Release PR 0.2.0

.github/workflows/build-docs.yml

@@ -18,8 +18,11 @@ jobs:
         with:
           python-version: 3.x
       - run: echo "cache_id=$(date --utc '+%V')" >> $GITHUB_ENV
-      - name: Obtain version from MANIFEST.MF
-        run: echo "pipeline_version=$(grep "version" nextflow.config | tail -1 | sed -e s'/[^=]*= //' | cut -d "'" -f 2)" >> $GITHUB_ENV
+      - name: Obtain version from nextflow config
+        run: |
+          version=$(grep "version" nextflow.config | tail -1 | sed -e s'/[^=]*= //' | cut -d "'" -f 2)
+          [[ $version == *"dev"* ]] && pipeline_version="dev" || pipeline_version=$version
+          echo "pipeline_version=$pipeline_version" >> $GITHUB_ENV
       - name: Setup git user
         run: |
           git config --global user.name "${{github.actor}}"
@@ -33,6 +36,7 @@ jobs:
       - name: Install dependencies
         run: pip install mkdocs-material pymdown-extensions pillow cairosvg mike
       - name: Build docs
-        run: mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
+        run: |
+          [[ ${{ env.pipeline_version }} == "dev" ]] && mike deploy --push ${{ env.pipeline_version }} || mike deploy --push --update-aliases ${{ env.pipeline_version }} latest
       - name: Set default docs
         run: mike set-default --push latest

CHANGELOG.md

@@ -1,10 +1,34 @@
 # nf-cmgg/structural: Changelog
+# nf-cmgg/structural: Changelog
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## v0.2.0 - [19 July 2024] - Mighty Manneken Pis
+
+### `Added`
+
+1. Added keyword shortcuts to the `--callers` parameter (these can also be used as comma-separated entries to the parameter):
+   - `all`: Use all callers available in the pipeline
+   - `sv`: Use all SV callers available in the pipeline
+   - `cnv`: Use all CNV callers available in the pipeline
+   - `rre`: Use all repeat region expansion callers available in the pipeline
+2. Added the possibilty to annotate on HPO terms. Add the right HPO terms to the samplesheet in the `hpo` field
+
+### `Changes`
+
+1. Updated all WisecondorX modules to version 1.2.6 and added the `--seed` argument to `WisecondorX predict`
+2. Removed support for the `phenotypes` VEP plugin. Common VEP plugin support will be added later
+3. Made the main workflow pluggable, making it possible to use this pipeline in a meta pipeline
+4. Updated all modules to their latest version
+
+### `Fixed`
+
+1. The smoove outputs are now correct when using `--output_callers`
+
 ## v0.1.0 - [3 April 2024] - Amazing Atomium
 
+Initial release of nf-cmgg/structural, created with the [nf-core](https://nf-co.re/) template.
 Initial release of nf-cmgg/structural, created with the [nf-core](https://nf-co.re/) template.
 
 ### `Added`

assets/multiqc_config.yml

@@ -1,6 +1,6 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/nf-core/structural/releases/tag/0.1.0" target="_blank">nf-core/structural</a> analysis pipeline. For information about how to interpret these results, please see the <a
-  href="https://nf-co.re/structural/0.1.0/docs/output" target="_blank">documentation</a>.
+  This report has been generated by the <a href="https://github.com/nf-core/structural/releases/tag/0.2.0" target="_blank">nf-core/structural</a> analysis pipeline. For information about how to interpret these results, please see the <a
+  href="https://nf-co.re/structural/0.2.0/docs/output" target="_blank">documentation</a>.
 report_section_order:
   "nf-cmgg-structural-methods-description":
     order: -1000

assets/schema_input.json

@@ -41,6 +41,11 @@
                 "type": "string",
                 "meta": ["sex"],
                 "enum": ["male", "female"]
+            },
+            "hpo": {
+                "type": "string",
+                "meta": ["hpo"],
+                "description": "HPO terms to be used for annotation with AnnotSV. Should be space or semicolon separated."
             }
         },
         "required": ["sample", "cram"]