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Merged
m-jahn merged 3 commits into from
Mar 21, 2026
Merged

feat: update docs, CI workflows #31

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7c2bcc6
fix: update CI workflows
m-jahn Mar 20, 2026
1549c34
feat: update README and config schema
m-jahn Mar 20, 2026
d619663
fix: update badges
m-jahn Mar 21, 2026
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12 changes: 4 additions & 8 deletions .github/workflows/conventional-prs.yml
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@@ -1,4 +1,5 @@
name: Lint PR
name: Conventional PRs

on:
pull_request_target:
types:
Expand All @@ -11,10 +12,5 @@ permissions:
pull-requests: read

jobs:
main:
name: Validate PR title
runs-on: ubuntu-latest
steps:
- uses: amannn/action-semantic-pull-request@v5
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
conventional-prs:
uses: MPUSP/mpusp-github-actions/.github/workflows/conventional-prs.yml@main
17 changes: 17 additions & 0 deletions .github/workflows/deploy-apptainer.yml
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@@ -0,0 +1,17 @@
name: Deploy Apptainer

on:
workflow_run:
workflows: ["Release Please"]
types:
- completed
workflow_dispatch:

permissions:
contents: read
packages: write

jobs:
deploy-apptainer:
if: ${{ github.event_name == 'workflow_dispatch' || github.event.workflow_run.conclusion == 'success' }}
uses: MPUSP/mpusp-github-actions/.github/workflows/deploy-apptainer.yml@main
54 changes: 0 additions & 54 deletions .github/workflows/deploy_apptainer.yml
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56 changes: 0 additions & 56 deletions .github/workflows/main.yml
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14 changes: 4 additions & 10 deletions .github/workflows/release-please.yml
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@@ -1,20 +1,14 @@
name: Release Please

on:
push:
branches:
- main
branches: [main]

permissions:
contents: write
pull-requests: write
issues: write

name: release-please

jobs:
release-please:
runs-on: ubuntu-latest
steps:
- uses: googleapis/release-please-action@v4
with:
token: ${{ secrets.GITHUB_TOKEN }}
release-type: go # just keep a changelog, no version anywhere outside of git tags
uses: MPUSP/mpusp-github-actions/.github/workflows/release-please.yml@main
12 changes: 12 additions & 0 deletions .github/workflows/snakemake-tests.yml
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@@ -0,0 +1,12 @@
name: Snakemake Tests

on:
pull_request:
branches: [main]

jobs:
snakemake-tests:
uses: MPUSP/mpusp-github-actions/.github/workflows/snakemake-tests.yml@main
with:
cores: 2
dryrun: false
4 changes: 2 additions & 2 deletions README.md
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@@ -1,9 +1,9 @@
# Snakemake-simple-mapping

[![Snakemake](https://img.shields.io/badge/snakemake-≥8.0.0-brightgreen.svg)](https://snakemake.github.io)
[![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)
[![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)
[![run with conda](http://img.shields.io/badge/run%20with-conda-3EB049?labelColor=000000&logo=anaconda)](https://docs.conda.io/en/latest/)
[![run with apptainer](https://img.shields.io/badge/run%20with-singularity-1D355C.svg?labelColor=000000)](https://sylabs.io/docs/)
[![run with apptainer](https://img.shields.io/badge/run%20with-apptainer-1D355C.svg?labelColor=000000)](https://apptainer.org/)
[![workflow catalog](https://img.shields.io/badge/Snakemake%20workflow%20catalog-darkgreen)](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/MPUSP/snakemake-simple-mapping)

A Snakemake workflow for the mapping of reads to reference genomes, minimalistic and simple.
Expand Down
76 changes: 0 additions & 76 deletions config/README.md
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Expand Up @@ -33,79 +33,3 @@ The sample sheet listing read input files needs to have the following layout:
| ------- | ----------- | ------------------- | ------------------- |
| sample1 | strain XY | sample1_R1.fastq.gz | sample1_R2.fastq.gz |
| ... | ... | ... | ... |

### Parameters

This table lists all parameters that can be used to run the workflow.

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