skierfe' -include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_skierfe_pipeline' -include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_skierfe_pipeline' +include { NALLO } from './workflows/nallo' +include { PIPELINE_INITIALISATION } from './subworkflows/local/utils_nfcore_nallo_pipeline' +include { PIPELINE_COMPLETION } from './subworkflows/local/utils_nfcore_nallo_pipeline' -include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_skierfe_pipeline' +include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_nallo_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -30,7 +30,7 @@ include { getGenomeAttribute } from './subworkflows/local/utils_nfcore_skie // // WORKFLOW: Run main analysis pipeline depending on type of input // -workflow GENOMICMEDICINESWEDEN_SKIERFE { +workflow GENOMICMEDICINESWEDEN_NALLO { take: samplesheet // channel: samplesheet read in from --input @@ -39,12 +39,12 @@ workflow GENOMICMEDICINESWEDEN_SKIERFE { // // WORKFLOW: Run pipeline // - SKIERFE ( + NALLO ( samplesheet ) emit: - multiqc_report = Channel.empty()// SKIERFE.out.multiqc_report // channel: /path/to/multiqc_report.html + multiqc_report = Channel.empty()// NALLO.out.multiqc_report // channel: /path/to/multiqc_report.html } /* @@ -72,7 +72,7 @@ workflow { // // WORKFLOW: Run main workflow // - GENOMICMEDICINESWEDEN_SKIERFE ( + GENOMICMEDICINESWEDEN_NALLO ( PIPELINE_INITIALISATION.out.samplesheet ) @@ -86,7 +86,7 @@ workflow { params.outdir, params.monochrome_logs, params.hook_url, - GENOMICMEDICINESWEDEN_SKIERFE.out.multiqc_report + GENOMICMEDICINESWEDEN_NALLO.out.multiqc_report ) } diff --git a/modules.json b/modules.json index 4aeb5851..8609604a 100644 --- a/modules.json +++ b/modules.json @@ -1,6 +1,6 @@ { - "name": "genomic-medicine-sweden/skierfe", - "homePage": "https://github.com/genomic-medicine-sweden/skierfe", + "name": "genomic-medicine-sweden/nallo", + "homePage": "https://github.com/genomic-medicine-sweden/nallo", "repos": { "https://github.com/nf-core/modules.git": { "modules": { diff --git a/modules/local/samplesheet_check.nf b/modules/local/samplesheet_check.nf deleted file mode 100644 index 5241fd71..00000000 --- a/modules/local/samplesheet_check.nf +++ /dev/null @@ -1,29 +0,0 @@ -process SAMPLESHEET_CHECK { - tag "$samplesheet" - label 'process_single' - - conda "conda-forge::python=3.8.3" - container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? - 'https://depot.galaxyproject.org/singularity/python:3.8.3' : - 'biocontainers/python:3.8.3' }" - - input: - path samplesheet - - output: - path '*.csv' , emit: csv - path "versions.yml", emit: versions - - when: - task.ext.when == null || task.ext.when - - script: // This script is bundled with the pipeline, in fellen31/skierfe/bin/ - """ - mv ${samplesheet} ${samplesheet}.unchecked.csv - - cat <<-END_VERSIONS > versions.yml - "${task.process}": - python: \$(python --version | sed 's/Python //g') - END_VERSIONS - """ -} diff --git a/nextflow.config b/nextflow.config index 3b5c7d35..bfb260c1 100644 --- a/nextflow.config +++ b/nextflow.config @@ -1,6 +1,6 @@ /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ - genomic-medicine-sweden/skierfe Nextflow config file + genomic-medicine-sweden/nallo Nextflow config file ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ Default config options for all compute environments ---------------------------------------------------------------------------------------- @@ -100,12 +100,12 @@ try { System.err.println("WARNING: Could not load nf-core/config profiles: ${params.custom_config_base}/nfcore_custom.config") } -// Load genomic-medicine-sweden/skierfe custom profiles from different institutions. +// Load genomic-medicine-sweden/nallo custom profiles from different institutions. // Warning: Uncomment only if a pipeline-specific institutional config already exists on nf-core/configs! // try { -// includeConfig "${params.custom_config_base}/pipeline/skierfe.config" +// includeConfig "${params.custom_config_base}/pipeline/nallo.config" // } catch (Exception e) { -// System.err.println("WARNING: Could not load nf-core/config/skierfe profiles: ${params.custom_config_base}/pipeline/skierfe.config") +// System.err.println("WARNING: Could not load nf-core/config/nallo profiles: ${params.custom_config_base}/pipeline/nallo.config") // } profiles { debug { @@ -260,9 +260,9 @@ dag { } manifest { - name = 'genomic-medicine-sweden/skierfe' + name = 'genomic-medicine-sweden/nallo' author = """Felix Lenner""" - homePage = 'https://github.com/genomic-medicine-sweden/skierfe' + homePage = 'https://github.com/genomic-medicine-sweden/nallo' description = """Long-read variant calling pipeline""" mainScript = 'main.nf' nextflowVersion = '!>=23.04.0' diff --git a/nextflow_schema.json b/nextflow_schema.json index d2e62e26..a5e57df9 100644 --- a/nextflow_schema.json +++ b/nextflow_schema.json @@ -1,7 +1,7 @@ { "$schema": "http://json-schema.org/draft-07/schema", - "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/skierfe/master/nextflow_schema.json", - "title": "genomic-medicine-sweden/skierfe pipeline parameters", + "$id": "https://raw.githubusercontent.com/genomic-medicine-sweden/nallo/master/nextflow_schema.json", + "title": "genomic-medicine-sweden/nallo pipeline parameters", "description": "Long-read variant calling pipeline", "type": "object", "definitions": { diff --git a/subworkflows/local/utils_nfcore_skierfe_pipeline/main.nf b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf similarity index 99% rename from subworkflows/local/utils_nfcore_skierfe_pipeline/main.nf rename to subworkflows/local/utils_nfcore_nallo_pipeline/main.nf index 22dbb792..6a7eca5f 100644 --- a/subworkflows/local/utils_nfcore_skierfe_pipeline/main.nf +++ b/subworkflows/local/utils_nfcore_nallo_pipeline/main.nf @@ -1,5 +1,5 @@ // -// Subworkflow with functionality specific to the genomic-medicine-sweden/skierfe pipeline +// Subworkflow with functionality specific to the genomic-medicine-sweden/nallo pipeline // /* diff --git a/workflows/skierfe.nf b/workflows/nallo.nf similarity index 99% rename from workflows/skierfe.nf rename to workflows/nallo.nf index a553a713..17052bdb 100644 --- a/workflows/skierfe.nf +++ b/workflows/nallo.nf @@ -38,7 +38,7 @@ include { MULTIQC } from '../modules/nf-core/multiqc/main' include { paramsSummaryMap } from 'plugin/nf-validation' include { paramsSummaryMultiqc } from '../subworkflows/nf-core/utils_nfcore_pipeline' include { softwareVersionsToYAML } from '../subworkflows/nf-core/utils_nfcore_pipeline' -include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_skierfe_pipeline' +include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_nallo_pipeline' /* ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ @@ -46,7 +46,7 @@ include { methodsDescriptionText } from '../subworkflows/local/utils_nfcore_skie ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ */ -workflow SKIERFE { +workflow NALLO { take: ch_input