updating GATK

.github/workflows/ci.yml

@@ -221,6 +221,12 @@ jobs:
           - tags: "dragmap/align"
           - tags: "fastp"
           - tags: "fastqc"
+          - tags: "gatk4/applybqsr"
+          - tags: "gatk4/baserecalibrator"
+          - tags: "gatk4/genomicsdbimport"
+          - tags: "gatk4/haplotypecaller"
+          - tags: "gatk4/markduplicates"
+          - tags: "gatk4/mergevcfs"
           - tags: "multiqc"
           - tags: "samtools/mpileup"
           - tags: "samtools/stats"

CHANGELOG.md

@@ -25,6 +25,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1360](https://github.com/nf-core/sarek/pull/1360) - Sync `TEMPLATE` with `tools` `2.11`
 - [#1408](https://github.com/nf-core/sarek/pull/1408), [#1412](https://github.com/nf-core/sarek/pull/1412) - Updating samtools to v1.19.2 - except in GATK/markduplicates. (Temporarily disabled nf-test for bwamem2/mem.)
 - [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporarily disable sentieon related tests
+- [#1419](https://github.com/nf-core/sarek/pull/1419) - Updating GATK to v4.5, and updating samtools to v1.19.2 in GATK/markduplicates.
 
 ### Fixed
 
@@ -45,6 +46,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
+| gatk       | 4.4.0.0     | 4.5.0.0     |
 | multiqc    | 1.17        | 1.18        |
 | samtools   | 1.17        | 1.19.2      |
 

modules.json

@@ -172,112 +172,112 @@
                     },
                     "gatk4/applybqsr": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/applyvqsr": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/baserecalibrator": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/calculatecontamination": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/cnnscorevariants": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "87e46f8fe8b056486a80c14b1d61e7cd6046bc06",
                         "installed_by": ["modules"]
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/estimatelibrarycomplexity": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filtermutectcalls": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filtervarianttranches": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/gatherbqsrreports": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/gatherpileupsummaries": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genomicsdbimport": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/genotypegvcfs": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/getpileupsummaries": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/haplotypecaller": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/intervallisttobed": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/learnreadorientationmodel": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/markduplicates": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergemutectstats": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergevcfs": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mutect2": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4/variantrecalibrator": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
                         "installed_by": ["modules"]
                     },
                     "gatk4spark/applybqsr": {