From 79b9674bfd7649f622b5a2881b51770e836c0985 Mon Sep 17 00:00:00 2001 From: Felix Lenner <52530259+fellen31@users.noreply.github.com> Date: Thu, 17 Oct 2024 14:03:31 +0200 Subject: [PATCH] Add additional mkdocs files (#431) --- .nf-core.yml | 1 + CHANGELOG.md | 3 + README.md | 2 +- CITATIONS.md => docs/CITATIONS.md | 0 docs/index.md | 111 ++++++++++++++++++++++++++++++ mkdocs.yml | 66 ++++++++++++++++++ 6 files changed, 182 insertions(+), 1 deletion(-) rename CITATIONS.md => docs/CITATIONS.md (100%) create mode 100644 docs/index.md create mode 100644 mkdocs.yml diff --git a/.nf-core.yml b/.nf-core.yml index 8a98a163..b53031cd 100644 --- a/.nf-core.yml +++ b/.nf-core.yml @@ -1,6 +1,7 @@ bump_version: null lint: files_exist: + - CITATIONS.md - CODE_OF_CONDUCT.md - assets/nf-core-nallo_logo_light.png - docs/README.md diff --git a/CHANGELOG.md b/CHANGELOG.md index 52dcb819..78c9608c 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -23,6 +23,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#408](https://github.com/genomic-medicine-sweden/nallo/pull/408) - Added a new subworkflow to annotate SVs - [#417](https://github.com/genomic-medicine-sweden/nallo/pull/417) - Added `FOUND_IN=deepvariant` tags to SNV calling output - [#419](https://github.com/genomic-medicine-sweden/nallo/pull/419) - Added support for SV filtering using input BED file ([#348](https://github.com/genomic-medicine-sweden/nallo/issues/348)) +- [#430](https://github.com/genomic-medicine-sweden/nallo/pull/430) - Added a GitHub action to build and publish docs to GitHub Pages +- [#431](https://github.com/genomic-medicine-sweden/nallo/pull/431) - Added files needed to automatically build and publish docs to GitHub Pages ### `Changed` @@ -53,6 +55,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0 - [#422](https://github.com/genomic-medicine-sweden/nallo/pull/422) - Updated nf-core/tools template to v3.0.1 - [#423](https://github.com/genomic-medicine-sweden/nallo/pull/423) - Updated metro map - [#428](https://github.com/genomic-medicine-sweden/nallo/pull/428) - Changed from using bcftools to SVDB for SV merging +- [#431](https://github.com/genomic-medicine-sweden/nallo/pull/431) - Changed `CITATIONS.md` to `docs/CITATIONS.md`, ### `Removed` diff --git a/README.md b/README.md index 4dd88d57..4d0856da 100644 --- a/README.md +++ b/README.md @@ -112,4 +112,4 @@ This pipeline uses code and infrastructure developed and maintained by the [nf-c > > _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). -An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. +An extensive list of references for the tools used by the pipeline can be found in the [`docs/CITATIONS.md`](CITATIONS.md) file. diff --git a/CITATIONS.md b/docs/CITATIONS.md similarity index 100% rename from CITATIONS.md rename to docs/CITATIONS.md diff --git a/docs/index.md b/docs/index.md new file mode 100644 index 00000000..1413a087 --- /dev/null +++ b/docs/index.md @@ -0,0 +1,111 @@ +--- +title: genomic-medicine-sweden/nallo +description: A bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. +--- + +## Introduction + +**genomic-medicine-sweden/nallo** is a bioinformatics analysis pipeline for long-reads from both PacBio and (targeted) ONT-data, focused on rare-disease. Heavily influenced by best-practice pipelines such as [nf-core/sarek](https://nf-co.re/sarek), [nf-core/raredisease](https://nf-co.re/raredisease), [nf-core/nanoseq](https://github.com/nf-core/nanoseq), [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). + +## Overview + + + genomic-medicine-sweden/nallo workflow + + +## Pipeline summary + +##### QC + +- Read QC with [FastQC](http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), [cramino](https://github.com/wdecoster/cramino) and [mosdepth](https://github.com/brentp/mosdepth) + +##### Alignment & assembly + +- Align reads to reference with [minimap2](https://github.com/lh3/minimap2) +- Assemble (trio-binned) haploid genomes with [hifiasm](https://github.com/chhylp123/hifiasm) (HiFi only) + +##### Variant calling + +- Call SNVs & joint genotyping with [deepvariant](https://github.com/google/deepvariant) and [GLNexus](https://github.com/dnanexus-rnd/GLnexus) +- Call SVs with [Severus](https://github.com/KolmogorovLab/Severus) or [Sniffles2](https://github.com/fritzsedlazeck/Sniffles) +- Call CNVs with [HiFiCNV](https://github.com/PacificBiosciences/HiFiCNV) +- Call tandem repeats with [TRGT](https://github.com/PacificBiosciences/trgt/tree/main) (HiFi only) +- Call paralogous genes with [Paraphase](https://github.com/PacificBiosciences/paraphase) +- Call variants from assembly with [dipcall](https://github.com/lh3/dipcall) (HiFi only) + +##### Phasing and methylation + +- Phase and haplotag reads with [LongPhase](https://github.com/twolinin/longphase), [whatshap](https://github.com/whatshap/whatshap) or [HiPhase](https://github.com/PacificBiosciences/HiPhase) +- Create methylation pileups with [modkit](https://github.com/nanoporetech/modkit) + +##### Annotation + +- Annotate SNVs and INDELs with databases of choice, i.e. [gnomAD](https://gnomad.broadinstitute.org), [CADD](https://cadd.gs.washington.edu) etc. with [echtvar](https://github.com/brentp/echtvar) and [VEP](https://github.com/Ensembl/ensembl-vep) +- Annotate repeat expansions with [stranger](https://github.com/Clinical-Genomics/stranger) +- Annotate SVs with [SVDB](https://github.com/J35P312/SVDB) and [VEP](https://github.com/Ensembl/ensembl-vep) + +##### Ranking + +- Rank SNVs with [GENMOD](https://github.com/Clinical-Genomics/genmod) + +## Usage + +> [!NOTE] +> If you are new to Nextflow and nf-core, please refer to [this page](https://nf-co.re/docs/usage/installation) on how to set-up Nextflow. Make sure to [test your setup](https://nf-co.re/docs/usage/introduction#how-to-run-a-pipeline) with `-profile test` before running the workflow on actual data. + +Prepare a samplesheet with input data: + +`samplesheet.csv` + +``` +project,sample,file,family_id,paternal_id,maternal_id,sex,phenotype +NIST,HG002,/path/to/HG002.fastq.gz,FAM1,HG003,HG004,1,2 +NIST,HG005,/path/to/HG005.bam,FAM1,HG003,HG004,2,1 +``` + +Supply a reference genome with `--fasta` and choose a matching `--preset` for your data (`revio`, `pacbio`, `ONT_R10`). Now, you can run the pipeline using: + +```bash +nextflow run genomic-medicine-sweden/nallo \ + -profile \ + --input samplesheet.csv \ + --preset \ + --fasta \ + --outdir +``` + +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**_; +> see [docs](https://nf-co.re/usage/configuration#custom-configuration-files). + +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 genomic-medicine-sweden/nallo +``` + +## Credits + +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: + +## Contributions and Support + +If you would like to contribute to this pipeline, please see the [contributing guidelines](.github/CONTRIBUTING.md). + +## Citations + +If you use genomic-medicine-sweden/nallo for your analysis, please cite it using the following doi: [10.5281/zenodo.13748210](https://doi.org/10.5281/zenodo.13748210). + +This pipeline uses code and infrastructure developed and maintained by the [nf-core](https://nf-co.re) community, reused here under the [MIT license](https://github.com/nf-core/tools/blob/main/LICENSE). + +> **The nf-core framework for community-curated bioinformatics pipelines.** +> +> Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen. +> +> _Nat Biotechnol._ 2020 Feb 13. doi: [10.1038/s41587-020-0439-x](https://dx.doi.org/10.1038/s41587-020-0439-x). + +An extensive list of references for the tools used by the pipeline can be found in the [`CITATIONS.md`](CITATIONS.md) file. diff --git a/mkdocs.yml b/mkdocs.yml new file mode 100644 index 00000000..418a2604 --- /dev/null +++ b/mkdocs.yml @@ -0,0 +1,66 @@ +# based on: https://github.com/nf-cmgg/structural/blob/master/mkdocs.yml +site_name: genomic-medicine-sweden/nallo +repo_name: genomic-medicine-sweden/nallo +repo_url: https://github.com/genomic-medicine-sweden/nallo +site_url: https://genomic-medicine-sweden.github.io/nallo + +nav: + - Home: index.md + - Usage: usage.md + - Output: output.md + - Parameters: parameters.md + - Citations: CITATIONS.md + +theme: + name: material + icon: + logo: octicons/checklist-16 + repo: fontawesome/brands/github + palette: + # Palette toggle for dark mode + - media: "(prefers-color-scheme: dark)" + scheme: slate + primary: custom + accent: custom + toggle: + icon: material/weather-sunny + name: Switch to light mode + # Palette toggle for light mode + - media: "(prefers-color-scheme: light)" + scheme: default + primary: custom + accent: custom + toggle: + icon: material/weather-night + name: Switch to dark mode + font: + text: Inter + features: + - content.code.annotate + - content.code.copy + - navigation.instant + - navigation.top + - navigation.tracking + - navigation.sections + - navigation.footer + - search.share + - toc.follow + +markdown_extensions: + - attr_list + - md_in_html + - admonition + - pymdownx.emoji: + emoji_index: !!python/name:material.extensions.emoji.twemoji + emoji_generator: !!python/name:material.extensions.emoji.to_svg + - pymdownx.highlight: + anchor_linenums: true + line_spans: __span + pygments_lang_class: true + - pymdownx.inlinehilite + - pymdownx.snippets + - pymdownx.superfences + +extra: + version: + provider: mike