Feat/fastq align dedup bismark

CHANGELOG.md

@@ -1,6 +1,6 @@
 # nf-core/methylseq
 
-## [v2.7.2](https://github.com/nf-core/methylseq/releases/tag/2.7.2) - []
+## [v2.8.0](https://github.com/nf-core/methylseq/releases/tag/2.8.0) - []
 
 ### Bug fixes & refactoring
 
@@ -9,6 +9,8 @@
 
 ### Pipeline Updates
 
+- 🔧 Install `fastq_align_dedup_bismark` subworkflow from nf-core/subworkflows [#453](https://github.com/nf-core/methylseq/pull/457)
+
 ## [v2.7.1](https://github.com/nf-core/methylseq/releases/tag/2.7.1) - [2024-10-27]
 
 ### Bug fixes & refactoring

modules.json

@@ -8,17 +8,17 @@
                     "bismark/align": {
                         "branch": "master",
                         "git_sha": "f5a291e827949778a3bb976479d6298b3abf99cd",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bismark", "modules"]
                     },
                     "bismark/coverage2cytosine": {
                         "branch": "master",
                         "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bismark", "modules"]
                     },
                     "bismark/deduplicate": {
                         "branch": "master",
                         "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bismark", "modules"]
                     },
                     "bismark/genomepreparation": {
                         "branch": "master",
@@ -28,17 +28,17 @@
                     "bismark/methylationextractor": {
                         "branch": "master",
                         "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bismark", "modules"]
                     },
                     "bismark/report": {
                         "branch": "master",
                         "git_sha": "79922141f1033bc3b56dabef0f0eff68b2b0fb03",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bismark", "modules"]
                     },
                     "bismark/summary": {
                         "branch": "master",
                         "git_sha": "dfd89399e3c6e2422c4cdcf0aaa8cf2393dc51c9",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bismark", "modules"]
                     },
                     "bwameth/align": {
                         "branch": "master",
@@ -113,12 +113,12 @@
                     "samtools/index": {
                         "branch": "master",
                         "git_sha": "b13f07be4c508d6ff6312d354d09f2493243e208",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bismark", "modules"]
                     },
                     "samtools/sort": {
                         "branch": "master",
                         "git_sha": "b7800db9b069ed505db3f9d91b8c72faea9be17b",
-                        "installed_by": ["modules"]
+                        "installed_by": ["fastq_align_dedup_bismark", "modules"]
                     },
                     "samtools/stats": {
                         "branch": "master",
@@ -139,19 +139,24 @@
             },
             "subworkflows": {
                 "nf-core": {
+                    "fastq_align_dedup_bismark": {
+                        "branch": "master",
+                        "git_sha": "af84433c2e619cf28e026d4140b1b8763ae3690b",
+                        "installed_by": ["subworkflows"]
+                    },
                     "utils_nextflow_pipeline": {
                         "branch": "master",
-                        "git_sha": "3aa0aec1d52d492fe241919f0c6100ebf0074082",
+                        "git_sha": "c2b22d85f30a706a3073387f30380704fcae013b",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfcore_pipeline": {
                         "branch": "master",
-                        "git_sha": "1b6b9a3338d011367137808b49b923515080e3ba",
+                        "git_sha": "1b89f75f1aa2021ec3360d0deccd0f6e97240551",
                         "installed_by": ["subworkflows"]
                     },
                     "utils_nfschema_plugin": {
                         "branch": "master",
-                        "git_sha": "bbd5a41f4535a8defafe6080e00ea74c45f4f96c",
+                        "git_sha": "2fd2cd6d0e7b273747f32e465fdc6bcc3ae0814e",
                         "installed_by": ["subworkflows"]
                     }
                 }

nf-test.config

@@ -16,7 +16,7 @@ config {
 
     // load the necessary plugins
     plugins {
-        load "nft-bam@0.3.0"
+        load "nft-bam@0.5.0"
         load "nft-utils@0.0.3"
     }
 }