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Merge pull request #31 from MPUSP/dev
feat: update docs, CI workflows
2 parents 19993ea + d619663 commit cb4f792

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‎.github/workflows/conventional-prs.yml‎

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name: Lint PR
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name: Conventional PRs
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on:
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pull_request_target:
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types:
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pull-requests: read
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jobs:
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main:
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name: Validate PR title
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runs-on: ubuntu-latest
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steps:
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- uses: amannn/action-semantic-pull-request@v5
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env:
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GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
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conventional-prs:
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uses: MPUSP/mpusp-github-actions/.github/workflows/conventional-prs.yml@main

‎.github/workflows/deploy-apptainer.yml‎

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name: Deploy Apptainer
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on:
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workflow_run:
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workflows: ["Release Please"]
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types:
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- completed
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workflow_dispatch:
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permissions:
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contents: read
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packages: write
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jobs:
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deploy-apptainer:
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if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
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uses: MPUSP/mpusp-github-actions/.github/workflows/deploy-apptainer.yml@main

‎.github/workflows/deploy_apptainer.yml‎

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‎.github/workflows/main.yml‎

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‎.github/workflows/release-please.yml‎

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name: Release Please
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on:
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push:
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branches:
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- main
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branches: [main]
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permissions:
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contents: write
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pull-requests: write
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issues: write
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name: release-please
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jobs:
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release-please:
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runs-on: ubuntu-latest
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steps:
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- uses: googleapis/release-please-action@v4
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with:
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token: ${{ secrets.GITHUB_TOKEN }}
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release-type: go # just keep a changelog, no version anywhere outside of git tags
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uses: MPUSP/mpusp-github-actions/.github/workflows/release-please.yml@main

‎.github/workflows/snakemake-tests.yml‎

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name: Snakemake Tests
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on:
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pull_request:
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branches: [main]
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jobs:
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snakemake-tests:
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uses: MPUSP/mpusp-github-actions/.github/workflows/snakemake-tests.yml@main
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with:
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cores: 2
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dryrun: false

‎README.md‎

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# Snakemake-simple-mapping
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[![Snakemake](https://img.shields.io/badge/snakemake-≥8.0.0-brightgreen.svg)](https://snakemake.github.io)
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[![GitHub actions status](https://github.com/MPUSP/snakemake-simple-mapping/actions/workflows/main.yml/badge.svg?branch=main)](https://github.com/MPUSP/snakemake-simple-mapping/actions/workflows/main.yml)
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[![GitHub Actions](https://github.com/MPUSP/snakemake-simple-mapping/actions/workflows/snakemake-tests.yml/badge.svg)](https://github.com/MPUSP/snakemake-simple-mapping/actions/workflows/snakemake-tests.yml)
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[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
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[![run with apptainer](https://img.shields.io/badge/run%20with-singularity-1D355C.svg?labelColor=000000)](https://sylabs.io/docs/)
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[![run with apptainer](https://img.shields.io/badge/run%20with-apptainer-1D355C.svg?labelColor=000000)](https://apptainer.org/)
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[![workflow catalog](https://img.shields.io/badge/Snakemake%20workflow%20catalog-darkgreen)](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/MPUSP/snakemake-simple-mapping)
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A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.

‎config/README.md‎

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| ------- | ----------- | ------------------- | ------------------- |
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| sample1 | strain XY | sample1_R1.fastq.gz | sample1_R2.fastq.gz |
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| ... | ... | ... | ... |
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### Parameters
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This table lists all parameters that can be used to run the workflow.
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| parameter | type | details | default |
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| ------------------------ | ------- | -------------------------------------------------------- | ----------------- |
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| **samplesheet** | string | path to the sample sheet in tsv format | |
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| **get_genome** | | | |
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| database | string | database to use for genome retrieval, 'ncbi' or 'manual' | `ncbi` |
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| assembly | string | Refseq ID to use for genome retrieval | `GCF_000307535.1` |
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| fasta | string | path to a custom FASTA file (optional) | |
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| gff | string | path to a custom GFF file (optional) | |
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| gff_source_type | array | mapping of GFF source types to feature types | |
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| **fastp** | | | |
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| extra | string | additional arguments to Fastp | |
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| **mapping** | | | |
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| tool | string | mapping tool to use, one of 'bowtie2', 'bwa_mem2' | `bwa_mem2` |
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| _bowtie2_ | | | |
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| index | string | additional arguments to bowtie build | |
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| extra | string | additional arguments to bowtie align | |
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| _bwa_mem2_ | | | |
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| extra | string | additional arguments to bwa-mem2 | |
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| sort | string | sorting tool to use | `samtools` |
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| sort_order | string | sorting order to use | `coordinate` |
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| sort_extra | string | additional arguments to the sorting tool | |
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| _samtools_sort_ | | | |
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| extra | string | additional arguments to Samtools sort | `-m 4G` |
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| index | object | Samtools index options | |
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| extra | string | additional arguments to Samtools index | |
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| _star_ | | | |
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| index | string | additional arguments to STAR index | |
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| extra | string | additional arguments to STAR align | |
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| _minimap2_ | | | |
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| index | string | additional arguments to minimap2 index | |
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| extra | string | additional arguments to minimap2 align | `-ax map-ont` |
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| sorting | string | sorting order to use | `coordinate` |
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| sort_extra | string | additional arguments to the sorting tool | |
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| **mapping_stats** | | | |
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| _gffread_ | | | |
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| extra | string | additional arguments to GFFread | |
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| _rseqc_infer_experiment_ | | | |
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| extra | string | additional arguments to RSeQC infer_experiment | |
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| _rseqc_bam_stat_ | | | |
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| extra | string | additional arguments to RSeQC bam_stat | |
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| _deeptools_coverage_ | | | |
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| genome_size | integer | genome size in base pairs | `1000` |
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| extra | string | additional arguments to DeepTools bamCoverage | |
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| **variant_calling** | | | |
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| _bcftools_pileup_ | | | |
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| uncompressed | boolean | whether to output uncompressed BCF files | `False` |
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| extra | string | additional arguments to BCFtools pileup | |
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| _bcftools_call_ | | | |
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| uncompressed | boolean | whether to output uncompressed VCF files | `False` |
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| caller | string | use '-c' for consensus or '-m' for multiallelic | `-c` |
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| extra | string | additional arguments to BCFtools view | |
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| _bcftools_view_ | | | |
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| extra | string | additional arguments to BCFtools call | |
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| _bcftools_filter_ | | | |
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| filter | string | expression by which to filter BCF/VCF result | `-e 'ALT=\".\"'` |
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| extra | string | additional arguments to BCFtools filter | |
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| _freebayes_ | | | |
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| extra | string | additional arguments to Freebayes call | |
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| **variant_annotation** | | | |
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| tool | string | annotation tool to use, one of 'vep', 'snpeff' | `vep` |
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| _vep_ | | | |
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| convert_gff | boolean | whether to convert NCBI GFF to Ensemble style GFF | `True` |
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| plugins | array | VEP plugins to use | `[]` |
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| extra | string | additional arguments to VEP | see config.yml |
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| _snpeff_ | | | |
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| extra | string | additional arguments to SnpEff | see config.yml |
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| **qc** | | | |
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| _fastqc_ | | | |
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| extra | string | additional arguments to FastQC | |
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| _multiqc_ | | | |
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| extra | string | additional arguments to MultiQC | |

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