Merge pull request #168 from hydra-genetics/rtd

docs: Added read the docs for all rules!

.github/workflows/test-build-mkdocs.yaml

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+name: build mkdocs
+
+on:
+  push:
+    branches:
+     - develop
+     - master
+  pull_request:
+    branches:
+     - develop
+     - master
+  workflow_dispatch:
+
+jobs:
+  build-mkdocs:
+    name: build mkdocs
+    runs-on: ubuntu-22.04
+    steps:
+      - uses: actions/checkout@v3
+      - name: Set up Python 3.8
+        uses: actions/setup-python@v3
+        with:
+          python-version: 3.8
+      - name: Install requirements.txt
+        run: |
+          pip install -r requirements.txt
+      - name: Install requirements.test.txt
+        run: |
+          pip install -r requirements.test.txt
+          pip install -r docs/requirements.txt
+      - name: build mkdocs
+        run: |
+          mkdocs build

.readthedocs.yaml

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+# .readthedocs.yaml
+# Read the Docs configuration file
+# See https://docs.readthedocs.io/en/stable/config-file/v2.html for details
+
+# Required
+version: 2
+
+# Set the version of Python and other tools you might need
+build:
+  os: ubuntu-22.04
+  tools:
+    python: "3.11"
+
+mkdocs:
+  configuration: mkdocs.yml
+
+# Optionally declare the Python requirements required to build your docs
+python:
+   install:
+   - requirements: docs/requirements.txt

README.md

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+<p align="center">
+<a href="https://hydra-genetics-cnv-sv.readthedocs.io">https://hydra-genetics-cnv-sv.readthedocs.io</a>
+</p>
+
 # <img src="images/hydragenetics.png" width=40 /> hydra-genetics/cnv_sv
 
 Snakemake module containing steps to call copy number variants and structural variants

docs/extra.css

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+.wy-nav-content {
+    max-width: 1600px !important;
+}
+h1,h2 {
+  margin-top: 50px;
+  margin-bottom: 10px !important;
+}
+h3 {
+  font-size: 18px;
+  margin-top: 30px;
+  margin-bottom: 10px !important;
+}
+h4 {
+  font-size: 17px;
+  font-style: italic;
+  margin-top: 30px;
+  margin-bottom: 10px !important;
+
+}
+h5 {
+  font-size: 16px;
+  font-style: italic;
+  margin-top: 30px;
+  margin-bottom: 10px !important;
+
+}
+p {
+  margin-top: 5px  !important;
+}
+* {
+  margin-bottom: 0px  !important;
+}
+
+table td {
+  min-width: 10px;
+  max-width: 600px;
+}
+table td:last-child {
+  width: 100%;
+}
+
+hr {
+  margin-top: 50px;
+  border: 1px solid black;
+}
+
+.twemoji {
+  width: 20px;
+  color: black;
+}

docs/images/generate_dag.txt

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+# Generate a dag graph and place it here
+# snakemake --rulegraph | dot -Tsvg > dag.svg

docs/includes/abbreviations.md

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+*[hg19]: UCSC human genome version 19
+*[API]: Application programming interface
+*[BAF]: Binary allele frequency
+*[cDNA]: coding DNA
+*[gDNA]: genomic DNA
+*[DNA]: Deoxyribonucleic acid
+*[DRMAA]: Distributed resource management application API
+*[CNV]: Copy number variation
+*[CNVs]: Copy number variations
+*[FFPE]: Formalin-fixed paraffin-embedded
+*[GMS]: Genomic Medicine Sweden
+*[HLA]: Human leukocyte antigen
+*[HRD]: Homologous recombination deficiency
+*[MAF]: Minor allele frequency
+*[MSI]: Microsatellite instability
+*[MSS]: Microsatellite stable 
+*[PoN]: Panel of normal
+*[QC]: Quality control
+*[RNA]: Ribonucleic acid
+*[sSNVs]: Synonymous single nucleotide variations
+*[nsSNVs]: Non-synonymous single nucleotide variations
+*[SNV]: Single nucleotide variation
+*[SNVs]: Single nucleotide variations
+*[INDEL]: Insertion and deletion
+*[INDELs]: Insertions and deletions
+*[TMB]: Tumor mutational burden

docs/index.md

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+# [CNV_SV module](https://github.com/hydra-genetics/cnv_sv)
+The cnv_sv module consists of a collection of tools calling larger structural genomic aberrations in DNA. Most tools use aligned `.bam` files as input, but many tools also make use of small variants calls in the form of a `.vcf` file.
+
+# [Hydra-genetics](https://hydra-genetics.readthedocs.io/en/latest/)
+
+We are an organization/community with the goal of making [snakemake](https://snakemake.readthedocs.io/en/stable/index.html) pipeline development easier, faster, a bit more structured and of higher quality.
+
+We do this by providing [snakemake modules](https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html#modules) that can be combined to create a complete analysis or included in already existing pipelines. All modules are subjected to extensive testing to make sure that new releases doesn't unexpectedly break existing pipeline or deviate from guidelines and best practices on how to write code.
+<p align="center" width="100%">
+    <img width="10%" src="images/hydragenetics.png">
+</p>

docs/intro.md

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+# Hydra-genetics snv_sv module
+The cnv_sv module consists of a collection of tools calling larger structural genomic aberrations in DNA. Most tools use aligned `.bam` files as input, but many tools also make use of small variants calls in the form of a `.vcf` file.
+
+## CNV_SV
+
+![CNV_SV steps](images/cnv_sv_dag.svg)
+
+## Module input files
+Aligned and merged `.bam` files as well as different `.vcf` files depending on application.
+
+* `alignment/samtools_merge_bam/{sample}_{type}.bam`
+* `snv_indels/bcbio_variation_recall_ensemble/{sample}_{type}.ensembled.vcf`
+* `snv_indels/bcbio_variation_recall_ensemble/{sample}_{type}.germline.vcf`
+* `snv_indels/glnexus/{sample}_{type}.vep_annotated.vcf.gz`
+
+## Module output files
+The output consists of results files that describe different kinds of larger genomic aberrations, such as copy number aberrations (CNVs), structural variants (SVs) and repeat expansions.
+
+* `cnv_sv/automap/{sample}_{type}/{sample}_{type}.HomRegions.tsv`
+* `cnv_sv/cnvkit_call/{sample}_{type}.{tc_method}.loh.cns`
+* `cnv_sv/cnvpytor/{sample}_{type}.filtered.vcf`
+* `cnv_sv/exomedepth_call/{sample}_{type}.txt`
+* `cnv_sv/expansionhunter/{sample}_{type}.vcf`
+* `cnv_sv/gatk_call_copy_ratio_segments/{sample}_{type}.clean.calledCNVs.seg`
+* `cnv_sv/manta_run_workflow_tn/{sample}/results/variants/somaticSV.vcf.gz`
+* `cnv_sv/manta_run_workflow_t/{sample}/results/variants/tumorSV.vcf.gz`
+* `cnv_sv/manta_run_workflow_n/{sample}/results/variants/candidateSV.vcf.gz`
+* `cnv_sv/pindel_vcf/{sample}_{type}.no_tc.vcf`
+* `cnv_sv/purecn_purity_file/{sample}_{type}.purity.txt`
+* `cnv_sv/reviewer/{sample}_{type}/{sample}_{type}.phasing.tsv`
+* `cnv_sv/smn_caller/{sample}_{type}.tsv`
+* `cnv_sv/svdb_query/{sample}_{type}.{tc_method}.svdb_query.vcf`
+* `cnv_sv/tiddit/{sample}_{type}.vcf`
+* `cnv_sv/upd/{sample}_{type}.upd_regions.bed`
+* `cnv_sv/upd/{sample}_{type}.upd_sites.bed`

docs/requirements.txt

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+jinja2<3.1.0
+mkdocs==1.4.2
+pymdown-extensions==10.0
+mkdocs-schema-reader==0.11.1
+mkdocs-simple-hooks==0.1.5
+mdx_spanner==0.0.5
+mkdocs-yaml-schema-plugin==0.2.3
+mkdocs-snakemake-rule-plugin==0.4.0
+mkdocs-material==9.1.7