Merge pull request #38 from MPUSP/dev

feat: update CI and config schema

Author: m-jahn

.github/workflows/conventional-prs.yml

@@ -1,4 +1,5 @@
-name: Lint PR
+name: Conventional PRs
+
 on:
   pull_request_target:
     types:
@@ -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

.github/workflows/deploy-apptainer.yml

@@ -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

.github/workflows/deploy_apptainer.yml

@@ -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

.github/workflows/main.yml

@@ -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: true

.github/workflows/release-please.yml

@@ -1,18 +1,20 @@
 # snakemake-ont-basecalling
 
-[![Snakemake](https://img.shields.io/badge/snakemake-≥8.24.1-brightgreen.svg)](https://snakemake.github.io)
-[![GitHub actions status](https://github.com/MPUSP/snakemake-ont-basecalling/actions/workflows/main.yml/badge.svg)](https://github.com/MPUSP/snakemake-ont-basecalling/actions/workflows/main.yml)
+[![Snakemake](https://img.shields.io/badge/snakemake-≥9.0.0-brightgreen.svg)](https://snakemake.github.io)
+[![GitHub Actions](https://github.com/MPUSP/snakemake-ont-basecalling/actions/workflows/snakemake-tests.yml/badge.svg)](https://github.com/MPUSP/snakemake-ont-basecalling/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-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)
+[![workflow catalog](https://img.shields.io/badge/Snakemake%20workflow%20catalog-darkgreen)](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/MPUSP/snakemake-ont-basecalling)
 
 A Snakemake workflow to perform basecalling and demultiplexing of Oxford Nanopore ONT data using Dorado.
 
 ## Usage
 
 The usage of this workflow is described in the [Snakemake Workflow Catalog](https://snakemake.github.io/snakemake-workflow-catalog/docs/workflows/MPUSP/snakemake-ont-basecalling).
 
-If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository.
+Detailed information about input data and workflow configuration can also be found in the [`config/README.md`](config/README.md).
+
+If you use this workflow in a paper, don't forget to give credits to the authors by citing the URL of this repository or its DOI.
 
 ## Workflow overview
 

.github/workflows/snakemake-tests.yml

@@ -49,23 +49,3 @@ snakemake --cores 3 --sdm conda --workflow-profile workflow/profiles/slurm/ --di
 
 **Note:**
 It is recommended to start the snakemake pipeline on the cluster using a session multiplexer like [screen](https://www.gnu.org/software/screen/manual/screen.html) or [tmux](https://www.redhat.com/en/blog/introduction-tmux-linux).
-
-### Parameters
-
-This table lists all parameters that can be used to run the workflow.
-
-| Parameter        | Type   | Details                                   | Default                  |
-| ---------------- | ------ | ----------------------------------------- | ------------------------ |
-| **input**        |        |                                           |                          |
-| runs             | string | table with sequencing runs                | `config/runs.csv`        |
-| file_extension   | string | extension for input files                 | `pod5`                   |
-| file_regex       | string | pattern to match input files              | `[A-Z]{3}[0-9]{5}...`    |
-| barcodes         | string | used barcodes for demultiplexing          | `1-24`                   |
-| **dorado**       |        |                                           |                          |
-| path             | string | path to the Dorado executable             |                          |
-| simplex / cuda   | string | CUDA device: `auto`, `cuda:0`, `cuda:all` | `cuda:all`               |
-| simplex / trim   | string | `all` or `none`                           | `none`                   |
-| simiplex / extra | string | params passed to dorado basecaller        | `""`                     |
-| demultiplexing   | bool   | whether to perform demultiplexing         | `True`                   |
-| **report**       |        |                                           |                          |
-| tools            | array  | list of tools to include in the report    | `["pycoQC", "NanoPlot"]` |

README.md

@@ -7,12 +7,20 @@ properties:
     properties:
       runs:
         type: string
+        description: "table with sequencing runs"
+        default: config/runs.csv
       file_extension:
         type: string
+        description: "file extension for input files"
+        default: ".pod5"
       file_regex:
         type: string
+        description: "regular expression to match input files"
+        default: "[A-Z]{3}[0-9]{5}..."
       barcodes:
         type: string
+        description: "range of barcodes to process"
+        default: "1-24"
     required:
       - runs
       - file_extension
@@ -23,20 +31,30 @@ properties:
     properties:
       path:
         type: string
+        description: "path to the Dorado executable"
+        default: "none"
       simplex:
         type: object
         properties:
           cuda:
             type: string
+            description: "CUDA device, one of: 'auto', 'cuda:0', 'cuda:all'"
+            default: "cuda:all"
           trim:
             type: string
+            description: "trimming option for Dorado, 'all' or 'none'"
+            default: "none"
           extra:
             type: string
+            description: "extra options for Dorado"
+            default: ""
         required:
           - cuda
           - trim
       demultiplexing:
         type: boolean
+        description: "whether to perform demultiplexing"
+        default: true
     required:
       - path
       - simplex
@@ -47,6 +65,8 @@ properties:
         type: array
         items:
           type: string
+        description: "list of tools to include in the report"
+        default: ["pycoQC", "NanoPlot"]
     required:
       - tools
 required: