Merge branch 'dev' into cleanup

nf-core · Jun 5, 2024 · d89f112 · d89f112
2 parents adf00db + ddd6fb6
commit d89f112
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Showing 31 changed files with 135 additions and 142 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,13 +19,15 @@ 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
+- [#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
 
 ### Fixed
 
 - [#1536](https://github.com/nf-core/sarek/pull/1536) - Correct typo `Strelka2` to `Strelka`
 - [#1541](https://github.com/nf-core/sarek/pull/1541) - Getting bam and bai published in the same folder
 - [#1542](https://github.com/nf-core/sarek/pull/1542) - Removing legacy configs of `CUSTOM_DUMPSOFTWAREVERSIONS`
+- [#1547](https://github.com/nf-core/sarek/pull/1547) - Correct typo in help text in nextflow_schema.json
 
 ### Removed
 
@@ -35,12 +37,9 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | ---------- | ----------- | ----------- |
 | `bwa`      | 0.7.17      | 0.7.18      |
 | `cnvkit`   | 0.9.10      | 0.9.11      |
-| `gawk`     | 5.1.0       | 5.3.0       |
 | `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

diff --git a/conf/test.config b/conf/test.config
@@ -19,7 +19,7 @@ params {
     max_time   = '8.h'
 
     // Base directory for nf-core/modules test data
-    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules'
+    modules_testdata_base_path = 's3://ngi-igenomes/testdata/nf-core/modules/'
 
     // Input data
     input = "${projectDir}/tests/csv/3.0/fastq_single.csv"

diff --git a/modules.json b/modules.json
@@ -356,47 +356,47 @@
                     },
                     "samtools/bam2fq": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/collatefastq": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/convert": {
                         "branch": "master",
-                        "git_sha": "b42fec6f7c6e5d0716685cabb825ef6bf6e386b5",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
                         "branch": "master",
-                        "git_sha": "f153f1f10e1083c49935565844cccb7453021682",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/index": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/merge": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/mpileup": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
-                        "git_sha": "f4596fe0bdc096cf53ec4497e83defdb3a94ff62",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "samtools/view": {
                         "branch": "master",
-                        "git_sha": "0bd7d2333a88483aa0476acea172e9f5f6dd83bb",
+                        "git_sha": "04fbbc7c43cebc0b95d5b126f6d9fe4effa33519",
                         "installed_by": ["modules"]
                     },
                     "sentieon/applyvarcal": {

diff --git a/modules/nf-core/samtools/bam2fq/environment.yml b/modules/nf-core/samtools/bam2fq/environment.yml
diff --git a/modules/nf-core/samtools/bam2fq/main.nf b/modules/nf-core/samtools/bam2fq/main.nf
diff --git a/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap b/modules/nf-core/samtools/bam2fq/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/collatefastq/environment.yml b/modules/nf-core/samtools/collatefastq/environment.yml
diff --git a/modules/nf-core/samtools/collatefastq/main.nf b/modules/nf-core/samtools/collatefastq/main.nf
diff --git a/modules/nf-core/samtools/convert/environment.yml b/modules/nf-core/samtools/convert/environment.yml
diff --git a/modules/nf-core/samtools/convert/main.nf b/modules/nf-core/samtools/convert/main.nf
diff --git a/modules/nf-core/samtools/convert/tests/main.nf.test.snap b/modules/nf-core/samtools/convert/tests/main.nf.test.snap
diff --git a/modules/nf-core/samtools/faidx/environment.yml b/modules/nf-core/samtools/faidx/environment.yml
diff --git a/modules/nf-core/samtools/faidx/main.nf b/modules/nf-core/samtools/faidx/main.nf
diff --git a/modules/nf-core/samtools/faidx/tests/main.nf.test.snap b/modules/nf-core/samtools/faidx/tests/main.nf.test.snap