Merge pull request #648 from nf-core/update_configs

Fix tests

CHANGELOG.md

@@ -13,6 +13,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- d4 files are not generated by default anymore [#648](https://github.com/nf-core/raredisease/pull/648)
 - Suffix used to identify unique fastq pairs from "\_T" to "\_LNUMBER" [#638](https://github.com/nf-core/raredisease/pull/638)
 - Merge output from germlinecnvcaller [#635](https://github.com/nf-core/raredisease/pull/635)
 - Update tools [#623](https://github.com/nf-core/raredisease/pull/623)
@@ -25,7 +26,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - Restrict deepvariant analysis of WES samples to bait regions [#633](https://github.com/nf-core/raredisease/pull/633)
 - bcftools annotate declaration in annotate CADD subworkflow [#624](https://github.com/nf-core/raredisease/pull/624)
 - Rhocallviz subworkflow will only be invocated once per sample [#621](https://github.com/nf-core/raredisease/pull/621)
-- Allow for VEP version 112 to be used and set it to default [#617](https://github.com/nf-core/raredisease/pull/617)
 - Updated createCaseChannel function to include a check for maternal and paternal ids being set to a numeric 0 [#643](https://github.com/nf-core/raredisease/pull/643)
 
 ### Parameters
@@ -40,7 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Tool       | Old version | New version |
 | ---------- | ----------- | ----------- |
 | bcftools   | 1.18        | 1.20        |
-| ensemblvep | 112         | 113         |
+| ensemblvep | 112         | 110         |
 | genmod     | 3.8.2       | 3.9         |
 | mosdepth   | 0.3.6       | 0.3.8       |
 | multiqc    | 1.21        | 1.25.1      |

conf/modules/qc_bam.config

@@ -55,7 +55,6 @@ process {
     }
 
     withName: '.*QC_BAM:MOSDEPTH' {
-        ext.args = '--d4'
         ext.prefix = { "${meta.id}_mosdepth" }
     }
 

conf/modules/raredisease.config

@@ -36,7 +36,7 @@ process {
         ext.args = {
         (params.genome == 'GRCh37') ? '--genome 37' : '--genome 38'
         }
-        ext.prefix = { "${meta.id}" }
+        ext.prefix = { "${meta.id}_smncopynumbercaller" }
         publishDir = [
             path: { "${params.outdir}/smncopynumbercaller" },
             mode: params.publish_dir_mode,

docs/output.md

@@ -171,7 +171,6 @@ The FastQC plots displayed in the MultiQC report shows _untrimmed_ reads. They m
 
 - `{outputdir}/qc_bam/`
   - `<sampleid>_mosdepth.global.dist.txt`: This file contains a cumulative distribution indicating the proportion of total bases that were covered for at least a given coverage value across each chromosome and the whole genome.
-  - `<sampleid>_mosdepth.per-base.d4`: This file contains a coverage for each base in the genome in d4 format.
   - `<sampleid>_mosdepth.summary.txt`: This file contains summary statistics, such as mean, minimum and maximum coverage per genomic contig.
 
 </details>

modules.json

@@ -128,7 +128,7 @@
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "6e3585d9ad20b41adc7d271009f8cb5e191ecab4",
+                        "git_sha": "9f9e1fc31cb35876922070c0e601ae05abae5cae",
                         "installed_by": ["modules"]
                     },
                     "expansionhunter": {