Merge branch 'dev' into rename-parameters

.github/workflows/ci.yml

@@ -51,10 +51,6 @@ jobs:
         uses: actions/checkout@b4ffde65f46336ab88eb53be808477a3936bae11 # v4
         with:
           fetch-depth: 0
-      - name: Fetch ${{ github.event.pull_request.base.ref }} branch
-        run: |
-          git remote add upstream ${{ github.event.repository.clone_url }}
-          git fetch upstream ${{ github.event.pull_request.base.ref }}
 
       - name: Set up Nextflow
         uses: nf-core/setup-nextflow@v2
@@ -75,7 +71,7 @@ jobs:
         run: |
           nf-test test \
             --ci \
-            --changed-since upstream/${{ github.event.pull_request.base.ref }} \
+            --changed-since HEAD^ \
             --verbose \
             --tag ${{ matrix.tags }} \
             --profile "+${{ matrix.profile }}" \

CHANGELOG.md

@@ -89,6 +89,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#489](https://github.com/genomic-medicine-sweden/nallo/pull/489) - Updated nf-core template to 3.0.2
 - [#493](https://github.com/genomic-medicine-sweden/nallo/pull/493) - Refactored `nallo.nf` to remove many nested ifs and easier to follow logic
 - [#493](https://github.com/genomic-medicine-sweden/nallo/pull/493) - Updated rank_variants dependencies with sv_annotation
+- [#498](https://github.com/genomic-medicine-sweden/nallo/pull/498) - Updated CI to fix CI failures after merge
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Changed to annotating and ranking SNVs per family instead of per project
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Changed output documentation and structure to match `sample` and `family` for all variants
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Changed the way of validating the samplesheet to remove outputing false errors with `ifEmpty`
 
 ### `Removed`
 
@@ -97,6 +101,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#379](https://github.com/genomic-medicine-sweden/nallo/pull/379) - Removed VEP Plugins from testdata ([genomic-medicine-sweden/test-datasets#16](https://github.com/genomic-medicine-sweden/test-datasets/pull/16))
 - [#388](https://github.com/genomic-medicine-sweden/nallo/pull/388) - Removed support for co-phasing SVs with HiPhase, as the officially supported caller (pbsv) is not in the pipeline
 - [#412](https://github.com/genomic-medicine-sweden/nallo/pull/412) - Removed `bcftools/index`, as indexing is handled by other modules and no references remained. ([#377](https://github.com/genomic-medicine-sweden/nallo/issues/377))
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Removed support for automatically creating an echvar database with SNVs and INDELs
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Removed `containts_affected` logic from the snv-calling workflow, since this was previously changed to be checked before pipeline start
 
 ### `Fixed`
 
@@ -107,6 +113,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#402](https://github.com/genomic-medicine-sweden/nallo/pull/402) - Fixed double sample names in HiFiCNV output
 - [#438](https://github.com/genomic-medicine-sweden/nallo/pull/438) - Fixed missing/malformed software versions in `ADD_FOUND_IN_TAG`, `ADD_MOST_SEVERE_CSQ`, `ADD_MOST_SEVERE_PLI`, `SAMPLESHEET_PED`, `SOMALIER_PED` and `TRGT`
 - [#444](https://github.com/genomic-medicine-sweden/nallo/pull/444) - Fixed genmod assigning wrong models on chromosome X when named `chrX` ([#343](https://github.com/genomic-medicine-sweden/nallo/issues/343))
+- [#502](https://github.com/genomic-medicine-sweden/nallo/pull/502) - Fixed genmod only scoring compounds in one family [#501](https://github.com/genomic-medicine-sweden/nallo/issues/501)
 
 ### Parameters
 

conf/modules/call_svs.config

@@ -75,7 +75,7 @@ process {
             '--write-index=tbi'
         ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/svs/single_sample/${meta.id}" },
+            path: { "${params.outdir}/svs/sample/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]

conf/modules/general.config

@@ -27,7 +27,7 @@ process {
     withName: '.*:NALLO:BCFTOOLS_STATS' {
         ext.prefix = { "${vcf}" }
         publishDir = [
-            path: { "${params.outdir}/snvs/stats/single_sample" },
+            path: { "${params.outdir}/snvs/stats/sample" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -51,7 +51,7 @@ process {
             '--write-index=tbi'
         ].join(' ') }
         publishDir = [
-            path: { "${params.outdir}/snvs/multi_sample/${meta.id}" },
+            path: { "${params.outdir}/snvs/family/${meta.id}" },
             mode: params.publish_dir_mode,
             saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
         ]
@@ -64,7 +64,7 @@ process {
             '--write-index=tbi'
         ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/snvs/single_sample/" },
+            path: { "${params.outdir}/snvs/sample/" },
             mode: params.publish_dir_mode,
             // Can't use prefix as it would come from the original file
             saveAs: { filename ->
@@ -88,7 +88,7 @@ process {
             '--write-index=tbi'
         ].join(' ')
         publishDir = [
-            path: { "${params.outdir}/svs/single_sample/" },
+            path: { "${params.outdir}/svs/sample/" },
             mode: params.publish_dir_mode,
             // Can't use prefix as it would come from the original file
             saveAs: { filename ->
@@ -111,13 +111,6 @@ process {
         ]
     }
 
-    withName: '.*:NALLO:SOMALIER_PED' {
-        publishDir = [
-            path: { "${params.outdir}/pedigree/project/" },
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename },
-        ]
-    }
-
     withName: '.*:NALLO:SOMALIER_PED_FAMILY' {
         publishDir = [
             path: { "${params.outdir}/pedigree/family/" },
@@ -198,14 +191,6 @@ process {
         ]
     }
 
-    withName: '.*:NALLO:ECHTVAR_ENCODE' {
-        publishDir = [
-            path: { "${params.outdir}/databases/echtvar/encode/${meta.id}" },
-            mode: params.publish_dir_mode,
-            saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
-        ]
-    }
-
     /*
     ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
     Summary