Merge pull request #204 from nf-cmgg/fix-WES-validation

Fix wes validation + some general fixes

.github/workflows/linting.yml

@@ -42,16 +42,14 @@ jobs:
           architecture: "x64"
 
       - name: read .nf-core.yml
-        uses: pietrobolcato/action-read-yaml@1.0.0
+        uses: pietrobolcato/action-read-yaml@1.1.0
         id: read_yml
         with:
-          config: ${{ github.workspace }}/.nf-core.yaml
+          config: ${{ github.workspace }}/.nf-core.yml
 
       - name: Install dependencies
         run: |
-          python -m pip install --upgrade pip
-          pip install git+https://github.com/nf-core/tools@dev
-          #pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
+          pip install nf-core==${{ steps.read_yml.outputs['nf_core_version'] }}
 
       - name: Run nf-core pipelines lint
         env:

.nf-core.yml

@@ -29,7 +29,7 @@ lint:
   multiqc_config:
     - "report_comment"
   actions_ci: false # TODO readd this once the linting doesn't act up
-nf_core_version: 3.0.0dev
+nf_core_version: 3.0.0
 repository_type: pipeline
 template:
   author: nvnieuwk

CHANGELOG.md

@@ -3,9 +3,25 @@
 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).
 
+## v1.9.0dev
+
+### New features
+
+1. Added the `--min_callable_coverage` parameter to state what the lowest coverage should for a region to be classified as callable.
+
+### Changes
+
+1. Added the `--squash-ploidy` argument to the RTG vcfeval process.
+
+### Fixes
+
+1. Validation of all samples now use an intersect of the golden truth BED files with the BED file used to call the variants. This should fix the WES validation which was broken until this point.
+2. A couple of small fixes to the vardict flow.
+3. Only use the standard chromosomes for UPDio analysis.
+
 ## v1.8.2 - Outstanding Oostkamp - [September 30 2024]
 
-## Fixes
+### Fixes
 
 1. Fixed some issues where indices were not created
 2. Updated the docs

conf/modules.config

@@ -85,7 +85,7 @@ process {
 
     withName: "^.*CRAM_PREPARE_SAMTOOLS_BEDTOOLS:MOSDEPTH\$" {
         ext.args = [
-            "--quantize 0:1:4: --mapq 1 --flag 1804 --no-per-base",
+            "--quantize 0:1:${params.min_callable_coverage - 1}: --mapq 1 --flag 1804 --no-per-base",
             params.mosdepth_slow ? "" : "--fast-mode"
         ].join(" ")
         publishDir  = [
@@ -329,6 +329,7 @@ process {
 
         if(params.filter) {
             withName: "^.*CRAM_CALL_VARDICTJAVA:VCF_FILTER_BCFTOOLS:FILTER_1\$" {
+                ext.prefix = { "${meta.id}.filtered1" }
                 ext.args = "-i 'QUAL >= 0${params.only_pass ? " && FILTER=\"PASS\"" : ""}' --output-type z"
             }
 
@@ -506,7 +507,7 @@ process {
                     mode: params.publish_dir_mode,
                     saveAs: { filename -> filename.equals('versions.yml') ? null : filename }
                 ] // SAVE
-                ext.args   = {"--sample ${meta.sample} --decompose"}
+                ext.args   = {"--sample ${meta.sample} --decompose --squash-ploidy"}
                 ext.prefix = {"${meta.sample}"}
             }
 
@@ -544,6 +545,15 @@ process {
         }
 
         if(params.updio) {
+            withName: "^.*VCF_UPD_UPDIO:BCFTOOLS_FILTER\$" {
+                ext.prefix = { "${meta.id}.filtered" }
+                ext.args = [
+                    "--output-type z",
+                    "--write-index=tbi",
+                    "-r chr1,chr2,chr3,chr4,chr5,chr6,chr7,chr8,chr9,chr10,chr11,chr12,chr13,chr14,chr15,chr16,chr17,chr18,chr19,chr20,chr21,chr22,chrX,chrY"
+                ].join(" ")
+            }
+
             withName: "^.*VCF_UPD_UPDIO:UPDIO\$" {
                 ext.prefix = {"updio_${meta.caller}"}
                 ext.args = {[

modules.json

@@ -18,7 +18,7 @@
                     },
                     "bcftools/filter": {
                         "branch": "master",
-                        "git_sha": "33ef773a7ea36e88323902f63662aa53c9b88988",
+                        "git_sha": "f85dbddd7a335fc0f5ac331e8d22ca94123b654b",
                         "installed_by": ["modules"]
                     },
                     "bcftools/norm": {
@@ -141,7 +141,7 @@
                     },
                     "rtgtools/vcfeval": {
                         "branch": "master",
-                        "git_sha": "e743b2dea725bcfc4b76a209981808987332013a",
+                        "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd",
                         "installed_by": ["modules"]
                     },
                     "samtools/convert": {