Md cram update

CHANGELOG.md

@@ -5,6 +5,24 @@ All notable changes to this project will be documented in this file.
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/)
 and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0.html).
 
+## [dev]
+
+### Added
+
+### Changed
+
+- [#855](https://github.com/nf-core/sarek/pull/855) - Speed up duplicate marking by using `samtools` for CRAM conversion
+
+### Fixed
+
+- [#851](https://github.com/nf-core/sarek/pull/851) - Fix `schema` definition `None` for `cf_chrom_len`
+
+### Deprecated
+
+### Removed
+
+### Dependencies
+
 ## [3.1](https://github.com/nf-core/sarek/releases/tag/3.1) - Rapaätno
 
 Rapaätno is the river you can see from the Skierfe mountain.

conf/modules/markduplicates.config

@@ -57,7 +57,7 @@ process {
     }
 
     withName: 'GATK4_MARKDUPLICATES' {
-        ext.args         = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT --CREATE_INDEX true'
+        ext.args         = '-REMOVE_DUPLICATES false -VALIDATION_STRINGENCY LENIENT'
         ext.prefix       = { "${meta.id}.md.cram" }
         ext.when         = { !(params.skip_tools && params.skip_tools.split(',').contains('markduplicates')) }
         publishDir       = [

modules.json

@@ -197,7 +197,8 @@
                     },
                     "gatk4/markduplicates": {
                         "branch": "master",
-                        "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67"
+                        "git_sha": "7578005a576f3ac1b0d4f10c037dde34cdedfb67",
+                        "patch": "modules/nf-core/gatk4/markduplicates/gatk4-markduplicates.diff"
                     },
                     "gatk4/markduplicatesspark": {
                         "branch": "master",