Cleanup + update modules

.github/workflows/ci.yml

@@ -224,7 +224,9 @@ jobs:
           - tags: "bwamem2/mem"
           - tags: "cat/cat"
           - tags: "cat/fastq"
+          - tags: "cnvkit/antitarget"
           - tags: "cnvkit/batch"
+          - tags: "cnvkit/reference"
           - tags: "deepvariant"
           - tags: "dragmap/align"
           - tags: "dragmap/hashtable"
@@ -247,6 +249,7 @@ jobs:
           - tags: "gawk"
           - tags: "mosdepth"
           - tags: "multiqc"
+          - tags: "ngscheckmate/ncm"
           - tags: "samblaster"
           - tags: "samtools/convert"
           - tags: "samtools/mpileup"

.gitignore

@@ -10,3 +10,5 @@ testing*
 .nf-test*
 .nf-test/
 test-datasets/
+test.tap
+test.xml

.nf-core.yml

@@ -6,16 +6,11 @@ lint:
     - .github/workflows/awsfulltest.yml
     - .github/workflows/awstest.yml
     - conf/modules.config
-    - lib/WorkflowMain.groovy
-    - lib/NfcoreTemplate.groovy
-    - lib/WorkflowSarek.groovy
   files_unchanged:
     - .gitignore
     - .github/PULL_REQUEST_TEMPLATE.md
     - assets/nf-core-sarek_logo_light.png
     - docs/images/nf-core-sarek_logo_dark.png
     - docs/images/nf-core-sarek_logo_light.png
-    - lib/NfcoreTemplate.groovy
-    - lib/NfcoreSchema.groovy
   modules_config: False
   template_strings: False

CHANGELOG.md

@@ -19,7 +19,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1513](https://github.com/nf-core/sarek/pull/1513) - Back to dev
 - [#1518](https://github.com/nf-core/sarek/pull/1518) - Sync `TEMPLATE` with `tools` `2.14.1`
 - [#1521](https://github.com/nf-core/sarek/pull/1521) - Minor code refactoring to simplify syntax in args handling
+- [#1545](https://github.com/nf-core/sarek/pull/1545) - Update modules
 - [#1552](https://github.com/nf-core/sarek/pull/1552) - Update samtools to v1.20
+- [#1545](https://github.com/nf-core/sarek/pull/1545) - Update modules
 - [#1553](https://github.com/nf-core/sarek/pull/1553) - Update bcftools to v1.20
 
 ### Fixed
@@ -36,10 +38,11 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | Dependency | Old version | New version |
 | ---------- | ----------- | ----------- |
 | `bcftools` | 1.18        | 1.20        |
+| `bwa`      | 0.7.17      | 0.7.18      |
+| `cnvkit`   | 0.9.10      | 0.9.11      |
+| `htslib`   | 1.19.1      | 1.20        |
 | `samtools` | 1.19.2      | 1.20        |
 
-### Modules / Subworkflows
-
 ### Parameters
 
 ## [3.4.2](https://github.com/nf-core/sarek/releases/tag/3.4.2) - Sájtáristjåhkkå

modules.json

@@ -38,12 +38,12 @@
                     },
                     "bwa/index": {
                         "branch": "master",
-                        "git_sha": "6278bf9afd4a4b2d00fa6052250e73da3d91546f",
+                        "git_sha": "086fa66260595e123b0ea47a6512539b72a9afa3",
                         "installed_by": ["modules"]
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "b97197968ac12dde2463fa54541f6350c46f2035",
+                        "git_sha": "0c34b8159f62cde451c4ff249629c9d0a4f3f9c3",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -63,12 +63,12 @@
                     },
                     "cat/fastq": {
                         "branch": "master",
-                        "git_sha": "0997b47c93c06b49aa7b3fefda87e728312cf2ca",
+                        "git_sha": "4fc983ad0b30e6e32696fa7d980c76c7bfe1c03e",
                         "installed_by": ["modules"]
                     },
                     "cnvkit/antitarget": {
                         "branch": "master",
-                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+                        "git_sha": "7d8eff8f0cbc20cb83ce624e86c58ede51397054",
                         "installed_by": ["modules"]
                     },
                     "cnvkit/batch": {
@@ -93,7 +93,7 @@
                     },
                     "cnvkit/reference": {
                         "branch": "master",
-                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
+                        "git_sha": "f8693ff46b884892982d658271ed260380111c53",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/assesssignificance": {
@@ -186,7 +186,7 @@
                     },
                     "gatk4/applyvqsr": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "cee8fe33d3ef1a220dee67dac75a32f7c872f63f",
                         "installed_by": ["modules"]
                     },
                     "gatk4/baserecalibrator": {
@@ -196,7 +196,7 @@
                     },
                     "gatk4/calculatecontamination": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "77ffba959bbe8b6e1d95d47688075d113e24f0d4",
                         "installed_by": ["modules"]
                     },
                     "gatk4/cnnscorevariants": {
@@ -206,7 +206,7 @@
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "e6fe277739f5894711405af3e717b2470bd956b5",
                         "installed_by": ["modules"]
                     },
                     "gatk4/estimatelibrarycomplexity": {
@@ -216,7 +216,7 @@
                     },
                     "gatk4/filtermutectcalls": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "7d814815f638e1483995b24a23f5f23229036bbf",
                         "installed_by": ["modules"]
                     },
                     "gatk4/filtervarianttranches": {
@@ -246,7 +246,7 @@
                     },
                     "gatk4/getpileupsummaries": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "b632dcbf8bd3d7b9cb22fd0b2416e9e6cb8f4045",
                         "installed_by": ["modules"]
                     },
                     "gatk4/haplotypecaller": {
@@ -271,7 +271,7 @@
                     },
                     "gatk4/mergemutectstats": {
                         "branch": "master",
-                        "git_sha": "d742e3143f2ccb8853c29b35cfcf50b5e5026980",
+                        "git_sha": "cafe91148ca110e52ceaa07f3e373b882800d04b",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergevcfs": {
@@ -306,7 +306,7 @@
                     },
                     "gawk": {
                         "branch": "master",
-                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
+                        "git_sha": "cf3ed075695639b0a0924eb0901146df1996dc08",
                         "installed_by": ["modules"]
                     },
                     "manta/germline": {
@@ -346,7 +346,7 @@
                     },
                     "ngscheckmate/ncm": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "0e04b949c90e686c8b07495576832d78ab9210cf",
                         "installed_by": ["bam_ngscheckmate"]
                     },
                     "samblaster": {