Merge pull request #623 from nf-core/module_updates

Update modules

CHANGELOG.md

@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### `Changed`
 
+- Update tools [#623](https://github.com/nf-core/raredisease/pull/623)
 - Update output file name prefix for upd and chromograph to sample-based [#620](https://github.com/nf-core/raredisease/pull/620)
 - Update tools [#619](https://github.com/nf-core/raredisease/pull/619)
 - Report only variants above 5% heteroplasmy in the clinical vcf file for mitochondria [#616](https://github.com/nf-core/raredisease/pull/616)
@@ -31,6 +32,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 | multiqc  | 1.21        | 1.25        |
 | picard   | 3.1.1       | 3.2.0       |
 | samtools | 1.19.2      | 1.21        |
+| sentieon | 202308.02   | 202308.03   |
 | stranger | 0.8.1       | 0.9.1       |
 | tabix    | 1.19.1      | 1.20        |
 

conf/modules/align_sentieon.config

@@ -19,21 +19,20 @@ process {
 
     withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_BWAMEM' {
         ext.args = { "-M -K 10000000 -R ${meta.read_group} " }
-        ext.prefix = { "${meta.id}_sorted" }
+        ext.prefix = { "${meta.id}_sorted.bam" }
     }
 
     withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DATAMETRICS' {
         ext.prefix = { "${meta.id}_datametrics" }
     }
 
     withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_READWRITER' {
-        ext.prefix = { "${meta.id}_merged" }
+        ext.prefix = { "${meta.id}_merged.bam" }
     }
 
     withName: '.*ALIGN:ALIGN_SENTIEON:SENTIEON_DEDUP' {
-        ext.args = { $params.rmdup ? "--rmdup" : '' }
-        ext.prefix = { "${meta.id}_dedup" }
-        ext.suffix = ".bam"
+        ext.args4 = { $params.rmdup ? "--rmdup" : '' }
+        ext.prefix = { "${meta.id}_dedup.bam" }
         publishDir = [
             enabled: !params.save_mapped_as_cram,
             path: { "${params.outdir}/alignment" },

modules.json

@@ -52,7 +52,7 @@
                     },
                     "bedtools/genomecov": {
                         "branch": "master",
-                        "git_sha": "81b90194ce9911dbd55bba2c65c6919f6677abc4",
+                        "git_sha": "bfa8975eefb8df3e480a44ac9e594f23f52b2963",
                         "installed_by": ["modules"]
                     },
                     "bwa/index": {
@@ -369,7 +369,7 @@
                     },
                     "rtgtools/vcfeval": {
                         "branch": "master",
-                        "git_sha": "666652151335353eef2fcd58880bcef5bc2928e1",
+                        "git_sha": "83e2df1e4ec594beb8a575b4db0b4197900f4ebd",
                         "installed_by": ["modules"]
                     },
                     "samtools/faidx": {
@@ -404,42 +404,42 @@
                     },
                     "sentieon/bwaindex": {
                         "branch": "master",
-                        "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/bwamem": {
                         "branch": "master",
-                        "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/datametrics": {
                         "branch": "master",
-                        "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dedup": {
                         "branch": "master",
-                        "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dnamodelapply": {
                         "branch": "master",
-                        "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/dnascope": {
                         "branch": "master",
-                        "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/readwriter": {
                         "branch": "master",
-                        "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "sentieon/wgsmetrics": {
                         "branch": "master",
-                        "git_sha": "e809c6b078d5343bdf8b5b2b78483096a2b5a973",
+                        "git_sha": "eb7b70119bfb1877334c996d13e520c61b21067d",
                         "installed_by": ["modules"]
                     },
                     "smncopynumbercaller": {