update all modules for correct registry usage

CHANGELOG.md

@@ -42,6 +42,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1015](https://github.com/nf-core/sarek/pull/1015) - Increase default value for `--nucleotides_per_second` to `200000` resulting in 21 groups for `GATK.GRCh38`
 - [#1019](https://github.com/nf-core/sarek/pull/1019) - Set a default registry outside of profile scope
 - [#1031](https://github.com/nf-core/sarek/pull/1031) - Update pipeline summary
+- [#1032](https://github.com/nf-core/sarek/pull/1032) - Update all modules
 
 ### Fixed
 
@@ -75,6 +76,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | ------------- | ----------- | ----------- |
 | `ascat`       | 3.0.0       | 3.1.1       |
 | `bcftools`    | 1.15.1      | 1.17        |
+| `deepvariant` | 1.4.0       | 1.5.0       |
 | `ensembl-vep` | 106.1       | 108.2       |
 | `multiqc`     | 1.13a       | 1.14        |
 | `samtools`    | 1.16        | 1.17        |

conf/modules/trimming.config

@@ -17,7 +17,7 @@ process {
 
     withName: 'FASTP' {
         ext.args = [ "",
-            params.trim_fastq              ?: "--disable_adapter_trimming",
+            !params.trim_fastq             ? "--disable_adapter_trimming"                 : "", // Disable adapter trimming
             params.clip_r1 > 0             ? "--trim_front1 ${params.clip_r1}"            : "", // Remove bp from the 5' end of read 1
             params.clip_r2   > 0           ? "--trim_front2 ${params.clip_r2}"            : "", // Remove bp from the 5' end of read 2
             params.three_prime_clip_r1 > 0 ? "--trim_tail1 ${params.three_prime_clip_r1}" : "", // Remove bp from the 3' end of read 1 AFTER adapter/quality trimming has been performed

modules/local/add_info_to_vcf/main.nf

@@ -4,7 +4,7 @@ process ADD_INFO_TO_VCF {
     conda "anaconda::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'quay.io/biocontainers/gawk:5.1.0' }"
+        'biocontainers/gawk:5.1.0' }"
 
     input:
     tuple val(meta), path(vcf_gz)

modules/local/build_intervals/main.nf

@@ -4,7 +4,7 @@ process BUILD_INTERVALS {
     conda "anaconda::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'quay.io/biocontainers/gawk:5.1.0' }"
+        'biocontainers/gawk:5.1.0' }"
 
     input:
     tuple val(meta), path(fasta_fai)

modules/local/create_intervals_bed/main.nf

@@ -4,7 +4,7 @@ process CREATE_INTERVALS_BED {
     conda "anaconda::gawk=5.1.0"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
         'https://depot.galaxyproject.org/singularity/gawk:5.1.0' :
-        'quay.io/biocontainers/gawk:5.1.0' }"
+        'biocontainers/gawk:5.1.0' }"
 
     input:
     path(intervals)