From f7e3a864f0dabef9226329e4af64dee32c609dd6 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 13:57:50 +0100 Subject: [PATCH 1/9] todos --- nextflow.config | 85 +++++++++++++++++++++++++++++++---- ro-crate-metadata.json | 100 ++++++++++++++++++++++++++++++++++++++--- 2 files changed, 170 insertions(+), 15 deletions(-) diff --git a/nextflow.config b/nextflow.config index a30334b9..9926f977 100644 --- a/nextflow.config +++ b/nextflow.config @@ -279,7 +279,6 @@ profiles { includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" // Load nf-core/raredisease custom profiles from different institutions. -// TODO nf-core: Optionally, you can add a pipeline-specific nf-core config at https://github.com/nf-core/configs // includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/raredisease.config" : "/dev/null" // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile @@ -339,15 +338,85 @@ manifest { name = 'nf-core/raredisease' author = """Clinical Genomics Stockholm""" // The author field is deprecated from Nextflow version 24.10.0, use contributors instead contributors = [ - // TODO nf-core: Update the field with the details of the contributors to your pipeline. New with Nextflow version 24.10.0 [ - name: 'Clinical Genomics Stockholm', - affiliation: '', + name: 'Ramprasad Neethiraj', + affiliation: 'School of Engineering sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden', + email: 'rne@kth.se', + github: 'https://github.com/ramprasadn', + contribution: ['author', 'maintainer'], + orcid: 'https://orcid.org/0000-0001-7313-3734' + ], + [ + name: 'Anders Jemt', + affiliation: 'Genomics Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden', + email: 'anders.jemt@scilifelab.se', + github: 'https://github.com/jemten', + contribution: ['author', 'maintainer'], + orcid: 'https://orcid.org/0000-0002-2219-0197' + ], + [ + name: 'Lucía Peña-Pérez', + affiliation: 'Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden', + email: 'lucia.pena.perez@scilifelab.se', + github: 'https://github.com/Lucpen', + contribution: ['contributor'], + orcid: 'https://orcid.org/0000-0002-5044-7754' + ], + [ + name: 'Peter Pruisscher', + affiliation: 'Genomics Medicine Center Karolinska, Karolinska University Hospital, Stockholm, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden', + email: 'peter.pruisscher@scilifelab.se', + github: 'https://github.com/peterpru', + contribution: ['contributor'], + orcid: 'https://orcid.org/0000-0002-6987-5839' + ], + [ + name: 'Anders Sune Pedersen', + affiliation: 'Danish National Genome Center', + email: 'aspe@clin.au.dk', + github: 'https://github.com/asp8200', + contribution: ['contributor'], + orcid: 'https://orcid.org/0009-0008-1112-841X' + ], + [ + name: 'Gwenna Breton', + affiliation: 'Clinical Genomics Gothenburg, Sahlgrenska University Hospital and University of Gothenburg', + email: 'gwenna.breton@gu.se', + github: 'https://github.com/Gwennid', + contribution: ['contributor'], + orcid: 'https://orcid.org/0000-0002-4100-9963' + ], + [ + name: 'Sima Rahimi', + affiliation: 'Clinical Genomics Lund, Lund University', + email: 'sima.rahimi@med.lu.se', + github: 'https://github.com/sima-r', + contribution: ['contributor'] + ], + [ + name: 'Felix Lenner', + affiliation: 'Department of Immunology, Genetics and Pathology, Uppsala University, Sweden; Science for Life Laboratory, Department of Microbiology, Tumour and Cell Biology, Karolinska Institutet, Stockholm, Sweden', + email: 'felix.lenner@scilifelab.se', + github: 'https://github.com/fellen31', + contribution: ['contributor'], + orcid: 'https://orcid.org/0000-0002-9594-0710' + ], + [ + name: 'Maxime U Garcia', + affiliation: 'Seqera', + email: 'maxime.garcia@seqera.io', + github: 'https://github.com/maxulysse', + contribution: ['contributor'], + orcid: 'https://orcid.org/0000-0003-2827-9261' + ], + [ + name: 'and the nf-core/raredisease team', + affiliation: 'nf-core community', email: '', - github: '', - contribution: [], // List of contribution types ('author', 'maintainer' or 'contributor') + github: 'https://github.com/nf-core', + contribution: ['contributor'], orcid: '' - ], + ] ] homePage = 'https://github.com/nf-core/raredisease' description = """call and score variants from WGS/WES of rare disease patients""" @@ -355,7 +424,7 @@ manifest { defaultBranch = 'master' nextflowVersion = '!>=24.04.2' version = '2.3.0dev' - doi = '' + doi = '10.5281/zenodo.7995798' } // Load DSL2 module options from config files, where each file contains the options for modules used in the eponymous subworkflow. diff --git a/ro-crate-metadata.json b/ro-crate-metadata.json index 248e3d43..ab8334d0 100644 --- a/ro-crate-metadata.json +++ b/ro-crate-metadata.json @@ -22,8 +22,8 @@ "@id": "./", "@type": "Dataset", "creativeWorkStatus": "InProgress", - "datePublished": "2024-12-20T13:10:31+00:00", - "description": "

\n \n \n \"nf-core/raredisease\"\n \n

[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.XXXXXXX-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.XXXXXXX)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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)\n\n## Introduction\n\n**nf-core/raredisease** is a bioinformatics pipeline that ...\n\n\n\n\n1. Read QC ([`FastQC`](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/))2. Present QC for raw reads ([`MultiQC`](http://multiqc.info/))\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\n\n\nNow, you can run the pipeline using:\n\n\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nTo see the results of an example test run with a full size dataset refer to the [results](https://nf-co.re/raredisease/results) tab on the nf-core website pipeline page.\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was originally written by Clinical Genomics Stockholm.\n\nWe thank the following people for their extensive assistance in the development of this pipeline:\n\n\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\n\n\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n", + "datePublished": "2025-01-17T12:53:41+00:00", + "description": "

\n \n \n \"nf-core/raredisease\"\n \n

\n\n[![GitHub Actions CI Status](https://github.com/nf-core/raredisease/actions/workflows/ci.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/ci.yml)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n[![nf-test](https://img.shields.io/badge/unit_tests-nf--test-337ab7.svg)](https://www.nf-test.com)\n[![GitHub Actions Linting Status](https://github.com/nf-core/raredisease/actions/workflows/linting.yml/badge.svg)](https://github.com/nf-core/raredisease/actions/workflows/linting.yml)[![AWS CI](https://img.shields.io/badge/CI%20tests-full%20size-FF9900?labelColor=000000&logo=Amazon%20AWS)](https://nf-co.re/raredisease/results)[![Cite with Zenodo](http://img.shields.io/badge/DOI-10.5281/zenodo.7995798-1073c8?labelColor=000000)](https://doi.org/10.5281/zenodo.7995798)\n\n[![Nextflow](https://img.shields.io/badge/nextflow%20DSL2-%E2%89%A524.04.2-23aa62.svg)](https://www.nextflow.io/)\n[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)\n[![run with docker](https://img.shields.io/badge/run%20with-docker-0db7ed?labelColor=000000&logo=docker)](https://www.docker.com/)\n[![run with singularity](https://img.shields.io/badge/run%20with-singularity-1d355c.svg?labelColor=000000)](https://sylabs.io/docs/)\n[![Launch on Seqera Platform](https://img.shields.io/badge/Launch%20%F0%9F%9A%80-Seqera%20Platform-%234256e7)](https://cloud.seqera.io/launch?pipeline=https://github.com/nf-core/raredisease)\n\n[![Get help on Slack](http://img.shields.io/badge/slack-nf--core%20%23raredisease-4A154B?labelColor=000000&logo=slack)](https://nfcore.slack.com/channels/raredisease)[![Follow on Twitter](http://img.shields.io/badge/twitter-%40nf__core-1DA1F2?labelColor=000000&logo=twitter)](https://twitter.com/nf_core)[![Follow on Mastodon](https://img.shields.io/badge/mastodon-nf__core-6364ff?labelColor=FFFFFF&logo=mastodon)](https://mstdn.science/@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)\n\n#### TOC\n\n- [Introduction](#introduction)\n- [Pipeline summary](#pipeline-summary)\n- [Usage](#usage)\n- [Pipeline output](#pipeline-output)\n- [Credits](#credits)\n- [Contributions and Support](#contributions-and-support)\n- [Citations](#citations)\n\n## Introduction\n\n**nf-core/raredisease** is a best-practice bioinformatic pipeline for calling and scoring variants from WGS/WES data from rare disease patients. This pipeline is heavily inspired by [MIP](https://github.com/Clinical-Genomics/MIP).\n\nThe 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!\n\nOn 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/raredisease/results).\n\n## Pipeline summary\n\n \n \n \"nf-core/raredisease\n \n\n**1. Metrics:**\n\n- [FastQC](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)\n- [Mosdepth](https://github.com/brentp/mosdepth)\n- [MultiQC](http://multiqc.info/)\n- [Picard's CollectMutipleMetrics, CollectHsMetrics, and CollectWgsMetrics](https://broadinstitute.github.io/picard/)\n- [Qualimap](http://qualimap.conesalab.org/)\n- [Sentieon's WgsMetricsAlgo](https://support.sentieon.com/manual/usages/general/)\n- [TIDDIT's cov](https://github.com/J35P312/)\n\n**2. Alignment:**\n\n- [Bwa-mem2](https://github.com/bwa-mem2/bwa-mem2)\n- [BWA-MEME](https://github.com/kaist-ina/BWA-MEME)\n- [BWA](https://github.com/lh3/bwa)\n- [Sentieon DNAseq](https://support.sentieon.com/manual/DNAseq_usage/dnaseq/)\n\n**3. Variant calling - SNV:**\n\n- [DeepVariant](https://github.com/google/deepvariant)\n- [Sentieon DNAscope](https://support.sentieon.com/manual/DNAscope_usage/dnascope/)\n\n**4. Variant calling - SV:**\n\n- [Manta](https://github.com/Illumina/manta)\n- [TIDDIT's sv](https://github.com/SciLifeLab/TIDDIT)\n- Copy number variant calling:\n - [CNVnator](https://github.com/abyzovlab/CNVnator)\n - [GATK GermlineCNVCaller](https://github.com/broadinstitute/gatk)\n\n**5. Annotation - SNV:**\n\n- [bcftools roh](https://samtools.github.io/bcftools/bcftools.html#roh)\n- [vcfanno](https://github.com/brentp/vcfanno)\n- [CADD](https://cadd.gs.washington.edu/)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n- [UPD](https://github.com/bjhall/upd)\n- [Chromograph](https://github.com/Clinical-Genomics/chromograph)\n\n**6. Annotation - SV:**\n\n- [SVDB query](https://github.com/J35P312/SVDB#Query)\n- [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**7. Mitochondrial analysis:**\n\n- [Alignment and variant calling - GATK Mitochondrial short variant discovery pipeline ](https://gatk.broadinstitute.org/hc/en-us/articles/4403870837275-Mitochondrial-short-variant-discovery-SNVs-Indels-)\n- [eKLIPse](https://github.com/dooguypapua/eKLIPse/tree/master)\n- Annotation:\n - [HaploGrep2](https://github.com/seppinho/haplogrep-cmd)\n - [Hmtnote](https://github.com/robertopreste/HmtNote)\n - [vcfanno](https://github.com/brentp/vcfanno)\n - [CADD](https://cadd.gs.washington.edu/)\n - [VEP](https://www.ensembl.org/info/docs/tools/vep/index.html)\n\n**8. Variant calling - repeat expansions:**\n\n- [Expansion Hunter](https://github.com/Illumina/ExpansionHunter)\n- [Stranger](https://github.com/Clinical-Genomics/stranger)\n\n**9. Variant calling - mobile elements:**\n\n- [RetroSeq](https://github.com/tk2/RetroSeq)\n\n**10. Rank variants - SV and SNV:**\n\n- [GENMOD](https://github.com/Clinical-Genomics/genmod)\n\n**11. Variant evaluation:**\n\n- [RTG Tools](https://github.com/RealTimeGenomics/rtg-tools)\n\nNote that it is possible to include/exclude certain tools or steps.\n\n## Usage\n\n> [!NOTE]\n> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow.Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data.\n\nFirst, prepare a samplesheet with your input data that looks as follows:\n\n`samplesheet.csv`:\n\n```csv\nsample,lane,fastq_1,fastq_2,sex,phenotype,paternal_id,maternal_id,case_id\nhugelymodelbat,1,reads_1.fastq.gz,reads_2.fastq.gz,1,2,,,justhusky\n```\n\nEach row represents a fastq file (single-end) or a pair of fastq files (paired end).\n\nSecond, ensure that you have defined the path to reference files and parameters required for the type of analysis that you want to perform. More information about this can be found [here](https://github.com/nf-core/raredisease/blob/dev/docs/usage.md).\n\nNow, you can run the pipeline using:\n\n```bash\nnextflow run nf-core/raredisease \\\n -profile \\\n --input samplesheet.csv \\\n --outdir \n```\n\n> [!WARNING]\n> Please provide pipeline parameters via the CLI or Nextflow `-params-file` option. Custom config files including those provided by the `-c` Nextflow option can be used to provide any configuration _**except for parameters**_; see [docs](https://nf-co.re/docs/usage/getting_started/configuration#custom-configuration-files).\n\nFor more details and further functionality, please refer to the [usage documentation](https://nf-co.re/raredisease/usage) and the [parameter documentation](https://nf-co.re/raredisease/parameters).\n\n## Pipeline output\n\nFor more details about the output files and reports, please refer to the\n[output documentation](https://nf-co.re/raredisease/output).\n\n## Credits\n\nnf-core/raredisease was written in a collaboration between the Clinical Genomics nodes in Sweden, with major contributions from [Ramprasad Neethiraj](https://github.com/ramprasadn), [Anders Jemt](https://github.com/jemten), [Lucia Pena Perez](https://github.com/Lucpen), and [Mei Wu](https://github.com/projectoriented) at Clinical Genomics Stockholm.\n\nAdditional contributors were [Sima Rahimi](https://github.com/sima-r), [Gwenna Breton](https://github.com/Gwennid) and [Emma V\u00e4sterviga](https://github.com/EmmaCAndersson) (Clinical Genomics Gothenburg); [Halfdan Rydbeck](https://github.com/hrydbeck) and [Lauri Mesilaakso](https://github.com/ljmesi) (Clinical Genomics Link\u00f6ping); [Subazini Thankaswamy Kosalai](https://github.com/sysbiocoder) (Clinical Genomics \u00d6rebro); [Annick Renevey](https://github.com/rannick) and [Peter Pruisscher](https://github.com/peterpru) (Clinical Genomics Stockholm); [Ryan Kennedy](https://github.com/ryanjameskennedy) (Clinical Genomics Lund); [Anders Sune Pedersen](https://github.com/asp8200) (Danish National Genome Center) and [Lucas Taniguti](https://github.com/lmtani).\n\nWe thank the nf-core community for their extensive assistance in the development of this pipeline.\n\n## Contributions and Support\n\nIf you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md).\n\nFor further information or help, don't hesitate to get in touch on the [Slack `#raredisease` channel](https://nfcore.slack.com/channels/raredisease) (you can join with [this invite](https://nf-co.re/join/slack)).\n\n## Citations\n\nIf you use nf-core/raredisease for your analysis, please cite it using the following doi: [10.5281/zenodo.7995798](https://doi.org/10.5281/zenodo.7995798)\n\nAn extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file.\n\nYou can cite the `nf-core` publication as follows:\n\n> **The nf-core framework for community-curated bioinformatics pipelines.**\n>\n> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.\n>\n> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x).\n\nYou can read more about MIP's use in healthcare in,\n\n> Stranneheim H, Lagerstedt-Robinson K, Magnusson M, et al. Integration of whole genome sequencing into a healthcare setting: high diagnostic rates across multiple clinical entities in 3219 rare disease patients. Genome Med. 2021;13(1):40. doi:10.1186/s13073-021-00855-5\n", "hasPart": [ { "@id": "main.nf" @@ -31,6 +31,9 @@ { "@id": "assets/" }, + { + "@id": "bin/" + }, { "@id": "conf/" }, @@ -43,6 +46,9 @@ { "@id": "modules/" }, + { + "@id": "modules/local/" + }, { "@id": "modules/nf-core/" }, @@ -99,7 +105,7 @@ }, "mentions": [ { - "@id": "#183fe8e5-2c6e-405f-b892-34de0407e024" + "@id": "#e2c32c4a-673a-4590-9c0b-03aa9700c1c6" } ], "name": "nf-core/raredisease" @@ -126,8 +132,28 @@ "SoftwareSourceCode", "ComputationalWorkflow" ], + "creator": [ + { + "@id": "https://orcid.org/0000-0002-4100-9963" + }, + { + "@id": "https://orcid.org/0000-0003-1316-2845" + }, + { + "@id": "https://orcid.org/0000-0002-5044-7754" + }, + { + "@id": "https://orcid.org/0000-0001-7313-3734" + }, + { + "@id": "#25568561+projectoriented@users.noreply.github.com" + }, + { + "@id": "https://orcid.org/0000-0002-2219-0197" + } + ], "dateCreated": "", - "dateModified": "2024-12-20T13:10:31Z", + "dateModified": "2025-01-17T13:53:41Z", "dct:conformsTo": "https://bioschemas.org/profiles/ComputationalWorkflow/1.0-RELEASE/", "keywords": [ "nf-core", @@ -144,6 +170,20 @@ "license": [ "MIT" ], + "maintainer": [ + { + "@id": "https://orcid.org/0000-0002-4100-9963" + }, + { + "@id": "https://orcid.org/0000-0002-5044-7754" + }, + { + "@id": "https://orcid.org/0000-0001-7313-3734" + }, + { + "@id": "https://orcid.org/0000-0002-2219-0197" + } + ], "name": [ "nf-core/raredisease" ], @@ -174,11 +214,11 @@ "version": "!>=24.04.2" }, { - "@id": "#183fe8e5-2c6e-405f-b892-34de0407e024", + "@id": "#e2c32c4a-673a-4590-9c0b-03aa9700c1c6", "@type": "TestSuite", "instance": [ { - "@id": "#53b042a2-0505-4b40-9fb6-f5e7ec5d5ab5" + "@id": "#8d046aff-c7d4-46a9-b3ff-eadbc1d03d23" } ], "mainEntity": { @@ -187,7 +227,7 @@ "name": "Test suite for nf-core/raredisease" }, { - "@id": "#53b042a2-0505-4b40-9fb6-f5e7ec5d5ab5", + "@id": "#8d046aff-c7d4-46a9-b3ff-eadbc1d03d23", "@type": "TestInstance", "name": "GitHub Actions workflow for testing nf-core/raredisease", "resource": "repos/nf-core/raredisease/actions/workflows/ci.yml", @@ -209,6 +249,11 @@ "@type": "Dataset", "description": "Additional files" }, + { + "@id": "bin/", + "@type": "Dataset", + "description": "Scripts that must be callable from a pipeline process" + }, { "@id": "conf/", "@type": "Dataset", @@ -229,6 +274,11 @@ "@type": "Dataset", "description": "Modules used by the pipeline" }, + { + "@id": "modules/local/", + "@type": "Dataset", + "description": "Pipeline-specific modules" + }, { "@id": "modules/nf-core/", "@type": "Dataset", @@ -314,6 +364,42 @@ "@type": "Organization", "name": "nf-core", "url": "https://nf-co.re/" + }, + { + "@id": "https://orcid.org/0000-0002-4100-9963", + "@type": "Person", + "email": "Gwenna.breton@gu.se", + "name": "Gwenna Breton" + }, + { + "@id": "https://orcid.org/0000-0003-1316-2845", + "@type": "Person", + "email": "raysloks@gmail.com", + "name": "Emil Bertilsson" + }, + { + "@id": "https://orcid.org/0000-0002-5044-7754", + "@type": "Person", + "email": "lucia.pena.perez@scilifelab.se", + "name": "Luc\u00eda Pe\u00f1a-P\u00e9rez" + }, + { + "@id": "https://orcid.org/0000-0001-7313-3734", + "@type": "Person", + "email": "20065894+ramprasadn@users.noreply.github.com", + "name": "Ramprasad Neethiraj" + }, + { + "@id": "#25568561+projectoriented@users.noreply.github.com", + "@type": "Person", + "email": "25568561+projectoriented@users.noreply.github.com", + "name": "Mei Wu" + }, + { + "@id": "https://orcid.org/0000-0002-2219-0197", + "@type": "Person", + "email": "jemten@users.noreply.github.com", + "name": "Anders Jemt" } ] } \ No newline at end of file From 8d7fd4bed5cef78a87244b6273f84a5d8cc51f22 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 14:15:47 +0100 Subject: [PATCH 2/9] update contributors --- nextflow.config | 7 +++++++ 1 file changed, 7 insertions(+) diff --git a/nextflow.config b/nextflow.config index 9926f977..3dbea604 100644 --- a/nextflow.config +++ b/nextflow.config @@ -409,6 +409,13 @@ manifest { contribution: ['contributor'], orcid: 'https://orcid.org/0000-0003-2827-9261' ], + [ + name: 'Eva Caceres', + affiliation: 'Clinical Genomics Stockholm', + email: 'eva.caceres@scilifelab.se', + github: 'https://github.com/fevac', + contribution: ['contributor'] + ], [ name: 'and the nf-core/raredisease team', affiliation: 'nf-core community', From 12600acb37a321ea99630db02d1eb0ada52af312 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 15:05:13 +0100 Subject: [PATCH 3/9] update config --- conf/modules/annotate_cadd.config | 2 +- conf/modules/annotate_genome_snvs.config | 6 +++--- conf/modules/annotate_rhocallviz.config | 2 +- conf/modules/qc_bam.config | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/conf/modules/annotate_cadd.config b/conf/modules/annotate_cadd.config index 404e71e5..b71de347 100644 --- a/conf/modules/annotate_cadd.config +++ b/conf/modules/annotate_cadd.config @@ -17,7 +17,7 @@ process { withName: '.*:ANNOTATE_CADD.*' { - ext.when = { ( !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun) } + ext.when = { ( !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun) } } withName: '.*:ANNOTATE_CADD:BCFTOOLS_VIEW' { diff --git a/conf/modules/annotate_genome_snvs.config b/conf/modules/annotate_genome_snvs.config index ceac8ed5..b8ada200 100644 --- a/conf/modules/annotate_genome_snvs.config +++ b/conf/modules/annotate_genome_snvs.config @@ -42,13 +42,13 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:UPD_SITES' { ext.prefix = { "${meta.upd_child}_upd_sites" } ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} sites"} - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } } withName: '.*ANNOTATE_GENOME_SNVS:UPD_REGIONS' { ext.prefix = { "${meta.upd_child}_upd_regions" } ext.args = {"--af-tag GNOMADAF --proband ${meta.upd_child} --mother ${meta.mother} --father ${meta.father} regions --min-size 5 --min-sites 1"} - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } } withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_SITES' { @@ -65,7 +65,7 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:CHROMOGRAPH_REGIONS' { ext.prefix = { "${meta6.upd_child}_chromograph_regions" } ext.args = { '--euploid' } - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } tag = {"${meta6.upd_child}"} publishDir = [ path: { "${params.outdir}/annotate_snv/genome" }, diff --git a/conf/modules/annotate_rhocallviz.config b/conf/modules/annotate_rhocallviz.config index 32822b9d..5311bfd2 100644 --- a/conf/modules/annotate_rhocallviz.config +++ b/conf/modules/annotate_rhocallviz.config @@ -45,7 +45,7 @@ process { withName: '.*ANNOTATE_GENOME_SNVS:ANNOTATE_RHOCALLVIZ:CHROMOGRAPH_AUTOZYG' { ext.prefix = { "${autozyg.simpleName}_autozyg_chromograph" } ext.args = { "--euploid" } - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } publishDir = [ path: { "${params.outdir}/annotate_snv/genome/" }, mode: params.publish_dir_mode, diff --git a/conf/modules/qc_bam.config b/conf/modules/qc_bam.config index 5aa0d7f3..afa9f240 100644 --- a/conf/modules/qc_bam.config +++ b/conf/modules/qc_bam.config @@ -60,7 +60,7 @@ process { withName: '.*QC_BAM:NGSBITS_SAMPLEGENDER' { // NGSBITS_SAMPLEGENDER needs a chrX and chrY in order to run so we skip it for the two test profiles - ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon']).size() >= 1) || workflow.stubRun } + ext.when = { !(workflow.profile.tokenize(',').intersect(['test', 'test_one_sample', 'test_sentieon', 'test_full']).size() >= 1) || workflow.stubRun } ext.prefix = { "${meta.id}_ngsbits_sex" } publishDir = [ path: { "${params.outdir}/ngsbits_samplegender" }, From 08ae78a13a3a315f7a5e573b3551c64c94ead9a1 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 15:09:54 +0100 Subject: [PATCH 4/9] update config --- conf/modules/call_snv_MT.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/modules/call_snv_MT.config b/conf/modules/call_snv_MT.config index 2c3a28fd..22e6fcb0 100644 --- a/conf/modules/call_snv_MT.config +++ b/conf/modules/call_snv_MT.config @@ -50,7 +50,7 @@ process { } withName: '.*CALL_SNV_MT_SHIFT:HAPLOCHECK_MT' { - ext.when = null + ext.when = false } } From 7bb78a391fb748b419c472fb67a3092bad2d8764 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 15:11:48 +0100 Subject: [PATCH 5/9] update docs --- docs/output.md | 1 + 1 file changed, 1 insertion(+) diff --git a/docs/output.md b/docs/output.md index 0b8c5524..5d87a5c4 100644 --- a/docs/output.md +++ b/docs/output.md @@ -58,6 +58,7 @@ The pipeline is built using [Nextflow](https://www.nextflow.io/) and processes d - [SVDB query](#svdb-query) - [VEP](#vep-1) - [Mitochondrial analysis](#mitochondrial-analysis) + - [Haplocheck](#haplocheck) - [Alignment and variant calling](#alignment-and-variant-calling) - [MT deletion script](#mt-deletion-script) - [eKLIPse](#eklipse) From bfe6440b68d03b0ea0a9a2d5ef4a478d369c0b21 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 17:15:12 +0100 Subject: [PATCH 6/9] Add Mei --- nextflow.config | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/nextflow.config b/nextflow.config index 3dbea604..3fd7703f 100644 --- a/nextflow.config +++ b/nextflow.config @@ -354,6 +354,11 @@ manifest { contribution: ['author', 'maintainer'], orcid: 'https://orcid.org/0000-0002-2219-0197' ], + [ + name: 'Mei Wu', + github: 'https://github.com/projectoriented', + contribution: ['contributor'] + ], [ name: 'Lucía Peña-Pérez', affiliation: 'Center for Inherited Metabolic Diseases, Karolinska University Hospital, Stockholm, Sweden; Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden', From 517a8d11c80ffa63ecca2831271e70eb6313004f Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 17:17:15 +0100 Subject: [PATCH 7/9] remove TODO --- .github/workflows/awsfulltest.yml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/awsfulltest.yml b/.github/workflows/awsfulltest.yml index 357a2a91..1843aa58 100644 --- a/.github/workflows/awsfulltest.yml +++ b/.github/workflows/awsfulltest.yml @@ -45,7 +45,6 @@ jobs: - name: Launch workflow via Seqera Platform uses: seqeralabs/action-tower-launch@v2 - # TODO nf-core: You can customise AWS full pipeline tests as required # Add full size test data (but still relatively small datasets for few samples) # on the `test_full.config` test runs with only one set of parameters with: From 644d53dbfa1a4fad23713645a7974af0b81f7e45 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 17:30:26 +0100 Subject: [PATCH 8/9] bump version --- .nf-core.yml | 2 +- CHANGELOG.md | 2 +- assets/multiqc_config.yml | 7 ++++--- nextflow.config | 2 +- 4 files changed, 7 insertions(+), 6 deletions(-) diff --git a/.nf-core.yml b/.nf-core.yml index 6b8986e2..4216b5ee 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -18,4 +18,4 @@ template: name: raredisease org: nf-core outdir: . - version: 2.3.0dev + version: 2.3.0 diff --git a/CHANGELOG.md b/CHANGELOG.md index 3f5ee062..ce4f6e9b 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -3,7 +3,7 @@ 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). -## 2.3.0dev - Getafix [xxxx-xx-xx] +## 2.3.0 - Getafix [xxxx-xx-xx] ### `Added` diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml index 53538d6c..f7e6b4cb 100644 --- a/assets/multiqc_config.yml +++ b/assets/multiqc_config.yml @@ -3,9 +3,10 @@ custom_logo_url: https://github.com/nf-core/raredisease/ custom_logo_title: "nf-core/raredisease" report_comment: > - This report has been generated by the nf-core/raredisease - analysis pipeline. For information about how to interpret these results, please see the - documentation. + This report has been generated by the nf-core/raredisease analysis pipeline. For information about + how to interpret these results, please see the documentation. report_section_order: "nf-core-raredisease-methods-description": order: -1000 diff --git a/nextflow.config b/nextflow.config index 3fd7703f..10351888 100644 --- a/nextflow.config +++ b/nextflow.config @@ -435,7 +435,7 @@ manifest { mainScript = 'main.nf' defaultBranch = 'master' nextflowVersion = '!>=24.04.2' - version = '2.3.0dev' + version = '2.3.0' doi = '10.5281/zenodo.7995798' } From 1c9eaa63f8de45ee94a29767f4904986a8947682 Mon Sep 17 00:00:00 2001 From: Ramprasad Neethiraj <20065894+ramprasadn@users.noreply.github.com> Date: Fri, 17 Jan 2025 17:35:30 +0100 Subject: [PATCH 9/9] custom configs --- nextflow.config | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nextflow.config b/nextflow.config index 10351888..021027eb 100644 --- a/nextflow.config +++ b/nextflow.config @@ -279,7 +279,7 @@ profiles { includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/nfcore_custom.config" : "/dev/null" // Load nf-core/raredisease custom profiles from different institutions. -// includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/raredisease.config" : "/dev/null" +includeConfig !System.getenv('NXF_OFFLINE') && params.custom_config_base ? "${params.custom_config_base}/pipeline/raredisease.config" : "/dev/null" // Set default registry for Apptainer, Docker, Podman, Charliecloud and Singularity independent of -profile // Will not be used unless Apptainer / Docker / Podman / Charliecloud / Singularity are enabled