Build branch main with version main (64aad6a)

Build pipeline: viash-hub.rnaseq.main-4gbdz Source commit: 64aad6a006 Source message: Merge pull request #22 from viash-hub/define_repositories_in_package_config define dependency repositories once in the package config
2024-09-14 09:49:51 +00:00
parent 92b5a42360
commit 9b29e37466
237 changed files with 3667 additions and 685 deletions
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -11,3 +11,13 @@ info:
 config_mods: |
  .requirements.commands := ['ps']
  .runners[.type == 'nextflow'].directives.tag := '$id'
+
+repositories:
+  - name: biobox
+    type: vsh
+    repo: vsh/biobox
+    tag: v0.2.0
+  - name: craftbox
+    type: vsh
+    repo: craftbox
+    tag: v0.1.0
--- a/src/workflows/genome_alignment_and_quant/config.vsh.yaml
+++ b/src/workflows/genome_alignment_and_quant/config.vsh.yaml
@@ -173,13 +173,6 @@ dependencies:
  - name: rsem/rsem_calculate_expression
    # repository: biobox

-repositories:
-  - name: biobox
-    type: vsh
-    repo: vsh/biobox
-    tag: v0.2.0
-
-
 runners: 
 - type: executable
 - type: nextflow
--- a/src/workflows/post_processing/config.vsh.yaml
+++ b/src/workflows/post_processing/config.vsh.yaml
@@ -155,12 +155,6 @@ dependencies:
  - name: ucsc/bedclip
  - name: ucsc/bedgraphtobigwig

-repositories:
-  - name: biobox
-    type: vsh
-    repo: vsh/biobox
-    tag: v0.2.0
-
 runners: 
 - type: executable
 - type: nextflow
--- a/src/workflows/pre_processing/config.vsh.yaml
+++ b/src/workflows/pre_processing/config.vsh.yaml
@@ -266,13 +266,7 @@ dependencies:
  - name: fq_subsample
  - name: salmon/salmon_quant
    repository: biobox
-
-repositories:
-  - name: biobox
-    type: vsh
-    repo: vsh/biobox
-    tag: v0.2.0
-    
+   
 runners: 
 - type: executable
 - type: nextflow
--- a/src/workflows/prepare_genome/config.vsh.yaml
+++ b/src/workflows/prepare_genome/config.vsh.yaml
@@ -164,16 +164,6 @@ dependencies:
    repository: biobox
  - name: kallisto/kallisto_index

-repositories:
-  - name: biobox
-    type: vsh
-    repo: biobox
-    tag: v0.2.0
-  - name: craftbox
-    type: vsh
-    repo: craftbox
-    tag: v0.1.0
-
 runners: 
 - type: executable
 - type: nextflow
--- a/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml
+++ b/src/workflows/pseudo_alignment_and_quant/config.vsh.yaml
@@ -83,12 +83,6 @@ dependencies:
    repository: biobox
  - name: kallisto/kallisto_quant

-repositories:
-  - name: biobox
-    type: vsh
-    repo: vsh/biobox
-    tag: v0.2.0
-
 runners: 
 - type: executable
 - type: nextflow
--- a/src/workflows/quality_control/config.vsh.yaml
+++ b/src/workflows/quality_control/config.vsh.yaml
@@ -652,13 +652,6 @@ dependencies:
    repository: biobox
  - name: workflows/merge_quant_results

-repositories:
-  - name: biobox
-    type: vsh
-    repo: vsh/biobox
-    tag: v0.2.0
-
-
 runners: 
 - type: executable
 - type: nextflow
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "fastp"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Robrecht Cannoodt"
  roles:
@@ -1066,7 +1066,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/fastp:0.23.4--hadf994f_2"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -1083,11 +1083,11 @@ build_info:
  output: "target/nextflow/fastp"
  executable: "target/nextflow/fastp/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -1097,7 +1097,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf
@@ -1,4 +1,4 @@
-// fastp 0.2.0
+// fastp v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2808,7 +2808,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "fastp",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Robrecht Cannoodt",
@@ -4001,7 +4001,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/fastp:0.23.4--hadf994f_2",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -4023,12 +4023,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/fastp",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -4037,7 +4037,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4632,7 +4632,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/fastp",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'fastp'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...).\n\nFeatures:\n\n  - comprehensive quality profiling for both before and after filtering data (quality curves, base contents, KMER, Q20/Q30, GC Ratio, duplication, adapter contents...)\n  - filter out bad reads (too low quality, too short, or too many N...)\n  - cut low quality bases for per read in its 5\' and 3\' by evaluating the mean quality from a sliding window (like Trimmomatic but faster).\n  - trim all reads in front and tail\n  - cut adapters. Adapter sequences can be automatically detected, which means you don\'t have to input the adapter sequences to trim them.\n  - correct mismatched base pairs in overlapped regions of paired end reads, if one base is with high quality while the other is with ultra low quality\n  - trim polyG in 3\' ends, which is commonly seen in NovaSeq/NextSeq data. Trim polyX in 3\' ends to remove unwanted polyX tailing (i.e. polyA tailing for mRNA-Seq data)\n  - preprocess unique molecular identifier (UMI) enabled data, shift UMI to sequence name.\n  - report JSON format result for further interpreting.\n  - visualize quality control and filtering results on a single HTML page (like FASTQC but faster and more informative).\n  - split the output to multiple files (0001.R1.gz, 0002.R1.gz...) to support parallel processing. Two modes can be used, limiting the total split file number, or limitting the lines of each split file.\n  - support long reads (data from PacBio / Nanopore devices).\n  - support reading from STDIN and writing to STDOUT\n  - support interleaved input\n  - support ultra-fast FASTQ-level deduplication\n'
  author = 'Robrecht Cannoodt'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "featurecounts"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Sai Nirmayi Yasa"
  roles:
@@ -627,7 +627,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/subread:2.0.6--he4a0461_0"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -645,11 +645,11 @@ build_info:
  output: "target/nextflow/featurecounts"
  executable: "target/nextflow/featurecounts/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -659,7 +659,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf
@@ -1,4 +1,4 @@
-// featurecounts 0.2.0
+// featurecounts v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2808,7 +2808,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "featurecounts",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Sai Nirmayi Yasa",
@@ -3527,7 +3527,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/subread:2.0.6--he4a0461_0",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3549,12 +3549,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/featurecounts",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3563,7 +3563,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4115,7 +4115,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/featurecounts",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'featurecounts'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'featureCounts is a read summarization program for counting reads generated from either RNA or genomic DNA sequencing experiments by implementing highly efficient chromosome hashing and feature blocking techniques. It works with either single or paired-end reads and provides a wide range of options appropriate for different sequencing applications.\n'
  author = 'Sai Nirmayi Yasa'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "gffread"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Emma Rousseau"
  roles:
@@ -668,7 +668,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -685,11 +685,11 @@ build_info:
  output: "target/nextflow/gffread"
  executable: "target/nextflow/gffread/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -699,7 +699,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf
@@ -1,4 +1,4 @@
-// gffread 0.2.0
+// gffread v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2808,7 +2808,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "gffread",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Emma Rousseau",
@@ -3584,7 +3584,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/gffread:0.12.7--hdcf5f25_3",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3606,12 +3606,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/gffread",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3620,7 +3620,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4218,7 +4218,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/gffread",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'gffread'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Validate, filter, convert and perform various other operations on GFF files.'
  author = 'Emma Rousseau'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "multiqc"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Dorien Roosen"
  roles:
@@ -433,7 +433,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -456,11 +456,11 @@ build_info:
  output: "target/nextflow/multiqc"
  executable: "target/nextflow/multiqc/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -470,7 +470,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf
@@ -1,4 +1,4 @@
-// multiqc 0.2.0
+// multiqc v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2808,7 +2808,7 @@ meta = [
  "resources_dir": moduleDir.toRealPath().normalize(),
  "config": processConfig(readJsonBlob('''{
  "name" : "multiqc",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Dorien Roosen",
@@ -3335,7 +3335,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3366,12 +3366,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/multiqc",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3380,7 +3380,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3961,7 +3961,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/multiqc",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'multiqc'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n'
  author = 'Dorien Roosen'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rsem_prepare_reference"
 namespace: "rsem"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Sai Nirmayi Yasa"
  roles:
@@ -352,7 +352,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -416,11 +416,11 @@ build_info:
  output: "target/nextflow/rsem/rsem_prepare_reference"
  executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -430,7 +430,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf
@@ -1,4 +1,4 @@
-// rsem_prepare_reference 0.2.0
+// rsem_prepare_reference v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "rsem_prepare_reference",
  "namespace" : "rsem",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Sai Nirmayi Yasa",
@@ -3185,7 +3185,7 @@ meta = [
      "id" : "docker",
      "image" : "ubuntu:22.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3245,12 +3245,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/rsem/rsem_prepare_reference",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3259,7 +3259,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3731,7 +3731,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/rsem/rsem_prepare_reference",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'rsem/rsem_prepare_reference'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'RSEM is a software package for estimating gene and isoform expression levels from RNA-Seq data. This component prepares transcript references for RSEM.\n'
  author = 'Sai Nirmayi Yasa'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "salmon_index"
 namespace: "salmon"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Sai Nirmayi Yasa"
  roles:
@@ -260,7 +260,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -277,11 +277,11 @@ build_info:
  output: "target/nextflow/salmon/salmon_index"
  executable: "target/nextflow/salmon/salmon_index/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -291,7 +291,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf
@@ -1,4 +1,4 @@
-// salmon_index 0.2.0
+// salmon_index v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "salmon_index",
  "namespace" : "salmon",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Sai Nirmayi Yasa",
@@ -3107,7 +3107,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/salmon:1.10.2--hecfa306_0",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3129,12 +3129,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/salmon/salmon_index",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3143,7 +3143,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3619,7 +3619,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/salmon/salmon_index",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'salmon/salmon_index'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. This component creates a salmon index for the transcriptome to use Salmon in the mapping-based mode. It is generally recommend that you build a decoy-aware transcriptome file. This is done using the entire genome of the organism as the decoy sequence by concatenating the genome to the end of the transcriptome to be indexed and populating the decoys.txt file with the chromosome names.\n'
  author = 'Sai Nirmayi Yasa'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "salmon_quant"
 namespace: "salmon"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Sai Nirmayi Yasa"
  roles:
@@ -1156,7 +1156,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/salmon:1.10.2--hecfa306_0"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -1173,11 +1173,11 @@ build_info:
  output: "target/nextflow/salmon/salmon_quant"
  executable: "target/nextflow/salmon/salmon_quant/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -1187,7 +1187,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf
@@ -1,4 +1,4 @@
-// salmon_quant 0.2.0
+// salmon_quant v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "salmon_quant",
  "namespace" : "salmon",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Sai Nirmayi Yasa",
@@ -3942,7 +3942,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/salmon:1.10.2--hecfa306_0",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3964,12 +3964,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/salmon/salmon_quant",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3978,7 +3978,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -4634,7 +4634,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/salmon/salmon_quant",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'salmon/salmon_quant'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Salmon is a tool for wicked-fast transcript quantification from RNA-seq data. It can either make use of pre-computed alignments (in the form of a SAM/BAM file) to the transcripts rather than the raw reads, or can be run in the mapping-based mode. \n'
  author = 'Sai Nirmayi Yasa'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools_flagstat"
 namespace: "samtools"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Emma Rousseau"
  roles:
@@ -155,7 +155,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -173,11 +173,11 @@ build_info:
  output: "target/nextflow/samtools/samtools_flagstat"
  executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -187,7 +187,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf
@@ -1,4 +1,4 @@
-// samtools_flagstat 0.2.0
+// samtools_flagstat v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "samtools_flagstat",
  "namespace" : "samtools",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Emma Rousseau",
@@ -3006,7 +3006,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3028,12 +3028,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_flagstat",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3042,7 +3042,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3463,7 +3463,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/samtools/samtools_flagstat",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'samtools/samtools_flagstat'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Counts the number of alignments in SAM/BAM/CRAM files for each FLAG type.'
  author = 'Emma Rousseau'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools_idxstats"
 namespace: "samtools"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Emma Rousseau"
  roles:
@@ -165,7 +165,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -183,11 +183,11 @@ build_info:
  output: "target/nextflow/samtools/samtools_idxstats"
  executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -197,7 +197,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf
@@ -1,4 +1,4 @@
-// samtools_idxstats 0.2.0
+// samtools_idxstats v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "samtools_idxstats",
  "namespace" : "samtools",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Emma Rousseau",
@@ -3018,7 +3018,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3040,12 +3040,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_idxstats",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3054,7 +3054,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3473,7 +3473,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/samtools/samtools_idxstats",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'samtools/samtools_idxstats'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Reports alignment summary statistics for a BAM file.'
  author = 'Emma Rousseau'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools_index"
 namespace: "samtools"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Emma Rousseau"
  roles:
@@ -171,7 +171,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -189,11 +189,11 @@ build_info:
  output: "target/nextflow/samtools/samtools_index"
  executable: "target/nextflow/samtools/samtools_index/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -203,7 +203,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf
@@ -1,4 +1,4 @@
-// samtools_index 0.2.0
+// samtools_index v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "samtools_index",
  "namespace" : "samtools",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Emma Rousseau",
@@ -3031,7 +3031,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3053,12 +3053,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_index",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3067,7 +3067,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3497,7 +3497,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/samtools/samtools_index",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'samtools/samtools_index'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Index SAM/BAM/CRAM files.'
  author = 'Emma Rousseau'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools_sort"
 namespace: "samtools"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Emma Rousseau"
  roles:
@@ -314,7 +314,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -332,11 +332,11 @@ build_info:
  output: "target/nextflow/samtools/samtools_sort"
  executable: "target/nextflow/samtools/samtools_sort/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -346,7 +346,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf
@@ -1,4 +1,4 @@
-// samtools_sort 0.2.0
+// samtools_sort v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "samtools_sort",
  "namespace" : "samtools",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Emma Rousseau",
@@ -3203,7 +3203,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3225,12 +3225,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_sort",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3239,7 +3239,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3717,7 +3717,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/samtools/samtools_sort",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'samtools/samtools_sort'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Sort SAM/BAM/CRAM file.'
  author = 'Emma Rousseau'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "samtools_stats"
 namespace: "samtools"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Emma Rousseau"
  roles:
@@ -383,7 +383,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -401,11 +401,11 @@ build_info:
  output: "target/nextflow/samtools/samtools_stats"
  executable: "target/nextflow/samtools/samtools_stats/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -415,7 +415,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf
@@ -1,4 +1,4 @@
-// samtools_stats 0.2.0
+// samtools_stats v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "samtools_stats",
  "namespace" : "samtools",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Emma Rousseau",
@@ -3273,7 +3273,7 @@ meta = [
      "id" : "docker",
      "image" : "quay.io/biocontainers/samtools:1.19.2--h50ea8bc_1",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3295,12 +3295,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_stats",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3309,7 +3309,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3779,7 +3779,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/samtools/samtools_stats",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'samtools/samtools_stats'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Reports alignment summary statistics for a BAM file.'
  author = 'Emma Rousseau'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "star_align_reads"
 namespace: "star"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Angela Oliveira Pisco"
  roles:
@@ -2624,7 +2624,7 @@ engines:
  id: "docker"
  image: "python:3.12-slim"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -2663,11 +2663,11 @@ build_info:
  output: "target/nextflow/star/star_align_reads"
  executable: "target/nextflow/star/star_align_reads/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -2677,7 +2677,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf
@@ -1,4 +1,4 @@
-// star_align_reads 0.2.0
+// star_align_reads v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2810,7 +2810,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "star_align_reads",
  "namespace" : "star",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Angela Oliveira Pisco",
@@ -4570,7 +4570,7 @@ meta = [
        {
          "type" : "integer",
          "name" : "--seed_split_min",
-          "description" : "min length of the seed seque''' + '''nces split by Ns or mate gap",
+          "description" : "min length of the seed sequ''' + '''ences split by Ns or mate gap",
          "info" : {
            "orig_name" : "--seedSplitMin"
          },
@@ -5894,7 +5894,7 @@ meta = [
      "id" : "docker",
      "image" : "python:3.12-slim",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -5943,12 +5943,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/star/star_align_reads",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -5957,7 +5957,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -6671,7 +6671,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/star/star_align_reads",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'star/star_align_reads'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Aligns reads to a reference genome using STAR.\n'
  author = 'Angela Oliveira Pisco, Robrecht Cannoodt'
 }
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "star_genome_generate"
 namespace: "star"
-version: "0.2.0"
+version: "v0.2.0"
 authors:
 - name: "Sai Nirmayi Yasa"
  roles:
@@ -305,7 +305,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "0.2.0"
+  target_tag: "v0.2.0"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -333,11 +333,11 @@ build_info:
  output: "target/nextflow/star/star_genome_generate"
  executable: "target/nextflow/star/star_genome_generate/main.nf"
  viash_version: "0.9.0"
-  git_commit: "5526b3e939030daea80595fa98387b469329bbfa"
-  git_remote: "https://github.com/viash-hub/biobox"
+  git_commit: "7e530218844c373048bc33de58f021b6460642e5"
+  git_remote: "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
 package_config:
  name: "biobox"
-  version: "0.2.0"
+  version: "v0.2.0"
  description: "A collection of bioinformatics tools for working with sequence data.\n"
  info: null
  viash_version: "0.9.0"
@@ -347,7 +347,7 @@ package_config:
  - ".requirements.commands := ['ps']\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := '0.2.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
  keywords:
  - "bioinformatics"
  - "modules"
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf
@@ -1,4 +1,4 @@
-// star_genome_generate 0.2.0
+// star_genome_generate v0.2.0
 // 
 // This wrapper script is auto-generated by viash 0.9.0 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -2809,7 +2809,7 @@ meta = [
  "config": processConfig(readJsonBlob('''{
  "name" : "star_genome_generate",
  "namespace" : "star",
-  "version" : "0.2.0",
+  "version" : "v0.2.0",
  "authors" : [
    {
      "name" : "Sai Nirmayi Yasa",
@@ -3163,7 +3163,7 @@ meta = [
      "id" : "docker",
      "image" : "ubuntu:22.04",
      "target_registry" : "images.viash-hub.com",
-      "target_tag" : "0.2.0",
+      "target_tag" : "v0.2.0",
      "namespace_separator" : "/",
      "setup" : [
        {
@@ -3195,12 +3195,12 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/star/star_genome_generate",
    "viash_version" : "0.9.0",
-    "git_commit" : "5526b3e939030daea80595fa98387b469329bbfa",
-    "git_remote" : "https://github.com/viash-hub/biobox"
+    "git_commit" : "7e530218844c373048bc33de58f021b6460642e5",
+    "git_remote" : "https://x-access-token:ghs_kiUBq39QrAlnG6IaeAcTcXhllzqpOV4LDB3e@github.com/viash-hub/biobox"
  },
  "package_config" : {
    "name" : "biobox",
-    "version" : "0.2.0",
+    "version" : "v0.2.0",
    "description" : "A collection of bioinformatics tools for working with sequence data.\n",
    "viash_version" : "0.9.0",
    "source" : "src",
@@ -3209,7 +3209,7 @@ meta = [
      ".requirements.commands := ['ps']\n",
      ".engines += { type: \\"native\\" }",
      ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := '0.2.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.2.0'"
    ],
    "keywords" : [
      "bioinformatics",
@@ -3662,7 +3662,7 @@ meta["defaults"] = [
  "container" : {
    "registry" : "images.viash-hub.com",
    "image" : "vsh/biobox/star/star_genome_generate",
-    "tag" : "0.2.0"
+    "tag" : "v0.2.0"
  },
  "tag" : "$id"
 }'''),
--- a/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/nextflow.config
+++ b/target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/nextflow.config
@@ -2,7 +2,7 @@ manifest {
  name = 'star/star_genome_generate'
  mainScript = 'main.nf'
  nextflowVersion = '!>=20.12.1-edge'
-  version = '0.2.0'
+  version = 'v0.2.0'
  description = 'Create index for STAR\n'
  author = 'Sai Nirmayi Yasa'
 }
--- a/target/executable/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml
@@ -140,6 +140,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -229,14 +238,23 @@ build_info:
  output: "target/executable/bbmap_bbsplit"
  executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit
@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
 cp -r bbmap/* /usr/local/bin

 LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:10Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools_genomecov/.config.vsh.yaml
@@ -80,6 +80,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -169,14 +178,23 @@ build_info:
  output: "target/executable/bedtools_genomecov"
  executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools_genomecov/bedtools_genomecov
@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
 chmod a+x /usr/local/bin/bedtools

 LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cat_additional_fasta/.config.vsh.yaml
+++ b/target/executable/cat_additional_fasta/.config.vsh.yaml
@@ -90,6 +90,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -173,14 +182,23 @@ build_info:
  output: "target/executable/cat_additional_fasta"
  executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/cat_additional_fasta/cat_additional_fasta
+++ b/target/executable/cat_additional_fasta/cat_additional_fasta
@@ -480,9 +480,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:17Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:10Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cat_fastq/.config.vsh.yaml
+++ b/target/executable/cat_fastq/.config.vsh.yaml
@@ -77,6 +77,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -160,14 +169,23 @@ build_info:
  output: "target/executable/cat_fastq"
  executable: "target/executable/cat_fastq/cat_fastq"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/cat_fastq/cat_fastq
+++ b/target/executable/cat_fastq/cat_fastq
@@ -472,9 +472,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:11Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/deseq2_qc/.config.vsh.yaml
+++ b/target/executable/deseq2_qc/.config.vsh.yaml
@@ -126,6 +126,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -228,14 +237,23 @@ build_info:
  output: "target/executable/deseq2_qc"
  executable: "target/executable/deseq2_qc/deseq2_qc"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/deseq2_qc/deseq2_qc
+++ b/target/executable/deseq2_qc/deseq2_qc
@@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
  Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:30Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/dupradar/.config.vsh.yaml
+++ b/target/executable/dupradar/.config.vsh.yaml
@@ -165,6 +165,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -257,14 +266,23 @@ build_info:
  output: "target/executable/dupradar"
  executable: "target/executable/dupradar/dupradar"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/dupradar/dupradar
+++ b/target/executable/dupradar/dupradar
@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
  Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'

 LABEL org.opencontainers.image.description="Companion container for running component dupradar"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:19Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:12Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -101,6 +101,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -189,14 +198,23 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -490,9 +490,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -74,6 +74,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -168,14 +177,23 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -485,9 +485,9 @@ cargo install --locked --path . && \
 mv /usr/local/fq/target/release/fq /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/getchromsizes/.config.vsh.yaml
+++ b/target/executable/getchromsizes/.config.vsh.yaml
@@ -67,6 +67,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -158,14 +167,23 @@ build_info:
  output: "target/executable/getchromsizes"
  executable: "target/executable/getchromsizes/getchromsizes"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/getchromsizes/getchromsizes
+++ b/target/executable/getchromsizes/getchromsizes
@@ -480,9 +480,9 @@ make && \
 make install

 LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:04Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gtf2bed/.config.vsh.yaml
+++ b/target/executable/gtf2bed/.config.vsh.yaml
@@ -48,6 +48,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -136,14 +145,23 @@ build_info:
  output: "target/executable/gtf2bed"
  executable: "target/executable/gtf2bed/gtf2bed"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/gtf2bed/gtf2bed
+++ b/target/executable/gtf2bed/gtf2bed
@@ -466,9 +466,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:25Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gtf_filter/.config.vsh.yaml
+++ b/target/executable/gtf_filter/.config.vsh.yaml
@@ -63,6 +63,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -146,14 +155,23 @@ build_info:
  output: "target/executable/gtf_filter"
  executable: "target/executable/gtf_filter/gtf_filter"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/gtf_filter/gtf_filter
+++ b/target/executable/gtf_filter/gtf_filter
@@ -470,9 +470,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gunzip/.config.vsh.yaml
+++ b/target/executable/gunzip/.config.vsh.yaml
@@ -47,6 +47,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -135,14 +144,23 @@ build_info:
  output: "target/executable/gunzip"
  executable: "target/executable/gunzip/gunzip"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/gunzip/gunzip
+++ b/target/executable/gunzip/gunzip
@@ -466,9 +466,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component gunzip"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:05Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -56,6 +56,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -146,14 +155,23 @@ build_info:
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -154,6 +154,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -244,14 +253,23 @@ build_info:
  output: "target/executable/kallisto/kallisto_quant"
  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml
+++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml
@@ -70,6 +70,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -161,14 +170,23 @@ build_info:
  output: "target/executable/multiqc_custom_biotype"
  executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
+++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
@@ -481,9 +481,9 @@ RUN apt-get update && \
 RUN pip install --upgrade pip

 LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:12Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/picard_markduplicates/.config.vsh.yaml
+++ b/target/executable/picard_markduplicates/.config.vsh.yaml
@@ -107,6 +107,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -198,14 +207,23 @@ build_info:
  output: "target/executable/picard_markduplicates"
  executable: "target/executable/picard_markduplicates/picard_markduplicates"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/picard_markduplicates/picard_markduplicates
+++ b/target/executable/picard_markduplicates/picard_markduplicates
@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
 mv picard.jar /usr/local/bin 

 LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:20Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/prepare_multiqc_input/.config.vsh.yaml
+++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml
@@ -317,6 +317,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -400,14 +409,23 @@ build_info:
  output: "target/executable/prepare_multiqc_input"
  executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/prepare_multiqc_input/prepare_multiqc_input
+++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input
@@ -557,9 +557,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:24Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:16Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
+++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
@@ -46,6 +46,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -129,14 +138,23 @@ build_info:
  output: "target/executable/preprocess_transcripts_fasta"
  executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
+++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
@@ -462,9 +462,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/preseq_lcextrap/.config.vsh.yaml
+++ b/target/executable/preseq_lcextrap/.config.vsh.yaml
@@ -67,6 +67,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -182,14 +191,23 @@ build_info:
  output: "target/executable/preseq_lcextrap"
  executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/preseq_lcextrap/preseq_lcextrap
+++ b/target/executable/preseq_lcextrap/preseq_lcextrap
@@ -495,9 +495,9 @@ mkdir build && cd build && \
 make && make install && make HAVE_HTSLIB=1 all 

 LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:05Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/.config.vsh.yaml
+++ b/target/executable/qualimap/.config.vsh.yaml
@@ -158,6 +158,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -262,14 +271,23 @@ build_info:
  output: "target/executable/qualimap"
  executable: "target/executable/qualimap/qualimap"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/qualimap/qualimap
+++ b/target/executable/qualimap/qualimap
@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
  Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component qualimap"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:03Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -181,6 +181,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -299,14 +308,23 @@ build_info:
  output: "target/executable/rsem/rsem_calculate_expression"
  executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -545,9 +545,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
 /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"

 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
@@ -110,6 +110,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -193,14 +202,23 @@ build_info:
  output: "target/executable/rsem/rsem_merge_counts"
  executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
+++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
@@ -490,9 +490,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:17Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
@@ -61,6 +61,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -154,14 +163,23 @@ build_info:
  output: "target/executable/rseqc/rseqc_bamstat"
  executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
+++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:15Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
@@ -84,6 +84,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -177,14 +186,23 @@ build_info:
  output: "target/executable/rseqc/rseqc_inferexperiment"
  executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
+++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:13Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
@@ -169,6 +169,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -263,14 +272,23 @@ build_info:
  output: "target/executable/rseqc/rseqc_innerdistance"
  executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
+++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
-LABEL org.opencontainers.image.created="2024-09-13T10:19:22Z"
-LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
+LABEL org.opencontainers.image.created="2024-09-14T08:49:14Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="64aad6a006818388eceffe024b1701b3eae06bee"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
@@ -157,6 +157,15 @@ status: "enabled"
 requirements:
  commands:
  - "ps"
+repositories:
+- type: "vsh"
+  name: "biobox"
+  repo: "vsh/biobox"
+  tag: "v0.2.0"
+- type: "vsh"
+  name: "craftbox"
+  repo: "craftbox"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -251,14 +260,23 @@ build_info:
  output: "target/executable/rseqc/rseqc_junctionannotation"
  executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
  viash_version: "0.9.0"
-  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
-  git_remote: "https://github.com/viash-hub/rnaseq"
+  git_commit: "64aad6a006818388eceffe024b1701b3eae06bee"
+  git_remote: "https://x-access-token:ghs_sq8cBpPtIm1wZvLlQUshbKRwwqLLDl0UmbNu@github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
      dest: "testData"
+  repositories:
+  - type: "vsh"
+    name: "biobox"
+    repo: "vsh/biobox"
+    tag: "v0.2.0"
+  - type: "vsh"
+    name: "craftbox"
+    repo: "craftbox"
+    tag: "v0.1.0"
  viash_version: "0.9.0"
  source: "src"
  target: "target"
--- a/Show More
+++ b/Show More