fix: Update all modules and collect software versions with topic channels

CHANGELOG.md

@@ -39,6 +39,7 @@ Initial release of Clinical-Genomics/oncorefiner, created with the [nf-core](htt
 - Updated template for nf-core/tools version 3.5.2 to apply updated settings and changes missed in previous template update ([14](https://github.com/Clinical-Genomics/oncorefiner/pull/14)) [#35](https://github.com/Clinical-Genomics/oncorefiner/pull/35)
 - Fixed prepare_references config that was defined but not used [36](https://github.com/Clinical-Genomics/oncorefiner/pull/36)
 - Fixed bug and formatting in feature request template [#39](https://github.com/Clinical-Genomics/oncorefiner/pull/39)
+- Updated all modules and removed deprecated `ch_versions` to implement latest nf-core changes that use the `versions` topic channel to collect software versions [#34](https://github.com/Clinical-Genomics/oncorefiner/pull/34)
 
 ### `Dependencies`
 

modules.json

@@ -7,52 +7,52 @@
                 "nf-core": {
                     "bcftools/annotate": {
                         "branch": "master",
-                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
+                        "git_sha": "3d9c2f4beaa4f62b3f006928fd9095a496d1e5a8",
                         "installed_by": ["modules"]
                     },
                     "bcftools/filter": {
                         "branch": "master",
-                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
+                        "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6",
                         "installed_by": ["modules"]
                     },
                     "bcftools/index": {
                         "branch": "master",
-                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
+                        "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6",
                         "installed_by": ["modules"]
                     },
                     "bcftools/view": {
                         "branch": "master",
-                        "git_sha": "f17049e03697726ace7499d2fe342f892594f6f3",
+                        "git_sha": "6383d8fe58f9498eecd5aa303e71a4a932d1e9f6",
                         "installed_by": ["modules"]
                     },
                     "ensemblvep/vep": {
                         "branch": "master",
-                        "git_sha": "0567eee9276d4a358e5f9f01c810a149fbd241f8",
+                        "git_sha": "34505e1fc5e9f4fd641210ca440acff6bd33b842",
                         "installed_by": ["modules"]
                     },
                     "multiqc": {
                         "branch": "master",
-                        "git_sha": "af27af1be706e6a2bb8fe454175b0cdf77f47b49",
+                        "git_sha": "2c73cc8fa92cf48de3da0b643fdf357a8a290b36",
                         "installed_by": ["modules"]
                     },
                     "svdb/query": {
                         "branch": "master",
-                        "git_sha": "41dfa3f7c0ffabb96a6a813fe321c6d1cc5b6e46",
+                        "git_sha": "7d09b5f86908bdd951e42aef9994ad5bb0f6c307",
                         "installed_by": ["modules"]
                     },
                     "tabix/tabix": {
                         "branch": "master",
-                        "git_sha": "f2cfcf9d3f6a2d123e6c44aefa788aa232204a7a",
+                        "git_sha": "524a7d5ef99a0cbfb4feec8bf7062eb6a531931a",
                         "installed_by": ["modules"]
                     },
                     "untar": {
                         "branch": "master",
-                        "git_sha": "00ee87ebb541af0008596400ce6d5f66d79d5408",
+                        "git_sha": "447f7bc0fa41dfc2400c8cad4c0291880dc060cf",
                         "installed_by": ["modules"]
                     },
                     "vcfanno": {
                         "branch": "master",
-                        "git_sha": "15e7f217661be7e332950289735bd790079873fe",
+                        "git_sha": "2ad28db4a5a82972c1210dfa7c85f035bb80c4de",
                         "installed_by": ["modules"]
                     }
                 }