Merge pull request #115 from genomic-medicine-sweden/publish_research…

…_f_vep

Patch Publish research file vep

.github/workflows/download_pipeline.yml

@@ -72,4 +72,4 @@ jobs:
         env:
           NXF_SINGULARITY_CACHEDIR: ./
           NXF_SINGULARITY_HOME_MOUNT: true
-        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) -stub -profile test,singularity --outdir ./results
+        run: nextflow run ./${{ env.REPOTITLE_LOWERCASE }}/$( sed 's/\W/_/g' <<< ${{ env.REPO_BRANCH }}) --skip_drop_as true --skip_drop_ae true -stub -profile test,singularity --outdir ./results

CHANGELOG.md

@@ -14,14 +14,24 @@ Parameter has been added if just the new parameter information is present.
 Parameter has been removed if new parameter information isn't present.
 :::
 
-## 2.0.1 - [XXXX-XX-XX]
+## 2.0.2 - [XXXX-XX-XX]
 
 ### `Added`
 
 ### `Fixed`
 
 ### `Parameters`
 
+## 2.0.1 - Grinch [2024-04-25]
+
+### `Added`
+
+### `Fixed`
+
+- Vep annotated research results will be published [#115](https://github.com/genomic-medicine-sweden/tomte/pull/115)
+
+### `Parameters`
+
 ## 2.0.0 - Santa [2024-04-19]
 
 ### `Added`

assets/multiqc_config.yml

@@ -1,5 +1,5 @@
 report_comment: >
-  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/2.0.0" target="_blank">genomic-medicine-sweden/tomte</a>
+  This report has been generated by the <a href="https://github.com/genomic-medicine-sweden/tomte/releases/tag/2.0.1" target="_blank">genomic-medicine-sweden/tomte</a>
   analysis pipeline. For information about how to interpret these results, please see the
   <a href="https://github.com/genomic-medicine-sweden/tomte/blob/master/docs/output.md" target="_blank">documentation</a>.
 report_section_order:

conf/modules/annotate_snv.config

@@ -41,6 +41,11 @@ process {
     withName: '.*ANNOTATE_SNV:RENAME_FILES' {
         ext.when = { (!params.skip_vep) }
         ext.prefix = { "${meta.id}_vep_${meta.set}" }
+        publishDir = [
+            path: { "${params.outdir}/annotate_vep" },
+            mode: params.publish_dir_mode,
+            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
+        ]
     }
 
     withName: '.*ANNOTATE_SNV:TABIX_TABIX' {

nextflow.config

@@ -270,7 +270,7 @@ manifest {
     description     = """Pipeline to analyse RNAseq from raredisease patients"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '2.0.0'
+    version         = '2.0.1'
     doi             = '10.5281/zenodo.10828946'
 }