Fix workflow links and update wrapper prefix

.github/workflows/main.yaml

@@ -11,33 +11,32 @@ jobs:
   Linting:
     runs-on: ubuntu-latest
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v4
     - name: Lint workflow
-      uses: snakemake/snakemake-github-action@v1.23.0
+      uses: snakemake/snakemake-github-action@v1.25.1
       with:
         directory: .
         snakefile: workflow/Snakefile
         args: "--lint"
-
+        stagein: micromamba install snakemake -y -c conda-forge -c anaconda rsync conda
   Testing:
     runs-on: ubuntu-latest
     needs: Linting
     timeout-minutes: 30
     steps:
     - name: Checkout repository and submodules
-      uses: actions/checkout@v2
-      with:
-        submodules: recursive
+      uses: actions/checkout@v4
     - name: Test workflow (local test data)
-      uses: snakemake/snakemake-github-action@v1.23.0
+      uses: snakemake/snakemake-github-action@v1.25.1
       with:
         directory: .test
         snakefile: workflow/Snakefile
-        args: "--use-conda --show-failed-logs -j 10 --conda-cleanup-pkgs cache --conda-frontend mamba --wrapper-prefix file:///github/workspace/workflow/wrappers"
-        stagein: mamba install -y -c conda-forge rsync
+        args: "--use-conda --show-failed-logs -j 10 --retries 1 --rerun-incomplete --keep-going --conda-cleanup-pkgs cache --wrapper-prefix file:///github/workspace/workflow/wrappers"
+        stagein: micromamba config append channels conda-forge; micromamba install -n snakemake -y rsync conda mamba
     - name: Test report
-      uses: snakemake/snakemake-github-action@v1.21.0
+      uses: snakemake/snakemake-github-action@v1.25.1
       with:
         directory: .test
         snakefile: workflow/Snakefile
         args: "--report report.zip --wrapper-prefix file:///github/workspace/workflow/wrappers"
+        stagein: micromamba install -n snakemake -y -c conda-forge  rsync conda

.pre-commit-config.yaml

@@ -1,22 +1,65 @@
 repos:
   - repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v2.3.0
+    rev: v4.5.0
     hooks:
+      - id: check-merge-conflict
+      - id: check-added-large-files
+      - id: debug-statements
+      - id: mixed-line-ending
+      - id: check-case-conflict
       - id: check-yaml
-      - id: end-of-file-fixer
       - id: trailing-whitespace
+      - id: end-of-file-fixer
+  - repo: https://github.com/asottile/reorder_python_imports
+    rev: v3.12.0
+    hooks:
+      - id: reorder-python-imports
+        args: [--application-directories=python, --unclassifiable-application-module=_tskit]
+  - repo: https://github.com/asottile/pyupgrade
+    rev: v3.15.0
+    hooks:
+      - id: pyupgrade
+        args: [--py3-plus, --py37-plus]
   - repo: https://github.com/psf/black
-    rev: 21.8b0
+    rev: 23.3.0
     hooks:
       - id: black
+        language_version: python3
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    rev: "v0.1.11"
+    hooks:
+      - id: ruff
+        args:
+          [
+          "--ignore=F821",
+          ]
+  - repo: https://github.com/asottile/blacken-docs
+    rev: 1.16.0
+    hooks:
+      - id: blacken-docs
+        additional_dependencies: [black==22.12.0]
+        language_version: python3
   - repo: https://github.com/snakemake/snakefmt
-    rev: 0.4.3
+    rev: v0.8.5
     hooks:
       - id: snakefmt
   - repo: local
     hooks:
       - id: lint
         name: Snakemake lint
-        entry: snakemake --lint text
+        entry: snakemake --configfile config/config.yaml --configfile config/envmodules.yaml --lint text -v -s
         language: system
-        files: ''
+        log_file: 'snakemake-lint.txt'
+        files: '.*\.smk$|Snakefile'
+        exclude: .*/test-.*\.smk$
+  - repo: https://github.com/DavidAnson/markdownlint-cli2
+    rev: v0.11.0
+    hooks:
+      - id: markdownlint-cli2
+        files: \.(md|qmd)$
+        types: [file]
+        exclude: LICENSE.md
+      - id: markdownlint-cli2-fix
+        files: \.(md|qmd)$
+        types: [file]
+        exclude: LICENSE.md

README.md

@@ -1,7 +1,9 @@
 # Snakemake workflow: Assembly evaluation workflow
 
 [![Snakemake](https://img.shields.io/badge/snakemake-≥5.25.0-brightgreen.svg)](https://snakemake.bitbucket.io)
-[![Build status](https://github.com/NBISweden/assemblyeval-smk/workflows/Tests/badge.svg?branch=main)](https://github.com/NBISweden/assemblyeval-smk/actions?query=workflow%3ATests)  ![License](https://img.shields.io/badge/license-MIT-blue.svg)
+[![Build
+status](https://github.com/NBISweden/assemblyeval-smk/workflows/Tests/badge.svg?branch=main)](https://github.com/NBISweden/assemblyeval-smk/actions?query=workflow%3ATests)
+![License](https://img.shields.io/badge/license-MIT-blue.svg)
 
 Snakemake workflow for genome assembly evaluation.
 
@@ -15,11 +17,14 @@ available, its DOI (see above; currently N/A).
 
 ## Features
 
-- align transcripts to a reference sequence with [gmap](http://research-pub.gene.com/gmap/)
-- estimate gene body coverage with [genecovr](https://github.com/NBISweden/genecovr)
-- run [quast](http://bioinf.spbau.ru/quast), [jellyfish](http://www.genome.umd.edu/jellyfish.html), [busco](https://busco.ezlab.org), and [kraken2](https://ccb.jhu.edu/software/kraken2/)
-- summarize quality metrics with [MultiQC](https://multiqc.info)
-- (WIP): run some of the steps for adding reads, coverage files, and
+* align transcripts to a reference sequence with [gmap](http://research-pub.gene.com/gmap/)
+* estimate gene body coverage with [genecovr](https://github.com/NBISweden/genecovr)
+* run [quast](http://bioinf.spbau.ru/quast),
+  [jellyfish](http://www.genome.umd.edu/jellyfish.html),
+  [busco](https://busco.ezlab.org), and
+  [kraken2](https://ccb.jhu.edu/software/kraken2/)
+* summarize quality metrics with [MultiQC](https://multiqc.info)
+* (WIP): run some of the steps for adding reads, coverage files, and
   sequences to the [blobtoolkit](https://blobtoolkit.genomehubs.org) viewer
 
 ## Quickstart
@@ -50,14 +55,12 @@ details) . In addition, edit the following files:
 `reads.tsv`
     Raw sequence read files.
 
-
 NOTE: the config directory doesn't have to be in the workflow source
 directory, in which case snakemake must be invoked with the full path
 to the Snakemake file:
 
     snakemake -s /path/to/manticore-smk/workflow/Snakefile
 
-
 ### Step 3: Install Snakemake
 
 Install Snakemake using
@@ -117,7 +120,8 @@ The report contains documentation and results from the workflow.
 
 ### Step 6: Contribute back
 
-In case you have also changed or added steps, please consider contributing them back to the original repository:
+In case you have also changed or added steps, please consider
+contributing them back to the original repository:
 
 1. [Fork](https://help.github.com/en/articles/fork-a-repo) the
    original repo to a personal or lab account.
@@ -140,7 +144,6 @@ For a quick overview of example configuration files, see
 and the test configuration
 [.test/config/config.yaml](https://github.com/NBISweden/assemblyeval-smk/blob/main/.test/config/config.yaml)
 
-
 ### Schemas
 
 All configuration files are evaluated against [configuration
@@ -177,10 +180,14 @@ examples.
 The tabular input files can also be represented as lists in yaml
 format. For instance, the following tabular data
 
+<!-- markdownlint-disable MD010 -->
+
     species	version	fasta
     foo	v1	resources/assembly.v1.fasta
     foo	v2	resources/assembly.v2.fasta
 
+<!-- markdownlint-enable MD010 -->
+
 would be represented as follows in yaml format
 
     - species: foo
@@ -240,7 +247,6 @@ Quast will calculate quality metrics of an assembly.
     quast:
       ids: ["foo_v2", "foo_v1"]
 
-
 #### kraken2
 
 kraken2 assigns taxonomic ids to sequences and is used for
@@ -254,21 +260,19 @@ taxids over windows.
       window_size: 20000
       npartitions: 50
 
-
 #### MultiQC
 
 MultiQC doesn't have a configuration section per se. Instead, it will
 collect and plot results for the following applications:
 
-- busco
-- jellyfish
-- quast
-- kraken2
+* busco
+* jellyfish
+* quast
+* kraken2
 
 Plot configurations can be tweaked in a multiqc configuration file
 `multiqc_config.yaml`.
 
-
 ### Rule configuration
 
 Every rule has a corresponding configuration entry, with keywords for
@@ -281,17 +285,20 @@ instance, to change `options` for `jellyfish_count_chunk`, add
       jellyfish_count_chunk:
         options: --size 20G --canonical
 
-
-
 ## Testing
 
 Test cases are in the subfolder `.test`. They are automatically
 executed via continuous integration with [Github
 Actions](https://github.com/features/actions). To run the tests, cd to
 `.test` and issue
 
-    snakemake --use-conda --conda-frontend mamba --show-failed-logs --cores 2 --conda-cleanup-pkgs cache -s ../workflow/Snakefile --wrapper-prefix file://$(pwd)/../workflow/wrappers
+    snakemake --use-conda --conda-frontend mamba \
+        --show-failed-logs --cores 2 --conda-cleanup-pkgs cache \
+        -s ../workflow/Snakefile \
+        --wrapper-prefix file://$(pwd)/../workflow/wrappers
 
 Once the test run has finished, create a report and view it:
 
-    snakemake --cores 1 -s ../workflow/Snakefile --wrapper-prefix file://$(pwd)/../workflow/wrappers --report report.html
+    snakemake --cores 1 -s ../workflow/Snakefile \
+        --wrapper-prefix file://$(pwd)/../workflow/wrappers \
+        --report report.html

workflow/envs/samtools.yaml

@@ -2,3 +2,4 @@ channels:
   - bioconda
 dependencies:
   - samtools
+  - snakemake-wrapper-utils

workflow/report/workflow.rst

@@ -3,7 +3,7 @@ assemblyeval-smk
 
 The assemblyeval-smk_ workflow runs a suite of programs for evaluating
 genome assembly quality. This analysis is based on commit version {{
-snakemake.config["__workflow_commit__"] }}.
+snakemake.config["__workflow_commit__"] }}_.
 
 The analysis can be rerun with the following command:
 
@@ -85,7 +85,7 @@ MultiQC report
 The `MultiQC report`_ collects results from quast_, jellyfish_, busco_,
 and other QC programs for which `MultiQC tools`_ exist.
 
-.. _assemblyeval-smk: https://github.com/percyfal/assemblyeval-smk
+.. _assemblyeval-smk: https://github.com/NBISweden/assemblyeval-smk
 .. _genecovr: https://github.com/NBISweden/genecovr
 .. _gmap: http://research-pub.gene.com/gmap/
 .. _blobtoolkit: https://blobtoolkit.genomehubs.org/
@@ -96,3 +96,4 @@ and other QC programs for which `MultiQC tools`_ exist.
 .. _Snakemake wrappers: https://snakemake-wrappers.readthedocs.io/en/stable/
 .. _MultiQC report: ./reports/multiqc.html
 .. _MultiQC tools: https://multiqc.info/#supported-tools
+.. _{{ snakemake.config["__workflow_commit__"] }}: {{ snakemake.config["__workflow_commit_link__"] }}