Updating samtools in bwamem (nf-core#4943)

* Updating mulled-container and environment.yml to samtools v1.19.2. Fixing htslib to v1.19.1 * Pinning version of htslib in environment.yml for samblaster * Pinning version of htslib in environment.yml for svdb/merge * Updating snapShot for bwa/mem * Updating snapShot for umicollapse
asp8200 · Feb 19, 2024 · ba3f3df · ba3f3df
1 parent 8c49840
commit ba3f3df
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Showing 6 changed files with 48 additions and 30 deletions.
diff --git a/modules/nf-core/bwa/mem/environment.yml b/modules/nf-core/bwa/mem/environment.yml
@@ -6,5 +6,5 @@ channels:
 dependencies:
   - bwa=0.7.17
   # renovate: datasource=conda depName=bioconda/samtools
-  - samtools=1.18
-  - htslib=1.18
+  - samtools=1.19.2
+  - htslib=1.19.1
diff --git a/modules/nf-core/bwa/mem/main.nf b/modules/nf-core/bwa/mem/main.nf
@@ -4,8 +4,8 @@ process BWA_MEM {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:9c0128851101dafef65cef649826d2dbe6bedd7e-0' :
-        'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:9c0128851101dafef65cef649826d2dbe6bedd7e-0' }"
+        'https://depot.galaxyproject.org/singularity/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:a34558545ae1413d94bde4578787ebef08027945-0' :
+        'biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:a34558545ae1413d94bde4578787ebef08027945-0' }"
 
     input:
     tuple val(meta), path(reads)

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/samblaster/environment.yml b/modules/nf-core/samblaster/environment.yml
@@ -6,3 +6,4 @@ channels:
 dependencies:
   - bioconda::samblaster=0.1.26
   - bioconda::samtools=1.19.2
+  - bioconda::htslib=1.19.1
diff --git a/modules/nf-core/svdb/merge/environment.yml b/modules/nf-core/svdb/merge/environment.yml
@@ -7,3 +7,4 @@ dependencies:
   - svdb=2.8.1
   # renovate: datasource=conda depName=bioconda/samtools
   - samtools=1.19.2
+  - htslib=1.19.1
diff --git a/modules/nf-core/umicollapse/tests/main.nf.test.snap b/modules/nf-core/umicollapse/tests/main.nf.test.snap