Update Bismark to 3.1.0

CHANGELOG.md

@@ -7,6 +7,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Pipeline Updates
 
+- 🔧 Update Bismark to v3.1.0 ([#614](https://github.com/nf-core/methylseq/pull/614))
 - 🔧 Update Bismark to v3.0.0 and refresh the bismark, samtools, bwa, bwameth, methyldackel and parabricks nf-core modules and alignment subworkflows to their latest versions ([#610](https://github.com/nf-core/methylseq/pull/610))
   - Migrated module version reporting to Nextflow topic channels
   - Threaded a combined `[ meta, fasta, fai ]` channel through the alignment subworkflows

modules.json

@@ -12,37 +12,37 @@
                     },
                     "bismark/align": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/coverage2cytosine": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/deduplicate": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/genomepreparation": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fasta_index_bismark_bwameth", "fasta_index_methylseq"]
                     },
                     "bismark/methylationextractor": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/report": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bismark/summary": {
                         "branch": "master",
-                        "git_sha": "9089c2afa0daf7dfd2bea23b972d7d3b8c66cd4c",
+                        "git_sha": "7d264419ee98edd5a0886d3782fb87553628272b",
                         "installed_by": ["fastq_align_dedup_bismark"]
                     },
                     "bwa/index": {