Add additional mkdocs files (#431)

.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

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`
 

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.

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
+
+<picture align="center">
+    <img alt="genomic-medicine-sweden/nallo workflow" src="docs/images/nallo_metromap.png">
+  </picture>
+
+## 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 <docker/singularity/.../institute> \
+    --input samplesheet.csv \
+    --preset <revio/pacbio/ONT_R10> \
+    --fasta <reference.fasta> \
+    --outdir <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.

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