Merge pull request #1412 from asp8200/update_samtools_II

Update mulled-containers to samtools v1.19.2
nf-core · Feb 20, 2024 · fa75797 · fa75797
2 parents e92cfb3 + 1bcdf57
commit fa75797
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Showing 29 changed files with 452 additions and 75 deletions.
diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml
@@ -211,6 +211,7 @@ jobs:
         exclude:
           - tags: "bwa/index"
           - tags: "bwa/mem"
+          - tags: "bwamem2/mem"
           - tags: "cat/cat"
           - tags: "cat/fastq"
           - tags: "custom/dumpsoftwareversions"

diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -23,8 +23,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 - [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local modules
 - [#1359](https://github.com/nf-core/sarek/pull/1359) - Removing params usage from local subworkflows
 - [#1360](https://github.com/nf-core/sarek/pull/1360) - Sync `TEMPLATE` with `tools` `2.11`
-- [#1408](https://github.com/nf-core/sarek/pull/1408) - Updating samtools to v1.19.2 in "pure" samtools-modules, that is, samtools in mulled containers have NOT yet been updated.
-- [#1411](https://github.com/nf-core/sarek/pull/1411) - Temporally disable sentieon related tests
+- [#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
 
 ### Fixed
 

diff --git a/conf/modules/tiddit.config b/conf/modules/tiddit.config
@@ -47,7 +47,7 @@ process {
 
         // SVDB
         withName: 'NFCORE_SAREK:SAREK:BAM_VARIANT_CALLING_SOMATIC_ALL:BAM_VARIANT_CALLING_SOMATIC_TIDDIT:SVDB_MERGE' {
-            ext.prefix = { "${meta.id}.tiddit" }
+            ext.prefix = { "${meta.id}.tiddit_sv_merge" }
             publishDir = [
                 mode: params.publish_dir_mode,
                 path: { "${params.outdir}/variant_calling/tiddit/${meta.id}/" },

diff --git a/modules.json b/modules.json
@@ -43,7 +43,7 @@
                     },
                     "bwa/mem": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "ba3f3df395d2719dcef5c67189042a1dc555c701",
                         "installed_by": ["modules"]
                     },
                     "bwamem2/index": {
@@ -53,7 +53,7 @@
                     },
                     "bwamem2/mem": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "74363e1acc38eaedeede8d429477397c1a6f9e18",
                         "installed_by": ["modules"]
                     },
                     "cat/cat": {
@@ -68,22 +68,22 @@
                     },
                     "cnvkit/antitarget": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "cnvkit/batch": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "76c858e2589c7762c68d7d14191d78f6db98a445",
                         "installed_by": ["modules"]
                     },
                     "cnvkit/genemetrics": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "cnvkit/reference": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "a64788f5ad388f1d2ac5bd5f1f3f8fc81476148c",
                         "installed_by": ["modules"]
                     },
                     "controlfreec/assesssignificance": {
@@ -125,7 +125,7 @@
                     },
                     "dragmap/align": {
                         "branch": "master",
-                        "git_sha": "3c77ca9aac783e76c3614a06db3bfe4fef619bde",
+                        "git_sha": "575e1bc54b083fb15e7dd8b5fcc40bea60e8ce83",
                         "installed_by": ["modules"],
                         "patch": "modules/nf-core/dragmap/align/dragmap-align.diff"
                     },
@@ -342,7 +342,7 @@
                     },
                     "samblaster": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "8ad1f37288c6f5a36871c169aa85614832152fd1",
                         "installed_by": ["modules"]
                     },
                     "samtools/bam2fq": {
@@ -452,7 +452,7 @@
                     },
                     "svdb/merge": {
                         "branch": "master",
-                        "git_sha": "3f5420aa22e00bd030a2556dfdffc9e164ec0ec5",
+                        "git_sha": "8c498400bfa0f0e5c1750fab21496a27bc8d9ad0",
                         "installed_by": ["modules"]
                     },
                     "tabix/bgziptabix": {

diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml
diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf
diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test b/modules/nf-core/bwa/mem/tests/main.nf.test
diff --git a/modules/nf-core/bwa/mem/tests/main.nf.test.snap b/modules/nf-core/bwa/mem/tests/main.nf.test.snap
diff --git a/modules/nf-core/bwamem2/mem/environment.yml b/modules/nf-core/bwamem2/mem/environment.yml
diff --git a/modules/nf-core/bwamem2/mem/main.nf b/modules/nf-core/bwamem2/mem/main.nf