Merge pull request #392 from genomic-medicine-sweden/markdupprefix

Make cram prefix same as the default markduplicates prefix
nf-core · Jul 31, 2023 · a2ce37e · a2ce37e
2 parents f4d5d57 + 7817473
commit a2ce37e
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -16,6 +16,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### `Fixed`
 
 - Invalid GATK4 container which caused incorrect singularity downloads with nf-core download [nf-core/modules #3668](https://github.com/nf-core/modules/issues/3668)
+- Make the default cram prefix same as markduplicates prefix [#392](https://github.com/nf-core/raredisease/pull/392)
 
 ## v1.1.1 - Abu (Patch) [2023-07-26]
 

diff --git a/conf/modules/align.config b/conf/modules/align.config
@@ -19,8 +19,9 @@ process{
     }
 
     withName: '.*ALIGN:SAMTOOLS_VIEW' {
-        ext.args = { '--output-fmt cram --write-index' }
-        ext.when = params.save_mapped_as_cram
+        ext.args   = { '--output-fmt cram --write-index' }
+        ext.prefix = { "${meta.id}_sorted_md" }
+        ext.when   = params.save_mapped_as_cram
         publishDir = [
             path: { "${params.outdir}/alignment" },
             mode: params.publish_dir_mode,