diff --git a/.cache.tar.xz b/.cache.tar.xz
index d991c3fe6d..94bf49a1b8 100644
Binary files a/.cache.tar.xz and b/.cache.tar.xz differ
diff --git a/public/components.json b/public/components.json
index 36388bb169..f3a18cfac2 100644
--- a/public/components.json
+++ b/public/components.json
@@ -6068,6 +6068,10 @@
           "name": "rnafusion",
           "version": "3.0.2"
         },
+        {
+          "name": "rnafusion",
+          "version": "3.0.2"
+        },
         {
           "name": "rnafusion",
           "version": "3.0.2"
@@ -19479,6 +19483,14 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "pathogensurveillance",
           "version": "dev"
@@ -33932,7 +33944,7 @@
       "type": "module",
       "meta": {
         "name": "deepvariant",
-        "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
+        "description": "(DEPRECATED - see main.nf) DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
         "keywords": [
           "variant calling",
           "machine learning",
@@ -34086,6 +34098,499 @@
         }
       ]
     },
+    {
+      "name": "deepvariant_callvariants",
+      "path": "modules/nf-core/deepvariant/callvariants/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "deepvariant_callvariants",
+        "description": "Call variants from the examples produced by make_examples",
+        "keywords": [
+          "variant calling",
+          "machine learning",
+          "neural network"
+        ],
+        "tools": [
+          {
+            "deepvariant": {
+              "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
+              "homepage": "https://github.com/google/deepvariant",
+              "documentation": "https://github.com/google/deepvariant",
+              "tool_dev_url": "https://github.com/google/deepvariant",
+              "doi": "10.1038/nbt.4235",
+              "licence": [
+                "BSD-3-clause"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+            }
+          },
+          {
+            "make_examples_tfrecords": {
+              "type": "file",
+              "description": "The actual sharded input files, from DEEPVARIANT_MAKEEXAMPLES process",
+              "pattern": "*.gz"
+            }
+          }
+        ],
+        "output": [
+          {
+            "call_variants_tfrecords": {
+              "type": "list",
+              "description": "Each output contains: unique ID string from input channel, meta, tfrecord file with variant calls.\n"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing software version",
+              "pattern": "versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@abhi18av",
+          "@ramprasadn",
+          "@fa2k"
+        ],
+        "maintainers": [
+          "@abhi18av",
+          "@ramprasadn"
+        ]
+      }
+    },
+    {
+      "name": "deepvariant_makeexamples",
+      "path": "modules/nf-core/deepvariant/makeexamples/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "deepvariant_makeexamples",
+        "description": "Transforms the input alignments to a format suitable for the deep neural network variant caller",
+        "keywords": [
+          "variant calling",
+          "machine learning",
+          "neural network"
+        ],
+        "tools": [
+          {
+            "deepvariant": {
+              "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
+              "homepage": "https://github.com/google/deepvariant",
+              "documentation": "https://github.com/google/deepvariant",
+              "tool_dev_url": "https://github.com/google/deepvariant",
+              "doi": "10.1038/nbt.4235",
+              "licence": [
+                "BSD-3-clause"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+            }
+          },
+          {
+            "input": {
+              "type": "file",
+              "description": "BAM/CRAM file",
+              "pattern": "*.bam/cram"
+            }
+          },
+          {
+            "index": {
+              "type": "file",
+              "description": "Index of BAM/CRAM file",
+              "pattern": "*.bai/crai"
+            }
+          },
+          {
+            "intervals": {
+              "type": "file",
+              "description": "Interval file for targeted regions",
+              "pattern": "*.bed"
+            }
+          },
+          {
+            "meta2": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "fasta": {
+              "type": "file",
+              "description": "The reference fasta file",
+              "pattern": "*.fasta"
+            }
+          },
+          {
+            "meta3": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "fai": {
+              "type": "file",
+              "description": "Index of reference fasta file",
+              "pattern": "*.fai"
+            }
+          },
+          {
+            "meta4": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "gzi": {
+              "type": "file",
+              "description": "GZI index of reference fasta file"
+            }
+          },
+          {
+            "meta5": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n",
+              "pattern": "*.gzi"
+            }
+          },
+          {
+            "par_bed": {
+              "type": "file",
+              "description": "BED file containing PAR regions",
+              "pattern": "*.bed"
+            }
+          }
+        ],
+        "output": [
+          {
+            "examples": {
+              "type": "list",
+              "description": "Tuple containing sample metadata and examples that can be used for calling\n"
+            }
+          },
+          {
+            "gvcf": {
+              "type": "list",
+              "description": "Tuple containing sample metadata and the GVCF data in tfrecord format\n"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing the DeepVariant software version",
+              "pattern": "versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@abhi18av",
+          "@ramprasadn",
+          "@fa2k"
+        ],
+        "maintainers": [
+          "@abhi18av",
+          "@ramprasadn"
+        ]
+      }
+    },
+    {
+      "name": "deepvariant_postprocessvariants",
+      "path": "modules/nf-core/deepvariant/postprocessvariants/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "deepvariant_postprocessvariants",
+        "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
+        "keywords": [
+          "variant calling",
+          "machine learning",
+          "neural network"
+        ],
+        "tools": [
+          {
+            "deepvariant": {
+              "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
+              "homepage": "https://github.com/google/deepvariant",
+              "documentation": "https://github.com/google/deepvariant",
+              "tool_dev_url": "https://github.com/google/deepvariant",
+              "doi": "10.1038/nbt.4235",
+              "licence": [
+                "BSD-3-clause"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+            }
+          },
+          {
+            "variant_calls_tfrecord_files": {
+              "type": "file",
+              "description": "One or more data files containing variant calls from DEEPVARIANT_CALLVARIANTS\n",
+              "pattern": "*.tfrecord.gz"
+            }
+          },
+          {
+            "gvcf_tfrecords": {
+              "type": "file",
+              "description": "Sharded tfrecord file from DEEPVARIANT_MAKEEXAMPLES with the coverage information used for GVCF output\n",
+              "pattern": "*.gz"
+            }
+          },
+          {
+            "meta2": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "fasta": {
+              "type": "file",
+              "description": "The reference fasta file",
+              "pattern": "*.fasta"
+            }
+          },
+          {
+            "meta3": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "fai": {
+              "type": "file",
+              "description": "Index of reference fasta file",
+              "pattern": "*.fai"
+            }
+          },
+          {
+            "meta4": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "gzi": {
+              "type": "file",
+              "description": "GZI index of reference fasta file",
+              "pattern": "*.gzi"
+            }
+          }
+        ],
+        "output": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+            }
+          },
+          {
+            "vcf": {
+              "type": "file",
+              "description": "Compressed VCF file",
+              "pattern": "*.vcf.gz"
+            }
+          },
+          {
+            "vcf_tbi": {
+              "type": "file",
+              "description": "Index for VCF",
+              "pattern": "*.vcf.gz.tbi"
+            }
+          },
+          {
+            "gvcf": {
+              "type": "file",
+              "description": "Compressed GVCF file",
+              "pattern": "*.g.vcf.gz"
+            }
+          },
+          {
+            "gvcf_tbi": {
+              "type": "file",
+              "description": "Index for GVCF",
+              "pattern": "*.g.vcf.gz.tbi"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing software version",
+              "pattern": "versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@abhi18av",
+          "@ramprasadn",
+          "@fa2k"
+        ],
+        "maintainers": [
+          "@abhi18av",
+          "@ramprasadn"
+        ]
+      }
+    },
+    {
+      "name": "deepvariant_rundeepvariant",
+      "path": "modules/nf-core/deepvariant/rundeepvariant/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "deepvariant_rundeepvariant",
+        "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
+        "keywords": [
+          "variant calling",
+          "machine learning",
+          "neural network"
+        ],
+        "tools": [
+          {
+            "deepvariant": {
+              "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
+              "homepage": "https://github.com/google/deepvariant",
+              "documentation": "https://github.com/google/deepvariant",
+              "tool_dev_url": "https://github.com/google/deepvariant",
+              "doi": "10.1038/nbt.4235",
+              "licence": [
+                "BSD-3-clause"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+            }
+          },
+          {
+            "input": {
+              "type": "file",
+              "description": "BAM/CRAM file",
+              "pattern": "*.bam/cram"
+            }
+          },
+          {
+            "index": {
+              "type": "file",
+              "description": "Index of BAM/CRAM file",
+              "pattern": "*.bai/crai"
+            }
+          },
+          {
+            "interval": {
+              "type": "file",
+              "description": "Interval file for targeted regions",
+              "pattern": "*.bed"
+            }
+          },
+          {
+            "meta2": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "fasta": {
+              "type": "file",
+              "description": "The reference fasta file",
+              "pattern": "*.fasta"
+            }
+          },
+          {
+            "meta3": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "fai": {
+              "type": "file",
+              "description": "Index of reference fasta file",
+              "pattern": "*.fai"
+            }
+          },
+          {
+            "meta4": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "gzi": {
+              "type": "file",
+              "description": "GZI index of reference fasta file",
+              "pattern": "*.gzi"
+            }
+          },
+          {
+            "meta5": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "par_bed": {
+              "type": "file",
+              "description": "BED file containing PAR regions",
+              "pattern": "*.bed"
+            }
+          }
+        ],
+        "output": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test', single_end:false ]\n"
+            }
+          },
+          {
+            "vcf": {
+              "type": "file",
+              "description": "Compressed VCF file",
+              "pattern": "*.vcf.gz"
+            }
+          },
+          {
+            "gvcf": {
+              "type": "file",
+              "description": "Compressed GVCF file",
+              "pattern": "*.g.vcf.gz"
+            }
+          },
+          {
+            "version": {
+              "type": "file",
+              "description": "File containing software version",
+              "pattern": "*.{version.txt}"
+            }
+          }
+        ],
+        "authors": [
+          "@abhi18av",
+          "@ramprasadn"
+        ],
+        "maintainers": [
+          "@abhi18av",
+          "@ramprasadn"
+        ]
+      }
+    },
     {
       "name": "delly_call",
       "path": "modules/nf-core/delly/call/meta.yml",
@@ -55496,17 +56001,315 @@
         ],
         "output": [
           {
-            "vcf": {
-              "type": "file",
-              "description": "Compressed VCF file",
-              "pattern": "*.vcf.gz"
-            }
-          },
-          {
-            "tbi": {
+            "vcf": {
+              "type": "file",
+              "description": "Compressed VCF file",
+              "pattern": "*.vcf.gz"
+            }
+          },
+          {
+            "tbi": {
+              "type": "file",
+              "description": "Index of VCF file",
+              "pattern": "*.vcf.gz.tbi"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing software versions",
+              "pattern": "versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@kevinmenden",
+          "@ramprasadn"
+        ],
+        "maintainers": [
+          "@kevinmenden",
+          "@ramprasadn"
+        ]
+      },
+      "pipelines": [
+        {
+          "name": "pathogensurveillance",
+          "version": "dev"
+        },
+        {
+          "name": "raredisease",
+          "version": "2.1.0"
+        },
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
+        {
+          "name": "rnavar",
+          "version": "1.0.0"
+        },
+        {
+          "name": "variantcatalogue",
+          "version": "dev"
+        }
+      ]
+    },
+    {
+      "name": "gatk4_variantrecalibrator",
+      "path": "modules/nf-core/gatk4/variantrecalibrator/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "gatk4_variantrecalibrator",
+        "description": "Build a recalibration model to score variant quality for filtering purposes.\nIt is highly recommended to follow GATK best practices when using this module,\nthe gaussian mixture model requires a large number of samples to be used for the\ntool to produce optimal results. For example, 30 samples for exome data. For more details see\nhttps://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-\n",
+        "keywords": [
+          "gatk4",
+          "recalibration model",
+          "variantrecalibrator"
+        ],
+        "tools": [
+          {
+            "gatk4": {
+              "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n",
+              "homepage": "https://gatk.broadinstitute.org/hc/en-us",
+              "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s",
+              "doi": "10.1158/1538-7445.AM2017-3590"
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n"
+            }
+          },
+          {
+            "vcf": {
+              "type": "file",
+              "description": "input vcf file containing the variants to be recalibrated",
+              "pattern": "*.vcf.gz"
+            }
+          },
+          {
+            "tbi": {
+              "type": "file",
+              "description": "tbi file matching with -vcf",
+              "pattern": "*.vcf.gz.tbi"
+            }
+          },
+          {
+            "resource_vcf": {
+              "type": "file",
+              "description": "all resource vcf files that are used with the corresponding '--resource' label",
+              "pattern": "*.vcf.gz"
+            }
+          },
+          {
+            "resource_tbi": {
+              "type": "file",
+              "description": "all resource tbi files that are used with the corresponding '--resource' label",
+              "pattern": "*.vcf.gz.tbi"
+            }
+          },
+          {
+            "labels": {
+              "type": "string",
+              "description": "necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator"
+            }
+          },
+          {
+            "fasta": {
+              "type": "file",
+              "description": "The reference fasta file",
+              "pattern": "*.fasta"
+            }
+          },
+          {
+            "fai": {
+              "type": "file",
+              "description": "Index of reference fasta file",
+              "pattern": "fasta.fai"
+            }
+          },
+          {
+            "dict": {
+              "type": "file",
+              "description": "GATK sequence dictionary",
+              "pattern": "*.dict"
+            }
+          }
+        ],
+        "output": [
+          {
+            "recal": {
+              "type": "file",
+              "description": "Output recal file used by ApplyVQSR",
+              "pattern": "*.recal"
+            }
+          },
+          {
+            "idx": {
+              "type": "file",
+              "description": "Index file for the recal output file",
+              "pattern": "*.idx"
+            }
+          },
+          {
+            "tranches": {
+              "type": "file",
+              "description": "Output tranches file used by ApplyVQSR",
+              "pattern": "*.tranches"
+            }
+          },
+          {
+            "plots": {
+              "type": "file",
+              "description": "Optional output rscript file to aid in visualization of the input data and learned model.",
+              "pattern": "*plots.R"
+            }
+          },
+          {
+            "version": {
+              "type": "file",
+              "description": "File containing software versions",
+              "pattern": "*.versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@GCJMackenzie",
+          "@nickhsmith"
+        ],
+        "maintainers": [
+          "@GCJMackenzie",
+          "@nickhsmith"
+        ]
+      },
+      "pipelines": [
+        {
+          "name": "rnadnavar",
+          "version": "dev"
+        },
+        {
+          "name": "sarek",
+          "version": "3.4.4"
+        }
+      ]
+    },
+    {
+      "name": "gatk4_variantstotable",
+      "path": "modules/nf-core/gatk4/variantstotable/meta.yml",
+      "type": "module",
+      "meta": {
+        "name": "gatk4_variantstotable",
+        "description": "Extract fields from a VCF file to a tab-delimited table",
+        "keywords": [
+          "filter",
+          "gatk4",
+          "table",
+          "vcf"
+        ],
+        "tools": [
+          {
+            "gatk4": {
+              "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n",
+              "homepage": "https://gatk.broadinstitute.org/hc/en-us",
+              "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s",
+              "doi": "10.1158/1538-7445.AM2017-3590",
+              "licence": [
+                "Apache-2.0"
+              ]
+            }
+          }
+        ],
+        "input": [
+          {
+            "meta": {
+              "type": "map",
+              "description": "Groovy Map containing VCF information. Attribute `gatk_args` can be used to add arguments to gatk.\ne.g. [ id:'test', gatk_args:'-F CHROM -F POS -F TYPE -GF AD']\n"
+            }
+          },
+          {
+            "vcf": {
+              "type": "file",
+              "description": "VCF file",
+              "pattern": "*.{vcf,vcf.gz}"
+            }
+          },
+          {
+            "tbi": {
+              "type": "file",
+              "description": "Index of VCF file.",
+              "pattern": "*.{idx,tbi}"
+            }
+          },
+          {
+            "arguments_file": {
+              "type": "file",
+              "description": "optional GATK arguments file",
+              "pattern": "*.{txt,list,args,arguments}"
+            }
+          },
+          {
+            "include_intervals": {
+              "type": "file",
+              "description": "optional GATK region file",
+              "pattern": "*.{bed,bed.gz,interval,interval_list}"
+            }
+          },
+          {
+            "exclude_intervals": {
+              "type": "file",
+              "description": "optional GATK exclude region file",
+              "pattern": "*.{bed,bed.gz,interval,interval_list}"
+            }
+          },
+          {
+            "meta2": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "fasta": {
+              "type": "file",
+              "description": "Fasta file of reference genome",
+              "pattern": "*.fasta"
+            }
+          },
+          {
+            "meta3": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "fai": {
+              "type": "file",
+              "description": "Index of fasta file",
+              "pattern": "*.fasta.fai"
+            }
+          },
+          {
+            "meta4": {
+              "type": "map",
+              "description": "Groovy Map containing reference information\ne.g. [ id:'genome' ]\n"
+            }
+          },
+          {
+            "dict": {
+              "type": "file",
+              "description": "Sequence dictionary of fastea file",
+              "pattern": "*.dict"
+            }
+          }
+        ],
+        "output": [
+          {
+            "table": {
               "type": "file",
-              "description": "Index of VCF file",
-              "pattern": "*.vcf.gz.tbi"
+              "description": "GATK output",
+              "pattern": "*.tsv"
             }
           },
           {
@@ -55518,178 +56321,12 @@
           }
         ],
         "authors": [
-          "@kevinmenden",
-          "@ramprasadn"
-        ],
-        "maintainers": [
-          "@kevinmenden",
-          "@ramprasadn"
-        ]
-      },
-      "pipelines": [
-        {
-          "name": "pathogensurveillance",
-          "version": "dev"
-        },
-        {
-          "name": "raredisease",
-          "version": "2.1.0"
-        },
-        {
-          "name": "rnadnavar",
-          "version": "dev"
-        },
-        {
-          "name": "rnavar",
-          "version": "1.0.0"
-        },
-        {
-          "name": "variantcatalogue",
-          "version": "dev"
-        }
-      ]
-    },
-    {
-      "name": "gatk4_variantrecalibrator",
-      "path": "modules/nf-core/gatk4/variantrecalibrator/meta.yml",
-      "type": "module",
-      "meta": {
-        "name": "gatk4_variantrecalibrator",
-        "description": "Build a recalibration model to score variant quality for filtering purposes.\nIt is highly recommended to follow GATK best practices when using this module,\nthe gaussian mixture model requires a large number of samples to be used for the\ntool to produce optimal results. For example, 30 samples for exome data. For more details see\nhttps://gatk.broadinstitute.org/hc/en-us/articles/4402736812443-Which-training-sets-arguments-should-I-use-for-running-VQSR-\n",
-        "keywords": [
-          "gatk4",
-          "recalibration model",
-          "variantrecalibrator"
-        ],
-        "tools": [
-          {
-            "gatk4": {
-              "description": "Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools\nwith a primary focus on variant discovery and genotyping. Its powerful processing engine\nand high-performance computing features make it capable of taking on projects of any size.\n",
-              "homepage": "https://gatk.broadinstitute.org/hc/en-us",
-              "documentation": "https://gatk.broadinstitute.org/hc/en-us/categories/360002369672s",
-              "doi": "10.1158/1538-7445.AM2017-3590"
-            }
-          }
-        ],
-        "input": [
-          {
-            "meta": {
-              "type": "map",
-              "description": "Groovy Map containing sample information\ne.g. [ id:'test' ]\n"
-            }
-          },
-          {
-            "vcf": {
-              "type": "file",
-              "description": "input vcf file containing the variants to be recalibrated",
-              "pattern": "*.vcf.gz"
-            }
-          },
-          {
-            "tbi": {
-              "type": "file",
-              "description": "tbi file matching with -vcf",
-              "pattern": "*.vcf.gz.tbi"
-            }
-          },
-          {
-            "resource_vcf": {
-              "type": "file",
-              "description": "all resource vcf files that are used with the corresponding '--resource' label",
-              "pattern": "*.vcf.gz"
-            }
-          },
-          {
-            "resource_tbi": {
-              "type": "file",
-              "description": "all resource tbi files that are used with the corresponding '--resource' label",
-              "pattern": "*.vcf.gz.tbi"
-            }
-          },
-          {
-            "labels": {
-              "type": "string",
-              "description": "necessary arguments for GATK VariantRecalibrator. Specified to directly match the resources provided. More information can be found at https://gatk.broadinstitute.org/hc/en-us/articles/5358906115227-VariantRecalibrator"
-            }
-          },
-          {
-            "fasta": {
-              "type": "file",
-              "description": "The reference fasta file",
-              "pattern": "*.fasta"
-            }
-          },
-          {
-            "fai": {
-              "type": "file",
-              "description": "Index of reference fasta file",
-              "pattern": "fasta.fai"
-            }
-          },
-          {
-            "dict": {
-              "type": "file",
-              "description": "GATK sequence dictionary",
-              "pattern": "*.dict"
-            }
-          }
-        ],
-        "output": [
-          {
-            "recal": {
-              "type": "file",
-              "description": "Output recal file used by ApplyVQSR",
-              "pattern": "*.recal"
-            }
-          },
-          {
-            "idx": {
-              "type": "file",
-              "description": "Index file for the recal output file",
-              "pattern": "*.idx"
-            }
-          },
-          {
-            "tranches": {
-              "type": "file",
-              "description": "Output tranches file used by ApplyVQSR",
-              "pattern": "*.tranches"
-            }
-          },
-          {
-            "plots": {
-              "type": "file",
-              "description": "Optional output rscript file to aid in visualization of the input data and learned model.",
-              "pattern": "*plots.R"
-            }
-          },
-          {
-            "version": {
-              "type": "file",
-              "description": "File containing software versions",
-              "pattern": "*.versions.yml"
-            }
-          }
-        ],
-        "authors": [
-          "@GCJMackenzie",
-          "@nickhsmith"
+          "@lindenb"
         ],
         "maintainers": [
-          "@GCJMackenzie",
-          "@nickhsmith"
+          "@lindenb"
         ]
-      },
-      "pipelines": [
-        {
-          "name": "rnadnavar",
-          "version": "dev"
-        },
-        {
-          "name": "sarek",
-          "version": "3.4.4"
-        }
-      ]
+      }
     },
     {
       "name": "gatk4spark_applybqsr",
@@ -82834,6 +83471,10 @@
           "name": "genomeassembler",
           "version": "dev"
         },
+        {
+          "name": "genomeassembler",
+          "version": "dev"
+        },
         {
           "name": "genomeassembler",
           "version": "dev"
@@ -145398,6 +146039,104 @@
         }
       ]
     },
+    {
+      "name": "deepvariant",
+      "path": "subworkflows/nf-core/deepvariant/meta.yml",
+      "type": "subworkflow",
+      "meta": {
+        "name": "deepvariant",
+        "description": "DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data",
+        "keywords": [
+          "variant calling",
+          "machine learning",
+          "neural network"
+        ],
+        "components": [
+          "deepvariant/makeexamples",
+          "deepvariant/callvariants",
+          "deepvariant/postprocessvariants"
+        ],
+        "input": [
+          {
+            "ch_input": {
+              "type": "list",
+              "description": "Input aligned reads in bam or cram format, with index, and optional intervals BED file\nStructure: [ val(meta), path(bam_or_cram), path(bai_or_crai), path(intervals_bed) ]\n"
+            }
+          },
+          {
+            "ch_fasta": {
+              "type": "file",
+              "description": "Reference genome\nStructure: [ val(meta2), path(fasta) ]\n"
+            }
+          },
+          {
+            "ch_fai": {
+              "type": "string",
+              "description": "Reference genome index in fai format\nStructure: [ val(meta3), path(fai) ]\n"
+            }
+          },
+          {
+            "ch_gzi": {
+              "type": "string",
+              "description": "Reference genome index in gzi format (either gzi or fai should be used)\nStructure: [ val(meta4), val(gzi) ]\n"
+            }
+          },
+          {
+            "ch_par_bed": {
+              "type": "string",
+              "description": "bed file of pseudoautosomal regions (optional)\nStructure: [ val(meta5), val(par_bed) ]\n",
+              "pattern": "*.bed"
+            }
+          }
+        ],
+        "output": [
+          {
+            "vcf": {
+              "type": "file",
+              "description": "Variant calls\nStructure: [ val(meta), path(vcf) ]\n",
+              "pattern": "*.vcf.gz"
+            }
+          },
+          {
+            "vcf_tbi": {
+              "type": "file",
+              "description": "Index for variant call file\nStructure: [ val(meta), path(vcf_tbi) ]\n",
+              "pattern": "*.tbi"
+            }
+          },
+          {
+            "gvcf": {
+              "type": "file",
+              "description": "Variant call file with genomic coverage information\nStructure: [ val(meta), path(gvcf) ]\n",
+              "pattern": "*.g.vcf.gz"
+            }
+          },
+          {
+            "gvcf_tbi": {
+              "type": "file",
+              "description": "Index for the GVCF.\nStructure: [ val(meta), path(gvcf_tbi) ]\n",
+              "pattern": "*.tbi"
+            }
+          },
+          {
+            "versions": {
+              "type": "file",
+              "description": "File containing software versions\nStructure: path(versions.yml)\n",
+              "pattern": "versions.yml"
+            }
+          }
+        ],
+        "authors": [
+          "@abhi18av",
+          "@ramprasadn",
+          "@fa2k"
+        ],
+        "maintainers": [
+          "@abhi18av",
+          "@ramprasadn"
+        ]
+      }
+    },
     {
       "name": "fasta_binning_concoct",
       "path": "subworkflows/nf-core/fasta_binning_concoct/meta.yml",
diff --git a/public/pipelines.json b/public/pipelines.json
index 479590c9d6..edd133a878 100644
--- a/public/pipelines.json
+++ b/public/pipelines.json
@@ -10,12 +10,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/airrflow",
             "created_at": "2018-12-04T11:39:05Z",
-            "updated_at": "2024-09-05T09:35:33Z",
+            "updated_at": "2024-09-12T10:38:12Z",
             "pushed_at": "2024-08-20T19:41:29Z",
             "homepage": "https://nf-co.re/airrflow",
             "size": 8642,
-            "stargazers_count": 51,
-            "watchers_count": 51,
+            "stargazers_count": 52,
+            "watchers_count": 52,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": false,
@@ -40,7 +40,7 @@
             "visibility": "public",
             "forks": 33,
             "open_issues": 20,
-            "watchers": 51,
+            "watchers": 52,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -4759,12 +4759,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/clipseq",
             "created_at": "2020-11-19T17:00:02Z",
-            "updated_at": "2024-09-03T13:17:28Z",
+            "updated_at": "2024-09-12T07:27:22Z",
             "pushed_at": "2024-05-10T17:08:37Z",
             "homepage": "https://nf-co.re/clipseq",
             "size": 41548,
-            "stargazers_count": 18,
-            "watchers_count": 18,
+            "stargazers_count": 19,
+            "watchers_count": 19,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": true,
@@ -4788,7 +4788,7 @@
             "visibility": "public",
             "forks": 27,
             "open_issues": 17,
-            "watchers": 18,
+            "watchers": 19,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -5657,7 +5657,7 @@
             "forks_count": 25,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 21,
+            "open_issues_count": 22,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -5669,7 +5669,7 @@
             ],
             "visibility": "public",
             "forks": 25,
-            "open_issues": 21,
+            "open_issues": 22,
             "watchers": 25,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -8121,7 +8121,7 @@
             "forks_count": 36,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 19,
+            "open_issues_count": 20,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -8134,7 +8134,7 @@
             ],
             "visibility": "public",
             "forks": 36,
-            "open_issues": 19,
+            "open_issues": 20,
             "watchers": 41,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -9866,12 +9866,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/differentialabundance",
             "created_at": "2022-10-12T08:49:25Z",
-            "updated_at": "2024-09-05T16:02:16Z",
-            "pushed_at": "2024-09-10T14:16:25Z",
+            "updated_at": "2024-09-12T03:50:05Z",
+            "pushed_at": "2024-09-12T08:05:43Z",
             "homepage": "https://nf-co.re/differentialabundance",
-            "size": 8504,
-            "stargazers_count": 55,
-            "watchers_count": 55,
+            "size": 8508,
+            "stargazers_count": 56,
+            "watchers_count": 56,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": true,
@@ -9901,7 +9901,7 @@
             "visibility": "public",
             "forks": 31,
             "open_issues": 40,
-            "watchers": 55,
+            "watchers": 56,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -11834,7 +11834,7 @@
             "url": "https://api.github.com/repos/nf-core/fastquorum",
             "created_at": "2022-09-10T06:39:22Z",
             "updated_at": "2024-09-11T15:26:18Z",
-            "pushed_at": "2024-09-11T21:21:01Z",
+            "pushed_at": "2024-09-12T06:19:48Z",
             "homepage": "https://nf-co.re/fastquorum",
             "size": 5026,
             "stargazers_count": 18,
@@ -11849,7 +11849,7 @@
             "forks_count": 9,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 15,
+            "open_issues_count": 14,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -11861,7 +11861,7 @@
             ],
             "visibility": "public",
             "forks": 9,
-            "open_issues": 15,
+            "open_issues": 14,
             "watchers": 18,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -11949,7 +11949,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 2,
+            "open_pr_count": 1,
             "repository_url": "https://github.com/nf-core/fastquorum",
             "contributors": [
                 {
@@ -12041,8 +12041,8 @@
                 },
                 {
                     "tag_name": "dev",
-                    "published_at": "2024-09-10T15:56:15Z",
-                    "tag_sha": "df83374039561ecd7c61cfb9bdad600948fb28e0",
+                    "published_at": "2024-09-12T06:19:48Z",
+                    "tag_sha": "ac04dd9ac55f91d08057de70a366efa0040355fe",
                     "has_schema": true,
                     "doc_files": [
                         "docs/output.md",
@@ -18682,14 +18682,14 @@
             "forks_count": 4,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 4,
+            "open_issues_count": 5,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
             "topics": [],
             "visibility": "public",
             "forks": 4,
-            "open_issues": 4,
+            "open_issues": 5,
             "watchers": 2,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -18763,7 +18763,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": false,
-            "open_pr_count": 1,
+            "open_pr_count": 2,
             "repository_url": "https://github.com/nf-core/magmap",
             "contributors": [],
             "released_after_tools": false,
@@ -22181,14 +22181,14 @@
             "forks_count": 10,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 4,
+            "open_issues_count": 5,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
             "topics": [],
             "visibility": "public",
             "forks": 10,
-            "open_issues": 4,
+            "open_issues": 5,
             "watchers": 13,
             "default_branch": "dev",
             "temp_clone_token": "",
@@ -22296,7 +22296,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 1,
+            "open_pr_count": 2,
             "repository_url": "https://github.com/nf-core/multiplesequencealign",
             "contributors": [
                 {
@@ -23996,12 +23996,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/oncoanalyser",
             "created_at": "2022-12-22T05:01:49Z",
-            "updated_at": "2024-09-09T10:17:37Z",
-            "pushed_at": "2024-09-11T23:07:38Z",
+            "updated_at": "2024-09-12T11:39:17Z",
+            "pushed_at": "2024-09-12T07:54:20Z",
             "homepage": "https://nf-co.re/oncoanalyser",
-            "size": 4858,
-            "stargazers_count": 38,
-            "watchers_count": 38,
+            "size": 4865,
+            "stargazers_count": 39,
+            "watchers_count": 39,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": true,
@@ -24012,15 +24012,15 @@
             "forks_count": 6,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 15,
+            "open_issues_count": 14,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
             "topics": [],
             "visibility": "public",
             "forks": 6,
-            "open_issues": 15,
-            "watchers": 38,
+            "open_issues": 14,
+            "watchers": 39,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -24117,7 +24117,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 2,
+            "open_pr_count": 1,
             "repository_url": "https://github.com/nf-core/oncoanalyser",
             "contributors": [
                 {
@@ -24180,8 +24180,8 @@
                 },
                 {
                     "tag_name": "dev",
-                    "published_at": "2024-09-11T23:06:14Z",
-                    "tag_sha": "5a4bacacd25bfe929ea9941e0459a044ef8b1952",
+                    "published_at": "2024-09-12T07:54:04Z",
+                    "tag_sha": "1144edb5ce910f4badd3795dac1c523a46fe2cbd",
                     "has_schema": true,
                     "doc_files": [
                         "docs/output.md",
@@ -30094,9 +30094,9 @@
             "url": "https://api.github.com/repos/nf-core/rnafusion",
             "created_at": "2018-10-05T13:05:57Z",
             "updated_at": "2024-09-04T04:34:53Z",
-            "pushed_at": "2024-08-16T16:09:02Z",
+            "pushed_at": "2024-09-12T13:58:26Z",
             "homepage": "https://nf-co.re/rnafusion",
-            "size": 19545,
+            "size": 19591,
             "stargazers_count": 138,
             "watchers_count": 138,
             "language": "Nextflow",
@@ -30835,12 +30835,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/rnaseq",
             "created_at": "2018-03-29T13:10:58Z",
-            "updated_at": "2024-09-11T04:16:09Z",
+            "updated_at": "2024-09-12T12:17:57Z",
             "pushed_at": "2024-09-10T14:39:10Z",
             "homepage": "https://nf-co.re/rnaseq",
             "size": 70281,
-            "stargazers_count": 861,
-            "watchers_count": 861,
+            "stargazers_count": 863,
+            "watchers_count": 863,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": false,
@@ -30851,7 +30851,7 @@
             "forks_count": 689,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 64,
+            "open_issues_count": 65,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -30861,8 +30861,8 @@
             ],
             "visibility": "public",
             "forks": 689,
-            "open_issues": 64,
-            "watchers": 861,
+            "open_issues": 65,
+            "watchers": 863,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -33790,12 +33790,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/sarek",
             "created_at": "2019-04-30T15:43:00Z",
-            "updated_at": "2024-09-10T13:40:29Z",
+            "updated_at": "2024-09-12T11:30:22Z",
             "pushed_at": "2024-09-03T15:34:54Z",
             "homepage": "https://nf-co.re/sarek",
             "size": 86663,
-            "stargazers_count": 385,
-            "watchers_count": 385,
+            "stargazers_count": 387,
+            "watchers_count": 387,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": false,
@@ -33803,10 +33803,10 @@
             "has_wiki": false,
             "has_pages": false,
             "has_discussions": false,
-            "forks_count": 400,
+            "forks_count": 401,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 264,
+            "open_issues_count": 267,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -33824,9 +33824,9 @@
                 "whole-genome-sequencing"
             ],
             "visibility": "public",
-            "forks": 400,
-            "open_issues": 264,
-            "watchers": 385,
+            "forks": 401,
+            "open_issues": 267,
+            "watchers": 387,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": true,
@@ -33860,7 +33860,7 @@
                     "status": "disabled"
                 }
             },
-            "network_count": 400,
+            "network_count": 401,
             "subscribers_count": 127,
             "team_contributors_permission_push": true,
             "team_contributors_permission_admin": false,
@@ -37132,12 +37132,12 @@
             "fork": false,
             "url": "https://api.github.com/repos/nf-core/scrnaseq",
             "created_at": "2019-04-08T13:12:00Z",
-            "updated_at": "2024-09-03T19:13:42Z",
-            "pushed_at": "2024-08-30T08:59:28Z",
+            "updated_at": "2024-09-12T14:07:18Z",
+            "pushed_at": "2024-09-12T11:55:18Z",
             "homepage": "https://nf-co.re/scrnaseq",
-            "size": 44015,
-            "stargazers_count": 203,
-            "watchers_count": 203,
+            "size": 44022,
+            "stargazers_count": 204,
+            "watchers_count": 204,
             "language": "Nextflow",
             "has_issues": true,
             "has_projects": false,
@@ -37166,7 +37166,7 @@
             "visibility": "public",
             "forks": 165,
             "open_issues": 43,
-            "watchers": 203,
+            "watchers": 204,
             "default_branch": "master",
             "temp_clone_token": "",
             "allow_squash_merge": false,
@@ -39012,9 +39012,9 @@
             "url": "https://api.github.com/repos/nf-core/smrnaseq",
             "created_at": "2018-07-11T14:56:59Z",
             "updated_at": "2024-09-08T23:07:40Z",
-            "pushed_at": "2024-09-11T19:24:24Z",
+            "pushed_at": "2024-09-12T07:08:45Z",
             "homepage": "https://nf-co.re/smrnaseq",
-            "size": 8495,
+            "size": 8514,
             "stargazers_count": 71,
             "watchers_count": 71,
             "language": "Nextflow",
@@ -39027,7 +39027,7 @@
             "forks_count": 122,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 29,
+            "open_issues_count": 27,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -39037,7 +39037,7 @@
             ],
             "visibility": "public",
             "forks": 122,
-            "open_issues": 29,
+            "open_issues": 27,
             "watchers": 71,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -39125,7 +39125,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 1,
+            "open_pr_count": 0,
             "repository_url": "https://github.com/nf-core/smrnaseq",
             "contributors": [
                 {
@@ -39576,8 +39576,8 @@
                 },
                 {
                     "tag_name": "dev",
-                    "published_at": "2024-09-11T19:24:24Z",
-                    "tag_sha": "8fa10180a1063cc3f8387e5a8f84407085e17b96",
+                    "published_at": "2024-09-12T07:08:45Z",
+                    "tag_sha": "47ae1592f4467342afe93560d58e9d6991adffb2",
                     "has_schema": true,
                     "doc_files": [
                         "docs/output.md",
@@ -39598,6 +39598,7 @@
                             "samtools_index",
                             "samtools_sort",
                             "samtools_stats",
+                            "seqcluster_collapse",
                             "seqkit_grep",
                             "umicollapse",
                             "umitools_extract",
@@ -39626,7 +39627,7 @@
             "url": "https://api.github.com/repos/nf-core/spatialvi",
             "created_at": "2022-02-23T20:44:38Z",
             "updated_at": "2024-09-05T14:06:54Z",
-            "pushed_at": "2024-09-05T14:06:51Z",
+            "pushed_at": "2024-09-12T13:14:25Z",
             "homepage": "https://nf-co.re/spatialvi",
             "size": 7199,
             "stargazers_count": 48,
@@ -39641,7 +39642,7 @@
             "forks_count": 17,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 4,
+            "open_issues_count": 5,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -39660,7 +39661,7 @@
             ],
             "visibility": "public",
             "forks": 17,
-            "open_issues": 4,
+            "open_issues": 5,
             "watchers": 48,
             "default_branch": "dev",
             "temp_clone_token": "",
@@ -39763,7 +39764,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 0,
+            "open_pr_count": 1,
             "repository_url": "https://github.com/nf-core/spatialvi",
             "contributors": [
                 {
@@ -40235,9 +40236,9 @@
             "url": "https://api.github.com/repos/nf-core/taxprofiler",
             "created_at": "2022-02-18T06:56:10Z",
             "updated_at": "2024-09-11T21:12:09Z",
-            "pushed_at": "2024-09-11T08:28:38Z",
+            "pushed_at": "2024-09-12T09:51:19Z",
             "homepage": "https://nf-co.re/taxprofiler",
-            "size": 12773,
+            "size": 14654,
             "stargazers_count": 118,
             "watchers_count": 118,
             "language": "Nextflow",
@@ -40250,7 +40251,7 @@
             "forks_count": 34,
             "archived": false,
             "disabled": false,
-            "open_issues_count": 42,
+            "open_issues_count": 44,
             "allow_forking": true,
             "is_template": false,
             "web_commit_signoff_required": false,
@@ -40269,7 +40270,7 @@
             ],
             "visibility": "public",
             "forks": 34,
-            "open_issues": 42,
+            "open_issues": 44,
             "watchers": 118,
             "default_branch": "master",
             "temp_clone_token": "",
@@ -40537,7 +40538,7 @@
             "TEMPLATE_branch_protection_enforce_admins": -1,
             "TEMPLATE_restrict_push": true,
             "has_required_topics": true,
-            "open_pr_count": 3,
+            "open_pr_count": 5,
             "repository_url": "https://github.com/nf-core/taxprofiler",
             "contributors": [
                 {
@@ -41353,8 +41354,8 @@
                 },
                 {
                     "tag_name": "dev",
-                    "published_at": "2024-09-11T08:22:54Z",
-                    "tag_sha": "373c5465e2566d4f6ac958ca004f0c7ef310784e",
+                    "published_at": "2024-09-12T09:50:46Z",
+                    "tag_sha": "1247a77d36da7908ead39d72f842bfd7464b48c9",
                     "has_schema": true,
                     "doc_files": [
                         "docs/output.md",