CHORES: update all modules

CHANGELOG.md

@@ -19,6 +19,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1278](https://github.com/nf-core/sarek/pull/1278) - Hide sentieon parameters similar to other variant callers
 - [#1280](https://github.com/nf-core/sarek/pull/1280) - Replacing link to `SentieonDNAscopeModel1.1.model` in Sentieon's S3 with link to same file in igenomes' S3
 - [#1303](https://github.com/nf-core/sarek/pull/1303) - Ressurect vep_version params and changed its scope to pipeline to enable usage for vep loftee plugin
+- [#1304](https://github.com/nf-core/sarek/pull/1304) - Update modules
 
 ### Fixed
 
@@ -35,6 +36,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| fastqc     | 0.11.9      | 0.12.1      |
+| multiqc    | 1.15        | 1.17        |
+
+### Modules / Subworkflows
+
+| script                        | Old name                      | New name                      |
+| ----------------------------- | ----------------------------- | ----------------------------- |
+| `gatk4spark/applybqsr`        | `GATK4_APPLYBQSRSPARK`        | 'GATK4SPARK_APPLYBQSR'        |
+| `gatk4spark/baserecalibrator` | `GATK4_BASERECALIBRATORSPARK` | 'GATK4SPARK_BASERECALIBRATOR' |
+| `gatk4spark/markduplicates`   | `GATK4_MARKDUPLICATESSPARK`   | 'GATK4SPARK_MARKDUPLICATES'   |
 
 ## [3.3.2](https://github.com/nf-core/sarek/releases/tag/3.3.2) - Ráhpajávvre
 

conf/base.config

@@ -74,11 +74,11 @@ process {
         label           = "process_high"
         memory          = { check_max( 36.GB * task.attempt, 'memory' ) }
     }
-    withName: 'GATK4_MARKDUPLICATES|GATK4_MARKDUPLICATESSPARK' {
+    withName: 'GATK4_MARKDUPLICATES|GATK4SPARK_MARKDUPLICATES' {
         cpus           = { check_max( 6 * task.attempt, 'cpus' ) }
         memory         = { check_max( 30.GB * task.attempt, 'memory' ) }
     }
-    withName:'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK|GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK|GATK4_GATHERBQSRREPORTS'{
+    withName:'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR|GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR|GATK4_GATHERBQSRREPORTS'{
         cpus            = { check_max( 2 * task.attempt, 'cpus' ) }
         memory          = { check_max( 4.GB * task.attempt, 'memory' ) }
     }

conf/modules/annotate.config

@@ -64,7 +64,7 @@ process {
     if (params.tools && params.tools.split(',').contains('bcfann')) {
         withName: 'NFCORE_SAREK:SAREK:VCF_ANNOTATE_ALL:VCF_ANNOTATE_BCFTOOLS:BCFTOOLS_ANNOTATE' {
             ext.args         = '--output-type z'
-            ext.prefix       = { "${vcf.baseName.minus(".vcf")}_BCF.ann" }
+            ext.prefix       = { input.baseName - ".vcf" + "_BCF.ann" }
             publishDir       = [
                     mode: params.publish_dir_mode,
                     path: { "${params.outdir}/annotation/${meta.variantcaller}/${meta.id}/" },

conf/modules/prepare_recalibration.config

@@ -15,7 +15,7 @@
 
 process {
 
-    withName: 'GATK4_BASERECALIBRATOR|GATK4_BASERECALIBRATOR_SPARK' {
+    withName: 'GATK4_BASERECALIBRATOR|GATK4SPARK_BASERECALIBRATOR' {
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
         publishDir       = [
             mode: params.publish_dir_mode,

conf/modules/recalibrate.config

@@ -15,7 +15,7 @@
 
 process {
 
-    withName: 'GATK4_APPLYBQSR|GATK4_APPLYBQSR_SPARK' {
+    withName: 'GATK4_APPLYBQSR|GATK4SPARK_APPLYBQSR' {
         ext.prefix       = { meta.num_intervals <= 1 ? "${meta.id}.recal" : "${meta.id}_${intervals.simpleName}.recal" }
         publishDir       = [
             enabled: !params.save_output_as_bam,