FIX: Fix default memory issue with gatk4/createsequencedictionary

CHANGELOG.md

@@ -5,6 +5,17 @@ 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
+
+### Changed
+
+- [#1087](https://github.com/nf-core/sarek/pull/1087) - Back to dev
+- [#1087](https://github.com/nf-core/sarek/pull/1087) - Minor modules update
+
+### Fixed
+
+- [#1087](https://github.com/nf-core/sarek/pull/1087) - Fix wrong default memory in GATK4_CREATESEQUENCEDICTIONARY [#1085](https://github.com/nf-core/sarek/pull/1085)
+
 ## [3.2.1](https://github.com/nf-core/sarek/releases/tag/3.2.1) - Pierikjaure
 
 Pierikjaure is a previous spelling of Bierikjávrre.

modules.json

@@ -198,7 +198,7 @@
                     },
                     "gatk4/createsequencedictionary": {
                         "branch": "master",
-                        "git_sha": "2df2a11d5b12f2a73bca74f103691bc35d83c5fd",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/estimatelibrarycomplexity": {
@@ -213,7 +213,7 @@
                     },
                     "gatk4/filtervarianttranches": {
                         "branch": "master",
-                        "git_sha": "911696ea0b62df80e900ef244d7867d177971f73",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/gatherbqsrreports": {
@@ -263,7 +263,7 @@
                     },
                     "gatk4/markduplicatesspark": {
                         "branch": "master",
-                        "git_sha": "4b7d4863a5883b76e6bff13b6e52468fab090c5b",
+                        "git_sha": "541811d779026c5d395925895fa5ed35e7216cc0",
                         "installed_by": ["modules"]
                     },
                     "gatk4/mergemutectstats": {

nextflow.config

@@ -323,7 +323,7 @@ manifest {
     description     = """An open-source analysis pipeline to detect germline or somatic variants from whole genome or targeted sequencing"""
     mainScript      = 'main.nf'
     nextflowVersion = '!>=23.04.0'
-    version         = '3.2.1'
+    version         = '3.3dev'
     doi             = '10.12688/f1000research.16665.2, 10.5281/zenodo.4063683'
 }
 

tests/test_joint_germline.yml

@@ -13,13 +13,13 @@
     - path: results/preprocessing/recalibrated/test/test.recal.cram.crai
       should_exist: false
     - path: results/reports/bcftools/haplotypecaller/joint_variant_calling/joint_germline.bcftools_stats.txt
-      md5sum: 404d1208df301a6726f5543245625ef3
+    # Not stable enough
     - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.FILTER.summary
-      md5sum: 87a84b5f8ac3d3cbeeef7d60afcdbfe7
+    # Not stable enough
     - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.count
-      md5sum: 974f6922981c87bb017b124aa009f654
+    # Not stable enough
     - path: results/reports/vcftools/haplotypecaller/joint_variant_calling/joint_germline.TsTv.qual
-      md5sum: 1e34357e5848c318f8c2c7d3b041d229
+    # Not stable enough
     - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz
     # binary changes md5sums on reruns
     - path: results/variant_calling/haplotypecaller/joint_variant_calling/joint_germline.vcf.gz.tbi