diff --git a/.cache.tar.xz b/.cache.tar.xz
index 4958436918..d30bf0b2f2 100644
Binary files a/.cache.tar.xz and b/.cache.tar.xz differ
diff --git a/public/components.json b/public/components.json
index c9bc29c276..f4137d547c 100644
--- a/public/components.json
+++ b/public/components.json
@@ -2513,6 +2513,204 @@
         ]
       }
     },
+    {
+      "name": "anota2seq_anota2seqrun",
+      "path": "modules/nf-core/anota2seq/anota2seqrun/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "anota2seq_anota2seqrun",
+        "description": "Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq",
+        "keywords": [
+          "riboseq",
+          "rnaseq",
+          "translation",
+          "differential"
+        ],
+        "tools": [
+          {
+            "anota2seq": {
+              "description": "Generally applicable transcriptome-wide analysis of translational efficiency using anota2seq",
+              "homepage": "https://bioconductor.org/packages/release/bioc/html/anota2seq.html",
+              "documentation": "https://bioconductor.org/packages/release/bioc/vignettes/anota2seq/inst/doc/anota2seq.pdf",
+              "doi": "10.18129/B9.bioc.anota2seq",
+              "licence": [
+                "GPL v3"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing contrast information. e.g.  [ id:'contrast1',\nblocking:'patient' ]\n"
+            }
+          },
+          {
+            "sample_treatment_col": {
+              "type": "string",
+              "description": "The column in the sample sheet that should be used to define groups for\ncomparison\n"
+            }
+          },
+          {
+            "reference": {
+              "type": "string",
+              "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the reference samples\n"
+            }
+          },
+          {
+            "target": {
+              "type": "string",
+              "description": "The value within the contrast_variable column of the sample sheet that\nshould be used to derive the target samples\n"
+            }
+          },
+          {
+            "meta2": {
+              "type": "map",
+              "description": "Groovy map containing study-wide metadata related to the sample sheet\nand matrix\n"
+            }
+          },
+          {
+            "samplesheet": {
+              "type": "file",
+              "description": "CSV or TSV format sample sheet with sample metadata\n"
+            }
+          },
+          {
+            "counts": {
+              "type": "file",
+              "description": "Raw TSV or CSV format expression matrix\n"
+            }
+          }
+        ],
+        "output": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing contrast information. e.g.  [ id:'contrast1',\nblocking:'patient' ]\n"
+            }
+          },
+          {
+            "translated_mrna": {
+              "type": "file",
+              "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for Ribo-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.",
+              "pattern": ".translated_mRNA.anota2seq.results.tsv"
+            }
+          },
+          {
+            "total_mrna": {
+              "type": "file",
+              "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in RNA levels across conditions for RNA-seq samples. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.",
+              "pattern": ".translated_mRNA.anota2seq.results.tsv"
+            }
+          },
+          {
+            "translation": {
+              "type": "file",
+              "description": "anota2seq results for the 'translated mRNA' analysis, describing differences in translation across conditions, being differences in translated RNA levels not explained by total RNA levels. See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.",
+              "pattern": ".translation.anota2seq.results.tsv"
+            }
+          },
+          {
+            "buffering": {
+              "type": "file",
+              "description": "anota2seq results for the 'translated mRNA' analysis, describing buffering across conditions, being stable levels of translated RNA (from riboseq samples) across conditions, despite changes in total mRNA.  See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.",
+              "pattern": ".translated_mRNA.anota2seq.results.tsv"
+            }
+          },
+          {
+            "mrna_abundance": {
+              "type": "file",
+              "description": "anota2seq results for the 'mRNA abunance' analysis, describing changes across conditions consistent between total mRNA and translated RNA (RNA-seq and Riboseq samples).  See https://rdrr.io/bioc/anota2seq/man/anota2seqGetOutput.html for description of output columns.",
+              "pattern": ".translated_mRNA.anota2seq.results.tsv"
+            }
+          },
+          {
+            "rdata": {
+              "type": "file",
+              "description": "Serialised Anota2seqDataSet object",
+              "pattern": ".Anota2seqDataSet.rds"
+            }
+          },
+          {
+            "fold_change_plot": {
+              "type": "file",
+              "description": "A fold change plot in PNG format, from anota2seq's anota2seqPlotFC()\nmethod.\n",
+              "pattern": ".fold_change.png"
+            }
+          },
+          {
+            "interaction_p_distribution_plot": {
+              "type": "file",
+              "description": "The distribution of p-values and adjusted p-values for the omnibus\ninteraction (both using densities and histograms). The second page of\nthe pdf displays the same plots but for the RVM statistics if RVM is\nused.\n",
+              "pattern": ".interaction_p_distribution.pdf"
+            }
+          },
+          {
+            "residual_distribution_summary_plot": {
+              "type": "file",
+              "description": "Summary plot for assessing normal distribution of regression residuals.\n",
+              "pattern": ".residual_distribution_summary.jpeg"
+            }
+          },
+          {
+            "residual_vs_fitted_plot": {
+              "type": "file",
+              "description": "QC plot showing residuals against fitted values.\n",
+              "pattern": ".residual_vs_fitted.jpeg"
+            }
+          },
+          {
+            "rvm_fit_for_all_contrasts_group_plot": {
+              "type": "file",
+              "description": "QC plot showing the CDF of variance (theoretical vs empirical), all\ncontrasts.\n",
+              "pattern": ".rvm_fit_for_all_contrasts_group.jpg"
+            }
+          },
+          {
+            "rvm_fit_for_interactions_plot": {
+              "type": "file",
+              "description": "QC plot showing the CDF of variance (theoretical vs empirical), for\ninteractions.\n",
+              "pattern": ".rvm_fit_for_interactions.jpg"
+            }
+          },
+          {
+            "rvm_fit_for_omnibus_group_plot": {
+              "type": "file",
+              "description": "QC plot showing the CDF of variance (theoretical vs empirical), for\nomnibus group.\n",
+              "pattern": ".rvm_fit_for_omnibus_group.jpg"
+            }
+          },
+          {
+            "simulated_vs_obt_dfbetas_without_interaction_plot": {
+              "type": "file",
+              "description": "Bar graphs of the frequencies of outlier dfbetas using different\ndfbetas thresholds.\n",
+              "pattern": ".simulated_vs_obt_dfbetas_without_interaction.pdf"
+            }
+          },
+          {
+            "session_info": {
+              "type": "file",
+              "description": "dump of R SessionInfo",
+              "pattern": "*.log"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing software versions",
+              "pattern": "versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@pinin4fjords"
+        ],
+        "maintainers": [
+          "@pinin4fjords"
+        ]
+      }
+    },
     {
       "name": "antismash_antismashlite",
       "path": "modules/nf-core/antismash/antismashlite/meta.yml",
@@ -4549,6 +4747,10 @@
           "name": "rnafusion",
           "version": "3.0.1"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.1"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.1"
@@ -7962,6 +8164,102 @@
         }
       ]
     },
+    {
+      "name": "bbmap_bbmerge",
+      "path": "modules/nf-core/bbmap/bbmerge/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "bbmap_bbmerge",
+        "description": "Merging overlapping paired reads into a single read.",
+        "keywords": [
+          "paired reads merging",
+          "fastq",
+          "overlap-based merging"
+        ],
+        "tools": [
+          {
+            "bbmap": {
+              "description": "BBMap is a short read aligner, as well as various other bioinformatic tools.",
+              "homepage": "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/",
+              "documentation": "https://jgi.doe.gov/data-and-tools/bbtools/bb-tools-user-guide/",
+              "licence": [
+                "UC-LBL license (see package)"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
+            }
+          },
+          {
+            "reads": {
+              "type": "file",
+              "description": "List of input paired end fastq files\n",
+              "pattern": "*.{fastq,fq}.gz"
+            }
+          },
+          {
+            "interleave": {
+              "type": "boolean",
+              "description": "Indicates whether the input paired reads are interleaved or not\n"
+            }
+          }
+        ],
+        "output": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. `[ id:'sample1', single_end:false ]`\n"
+            }
+          },
+          {
+            "merged": {
+              "type": "file",
+              "description": "merged reads",
+              "pattern": "*_merged.fastq"
+            }
+          },
+          {
+            "unmerged": {
+              "type": "file",
+              "description": "unmerged reads",
+              "pattern": "*_unmerged.fastq"
+            }
+          },
+          {
+            "ihist": {
+              "type": "file",
+              "description": "insert size histogram",
+              "pattern": "*_ihist.txt"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing software versions",
+              "pattern": "versions.yml"
+            }
+          },
+          {
+            "log": {
+              "type": "file",
+              "description": "log file containing stdout and stderr from bbmerge.sh",
+              "pattern": "*.log"
+            }
+          }
+        ],
+        "authors": [
+          "@guille0387"
+        ],
+        "maintainers": [
+          "@guille0387"
+        ]
+      }
+    },
     {
       "name": "bbmap_bbnorm",
       "path": "modules/nf-core/bbmap/bbnorm/meta.yml",
@@ -26623,7 +26921,13 @@
         "maintainers": [
           "@pinin4fjords"
         ]
-      }
+      },
+      "pipelines": [
+        {
+          "name": "riboseq",
+          "version": "dev"
+        }
+      ]
     },
     {
       "name": "cutadapt",
@@ -39816,6 +40120,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -41641,6 +41949,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -46620,6 +46932,10 @@
           "name": "rnadnavar",
           "version": "dev"
         },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
         {
           "name": "rnadnavar",
           "version": "dev"
@@ -62062,6 +62378,24 @@
               "description": "A file containing all bootstrap trees,\nonly generated if bootstrap is on\nand the -wbt flag is passed in ext.args\n",
               "pattern": "*.{ufboot}"
             }
+          },
+          {
+            "report": {
+              "type": "file",
+              "description": "Main report file containing computational\nresults as well as a textual visualisation\nof the final tree.\n"
+            }
+          },
+          {
+            "mldist": {
+              "type": "file",
+              "description": "File containing the pairwise maximum\nlikelihood distances as a matrix.\n"
+            }
+          },
+          {
+            "log": {
+              "type": "file",
+              "description": "Log file of entire run"
+            }
           }
         ],
         "authors": [
@@ -63802,6 +64136,10 @@
         ]
       },
       "pipelines": [
+        {
+          "name": "riboseq",
+          "version": "dev"
+        },
         {
           "name": "rnaseq",
           "version": "3.14.0"
@@ -113986,7 +114324,13 @@
         "maintainers": [
           "@pinin4fjords"
         ]
-      }
+      },
+      "pipelines": [
+        {
+          "name": "riboseq",
+          "version": "dev"
+        }
+      ]
     },
     {
       "name": "survivor_filter",
@@ -119020,7 +119364,13 @@
         "maintainers": [
           "@pinin4fjords"
         ]
-      }
+      },
+      "pipelines": [
+        {
+          "name": "riboseq",
+          "version": "dev"
+        }
+      ]
     },
     {
       "name": "ucsc_bedclip",
@@ -134663,7 +135013,13 @@
           "@pinin4fjords",
           "@adamrtalbot"
         ]
-      }
+      },
+      "pipelines": [
+        {
+          "name": "riboseq",
+          "version": "dev"
+        }
+      ]
     },
     {
       "name": "utils_nextflow_pipeline",
diff --git a/public/pipelines.json b/public/pipelines.json
index bc4a657903..18e14c01db 100644
--- a/public/pipelines.json
+++ b/public/pipelines.json
@@ -534,7 +534,7 @@
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-            "subscribers_count": 145,
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             "team_contributors_permission_push": true,
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@@ -1326,7 +1326,7 @@
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             "archived": false,
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-            "open_issues_count": 32,
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             "allow_forking": true,
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@@ -1336,7 +1336,7 @@
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-            "open_issues": 32,
+            "open_issues": 33,
             "watchers": 159,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -1367,7 +1367,7 @@
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@@ -1953,7 +1953,7 @@
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-            "subscribers_count": 143,
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@@ -2286,7 +2286,7 @@
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@@ -2535,7 +2535,7 @@
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@@ -2842,7 +2842,7 @@
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@@ -3110,7 +3110,7 @@
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@@ -3344,7 +3344,7 @@
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@@ -3740,7 +3740,7 @@
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-            "subscribers_count": 149,
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@@ -4139,7 +4139,7 @@
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             "archived": false,
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-            "open_issues_count": 9,
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@@ -4156,7 +4156,7 @@
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-            "open_issues": 9,
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@@ -4187,7 +4187,7 @@
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@@ -4432,7 +4432,7 @@
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@@ -4652,7 +4652,7 @@
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@@ -4887,7 +4887,7 @@
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@@ -5089,7 +5089,7 @@
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@@ -5264,7 +5264,7 @@
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@@ -5595,7 +5595,7 @@
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             "allow_squash_merge": -1,
@@ -5793,7 +5793,7 @@
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-            "subscribers_count": 152,
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@@ -6395,7 +6395,7 @@
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@@ -7416,7 +7416,7 @@
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-            "subscribers_count": 83,
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@@ -8286,7 +8286,7 @@
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@@ -8500,7 +8500,7 @@
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@@ -8821,7 +8821,7 @@
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@@ -9311,7 +9311,7 @@
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@@ -9537,7 +9537,7 @@
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@@ -10214,7 +10214,7 @@
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@@ -10528,7 +10528,7 @@
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@@ -10687,7 +10687,7 @@
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@@ -10892,7 +10892,7 @@
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