Merge pull request #1552 from asp8200/update_samtools

Update samtools to v1.20
nf-core · Jun 4, 2024 · ddd6fb6 · ddd6fb6
2 parents d897e5c + 4c47673
commit ddd6fb6
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -19,6 +19,7 @@ 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
 
 ### Fixed
 
@@ -31,6 +32,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Dependencies
 
+| Dependency | Old version | New version |
+| ---------- | ----------- | ----------- |
+| `samtools` | 1.19.2      | 1.20        |
+
 ### Modules / Subworkflows
 
 ### Parameters

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
diff --git a/modules/nf-core/samtools/index/environment.yml b/modules/nf-core/samtools/index/environment.yml