Build branch v0.1 with version v0.1.1 (0f49a3f)

Build pipeline: vsh-ci-dev-w9454 Source commit: 0f49a3ff62 Source message: Bump version to v0.1.1
2024-10-17 17:31:01 +00:00
parent 69e0b1ebaf
commit 3e6bb670c5
246 changed files with 1539 additions and 1390 deletions
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -1,5 +1,7 @@
+name: rnaseq
+
 viash_version: 0.9.0
-version: v0.1.0
+version: v0.1.1

 source: src
 target: target
--- a/target/executable/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "bbmap_bbsplit"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -219,7 +219,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -238,10 +238,11 @@ build_info:
  output: "target/executable/bbmap_bbsplit"
  executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -263,5 +264,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# bbmap_bbsplit v0.1.0
+# bbmap_bbsplit v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bbmap_bbsplit v0.1.0"
+  echo "bbmap_bbsplit v0.1.1"
  echo ""
  echo "Split sequencing reads by mapping them to multiple references simultaneously."
  echo ""
@@ -506,10 +506,10 @@ 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="2024-10-04T11:21:39Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -645,7 +645,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "bbmap_bbsplit v0.1.0"
+            echo "bbmap_bbsplit v0.1.1"
            exit
            ;;
        --id)
@@ -852,7 +852,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/bbmap_bbsplit:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/bbmap_bbsplit:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools_genomecov/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "bedtools_genomecov"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -159,7 +159,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -178,10 +178,11 @@ build_info:
  output: "target/executable/bedtools_genomecov"
  executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -203,5 +204,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools_genomecov/bedtools_genomecov
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# bedtools_genomecov v0.1.0
+# bedtools_genomecov v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bedtools_genomecov v0.1.0"
+  echo "bedtools_genomecov v0.1.1"
  echo ""
  echo "Compute BEDGRAPH (-bg) summaries of feature coverage"
  echo ""
@@ -481,10 +481,10 @@ 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="2024-10-04T11:21:40Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -620,7 +620,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "bedtools_genomecov v0.1.0"
+            echo "bedtools_genomecov v0.1.1"
            exit
            ;;
        --strandedness)
@@ -766,7 +766,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/bedtools_genomecov:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/bedtools_genomecov:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/cat_additional_fasta/.config.vsh.yaml
+++ b/target/executable/cat_additional_fasta/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "cat_additional_fasta"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -169,7 +169,7 @@ engines:
  id: "docker"
  image: "python"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  entrypoint: []
  cmd: null
@@ -182,10 +182,11 @@ build_info:
  output: "target/executable/cat_additional_fasta"
  executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -207,5 +208,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/cat_additional_fasta/cat_additional_fasta
+++ b/target/executable/cat_additional_fasta/cat_additional_fasta
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# cat_additional_fasta v0.1.0
+# cat_additional_fasta v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cat_additional_fasta v0.1.0"
+  echo "cat_additional_fasta v0.1.1"
  echo ""
  echo "Concatenate addional fasta file to reference FASTA and GTF files."
  echo ""
@@ -480,10 +480,10 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:48Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -619,7 +619,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "cat_additional_fasta v0.1.0"
+            echo "cat_additional_fasta v0.1.1"
            exit
            ;;
        --fasta)
@@ -776,7 +776,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/cat_additional_fasta:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/cat_additional_fasta:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/cat_fastq/.config.vsh.yaml
+++ b/target/executable/cat_fastq/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "cat_fastq"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -156,7 +156,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  entrypoint: []
  cmd: null
@@ -169,10 +169,11 @@ build_info:
  output: "target/executable/cat_fastq"
  executable: "target/executable/cat_fastq/cat_fastq"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -194,5 +195,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/cat_fastq/cat_fastq
+++ b/target/executable/cat_fastq/cat_fastq
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# cat_fastq v0.1.0
+# cat_fastq v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "cat_fastq v0.1.0"
+  echo "cat_fastq v0.1.1"
  echo ""
  echo "Concatenate multiple fastq files"
  echo ""
@@ -472,10 +472,10 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:48Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -611,7 +611,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "cat_fastq v0.1.0"
+            echo "cat_fastq v0.1.1"
            exit
            ;;
        --read_1)
@@ -758,7 +758,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/cat_fastq:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/cat_fastq:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/deseq2_qc/.config.vsh.yaml
+++ b/target/executable/deseq2_qc/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "deseq2_qc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "input"
  arguments:
@@ -207,7 +207,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -239,10 +239,11 @@ build_info:
  output: "target/executable/deseq2_qc"
  executable: "target/executable/deseq2_qc/deseq2_qc"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -264,5 +265,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/deseq2_qc/deseq2_qc
+++ b/target/executable/deseq2_qc/deseq2_qc
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# deseq2_qc v0.1.0
+# deseq2_qc v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "deseq2_qc v0.1.0"
+  echo "deseq2_qc v0.1.1"
  echo ""
  echo "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the"
  echo "counts files"
@@ -502,10 +502,10 @@ 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="2024-10-04T11:21:58Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "deseq2_qc v0.1.0"
+            echo "deseq2_qc v0.1.1"
            exit
            ;;
        --counts)
@@ -831,7 +831,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/deseq2_qc:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/deseq2_qc:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/dupradar/.config.vsh.yaml
+++ b/target/executable/dupradar/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "dupradar"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -244,7 +244,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -266,10 +266,11 @@ build_info:
  output: "target/executable/dupradar"
  executable: "target/executable/dupradar/dupradar"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -291,5 +292,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/dupradar/dupradar
+++ b/target/executable/dupradar/dupradar
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# dupradar v0.1.0
+# dupradar v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "dupradar v0.1.0"
+  echo "dupradar v0.1.1"
  echo ""
  echo "Assessment of duplication rates in RNA-Seq datasets"
  echo ""
@@ -520,10 +520,10 @@ 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="2024-10-04T11:21:49Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -659,7 +659,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "dupradar v0.1.0"
+            echo "dupradar v0.1.1"
            exit
            ;;
        --id)
@@ -882,7 +882,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/dupradar:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/dupradar:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "fastqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -180,7 +180,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -198,10 +198,11 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -223,5 +224,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# fastqc v0.1.0
+# fastqc v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "fastqc v0.1.0"
+  echo "fastqc v0.1.1"
  echo ""
  echo "Fastqc component, please see"
  echo "https://www.bioinformatics.babraham.ac.uk/projects/fastqc/. This component can"
@@ -490,10 +490,10 @@ 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="2024-10-04T11:21:41Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -629,7 +629,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "fastqc v0.1.0"
+            echo "fastqc v0.1.1"
            exit
            ;;
        --paired)
@@ -792,7 +792,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/fastqc:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/fastqc:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "fq_subsample"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -153,7 +153,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -177,10 +177,11 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -202,5 +203,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# fq_subsample v0.1.0
+# fq_subsample v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "fq_subsample v0.1.0"
+  echo "fq_subsample v0.1.1"
  echo ""
  echo "fq subsample outputs a subset of records from single or paired FASTQ files. This"
  echo "requires a seed (--seed) to be set in ext.args"
@@ -485,10 +485,10 @@ 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="2024-10-04T11:21:41Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -624,7 +624,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "fq_subsample v0.1.0"
+            echo "fq_subsample v0.1.1"
            exit
            ;;
        --input)
@@ -765,7 +765,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/fq_subsample:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/fq_subsample:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/getchromsizes/.config.vsh.yaml
+++ b/target/executable/getchromsizes/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "getchromsizes"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -146,7 +146,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -167,10 +167,11 @@ build_info:
  output: "target/executable/getchromsizes"
  executable: "target/executable/getchromsizes/getchromsizes"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -192,5 +193,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/getchromsizes/getchromsizes
+++ b/target/executable/getchromsizes/getchromsizes
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# getchromsizes v0.1.0
+# getchromsizes v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "getchromsizes v0.1.0"
+  echo "getchromsizes v0.1.1"
  echo ""
  echo "Generates a FASTA file of chromosome sizes and a fasta index file."
  echo ""
@@ -480,10 +480,10 @@ make && \
 make install

 LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:41Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -619,7 +619,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "getchromsizes v0.1.0"
+            echo "getchromsizes v0.1.1"
            exit
            ;;
        --fasta)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/getchromsizes:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/getchromsizes:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/gtf2bed/.config.vsh.yaml
+++ b/target/executable/gtf2bed/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "gtf2bed"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -127,7 +127,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -145,10 +145,11 @@ build_info:
  output: "target/executable/gtf2bed"
  executable: "target/executable/gtf2bed/gtf2bed"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -170,5 +171,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/gtf2bed/gtf2bed
+++ b/target/executable/gtf2bed/gtf2bed
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# gtf2bed v0.1.0
+# gtf2bed v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "gtf2bed v0.1.0"
+  echo "gtf2bed v0.1.1"
  echo ""
  echo "Create BED annotation file from GTF."
  echo ""
@@ -466,10 +466,10 @@ 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="2024-10-04T11:21:54Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -605,7 +605,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "gtf2bed v0.1.0"
+            echo "gtf2bed v0.1.1"
            exit
            ;;
        --gtf)
@@ -718,7 +718,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gtf2bed:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gtf2bed:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/gtf_filter/.config.vsh.yaml
+++ b/target/executable/gtf_filter/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "gtf_filter"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -142,7 +142,7 @@ engines:
  id: "docker"
  image: "python"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  entrypoint: []
  cmd: null
@@ -155,10 +155,11 @@ build_info:
  output: "target/executable/gtf_filter"
  executable: "target/executable/gtf_filter/gtf_filter"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -180,5 +181,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/gtf_filter/gtf_filter
+++ b/target/executable/gtf_filter/gtf_filter
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# gtf_filter v0.1.0
+# gtf_filter v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "gtf_filter v0.1.0"
+  echo "gtf_filter v0.1.1"
  echo ""
  echo "Filters a GTF file based on sequence names in a FASTA file."
  echo ""
@@ -470,10 +470,10 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:57Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -609,7 +609,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "gtf_filter v0.1.0"
+            echo "gtf_filter v0.1.1"
            exit
            ;;
        --fasta)
@@ -738,7 +738,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gtf_filter:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gtf_filter:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/gunzip/.config.vsh.yaml
+++ b/target/executable/gunzip/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "gunzip"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -126,7 +126,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -144,10 +144,11 @@ build_info:
  output: "target/executable/gunzip"
  executable: "target/executable/gunzip/gunzip"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -169,5 +170,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/gunzip/gunzip
+++ b/target/executable/gunzip/gunzip
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# gunzip v0.1.0
+# gunzip v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "gunzip v0.1.0"
+  echo "gunzip v0.1.1"
  echo ""
  echo "Compress or uncompress a file or list of files."
  echo ""
@@ -466,10 +466,10 @@ 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="2024-10-04T11:21:42Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -605,7 +605,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "gunzip v0.1.0"
+            echo "gunzip v0.1.1"
            exit
            ;;
        --input)
@@ -718,7 +718,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/gunzip:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/gunzip:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "kallisto_index"
 namespace: "kallisto"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -135,7 +135,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -155,10 +155,11 @@ build_info:
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -180,5 +181,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# kallisto_index v0.1.0
+# kallisto_index v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "kallisto_index v0.1.0"
+  echo "kallisto_index v0.1.1"
  echo ""
  echo "Create Kallisto index."
  echo ""
@@ -471,10 +471,10 @@ 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="2024-10-04T11:21:55Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -610,7 +610,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "kallisto_index v0.1.0"
+            echo "kallisto_index v0.1.1"
            exit
            ;;
        --transcriptome_fasta)
@@ -734,7 +734,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/kallisto/kallisto_index:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/kallisto/kallisto_index:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "kallisto_quant"
 namespace: "kallisto"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -233,7 +233,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -253,10 +253,11 @@ build_info:
  output: "target/executable/kallisto/kallisto_quant"
  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -278,5 +279,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# kallisto_quant v0.1.0
+# kallisto_quant v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "kallisto_quant v0.1.0"
+  echo "kallisto_quant v0.1.1"
  echo ""
  echo "Computes equivalence classes for reads and quantifies abundances."
  echo ""
@@ -515,10 +515,10 @@ 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="2024-10-04T11:21:55Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -654,7 +654,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "kallisto_quant v0.1.0"
+            echo "kallisto_quant v0.1.1"
            exit
            ;;
        --input)
@@ -883,7 +883,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/kallisto/kallisto_quant:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/kallisto/kallisto_quant:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml
+++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "multiqc_custom_biotype"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -152,7 +152,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -173,10 +173,11 @@ build_info:
  output: "target/executable/multiqc_custom_biotype"
  executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -198,5 +199,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
+++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# multiqc_custom_biotype v0.1.0
+# multiqc_custom_biotype v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "multiqc_custom_biotype v0.1.0"
+  echo "multiqc_custom_biotype v0.1.1"
  echo ""
  echo "Calculate features percentage for biotype counts"
  echo ""
@@ -481,10 +481,10 @@ 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="2024-10-04T11:21:50Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -620,7 +620,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "multiqc_custom_biotype v0.1.0"
+            echo "multiqc_custom_biotype v0.1.1"
            exit
            ;;
        --biocounts)
@@ -766,7 +766,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/multiqc_custom_biotype:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/multiqc_custom_biotype:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/picard_markduplicates/.config.vsh.yaml
+++ b/target/executable/picard_markduplicates/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "picard_markduplicates"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -186,7 +186,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -207,10 +207,11 @@ build_info:
  output: "target/executable/picard_markduplicates"
  executable: "target/executable/picard_markduplicates/picard_markduplicates"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -232,5 +233,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/picard_markduplicates/picard_markduplicates
+++ b/target/executable/picard_markduplicates/picard_markduplicates
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# picard_markduplicates v0.1.0
+# picard_markduplicates v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "picard_markduplicates v0.1.0"
+  echo "picard_markduplicates v0.1.1"
  echo ""
  echo "Locate and tag duplicate reads in a BAM file"
  echo ""
@@ -494,10 +494,10 @@ 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="2024-10-04T11:21:57Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -633,7 +633,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "picard_markduplicates v0.1.0"
+            echo "picard_markduplicates v0.1.1"
            exit
            ;;
        --bam)
@@ -801,7 +801,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/picard_markduplicates:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/picard_markduplicates:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/prepare_multiqc_input/.config.vsh.yaml
+++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "prepare_multiqc_input"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -396,7 +396,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  entrypoint: []
  cmd: null
@@ -409,10 +409,11 @@ build_info:
  output: "target/executable/prepare_multiqc_input"
  executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -434,5 +435,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/prepare_multiqc_input/prepare_multiqc_input
+++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# prepare_multiqc_input v0.1.0
+# prepare_multiqc_input v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "prepare_multiqc_input v0.1.0"
+  echo "prepare_multiqc_input v0.1.1"
  echo ""
  echo "Prepare directory with all the input files for MultiQC."
  echo ""
@@ -557,10 +557,10 @@ 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="2024-10-04T11:21:53Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -696,7 +696,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "prepare_multiqc_input v0.1.0"
+            echo "prepare_multiqc_input v0.1.1"
            exit
            ;;
        --fail_trimming_multiqc)
@@ -1311,7 +1311,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/prepare_multiqc_input:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/prepare_multiqc_input:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
+++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "preprocess_transcripts_fasta"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -125,7 +125,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  entrypoint: []
  cmd: null
@@ -138,10 +138,11 @@ build_info:
  output: "target/executable/preprocess_transcripts_fasta"
  executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -163,5 +164,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
+++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# preprocess_transcripts_fasta v0.1.0
+# preprocess_transcripts_fasta v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "preprocess_transcripts_fasta v0.1.0"
+  echo "preprocess_transcripts_fasta v0.1.1"
  echo ""
  echo "Process transcripts FASTA if GTF file is GENOCODE format"
  echo ""
@@ -462,10 +462,10 @@ 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="2024-10-04T11:21:52Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -601,7 +601,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "preprocess_transcripts_fasta v0.1.0"
+            echo "preprocess_transcripts_fasta v0.1.1"
            exit
            ;;
        --transcript_fasta)
@@ -714,7 +714,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/preprocess_transcripts_fasta:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/preprocess_transcripts_fasta:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/preseq_lcextrap/.config.vsh.yaml
+++ b/target/executable/preseq_lcextrap/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "preseq_lcextrap"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -146,7 +146,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -191,10 +191,11 @@ build_info:
  output: "target/executable/preseq_lcextrap"
  executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -216,5 +217,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/preseq_lcextrap/preseq_lcextrap
+++ b/target/executable/preseq_lcextrap/preseq_lcextrap
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# preseq_lcextrap v0.1.0
+# preseq_lcextrap v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "preseq_lcextrap v0.1.0"
+  echo "preseq_lcextrap v0.1.1"
  echo ""
  echo "Computing the expected future yield of distinct reads and bounds on the number"
  echo "of total distinct reads in the library and the associated confidence intervals."
@@ -495,10 +495,10 @@ 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="2024-10-04T11:21:42Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -634,7 +634,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "preseq_lcextrap v0.1.0"
+            echo "preseq_lcextrap v0.1.1"
            exit
            ;;
        --input)
@@ -769,7 +769,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/preseq_lcextrap:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/preseq_lcextrap:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/qualimap/.config.vsh.yaml
+++ b/target/executable/qualimap/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "qualimap"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -237,7 +237,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -271,10 +271,11 @@ build_info:
  output: "target/executable/qualimap"
  executable: "target/executable/qualimap/qualimap"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -296,5 +297,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/qualimap/qualimap
+++ b/target/executable/qualimap/qualimap
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# qualimap v0.1.0
+# qualimap v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "qualimap v0.1.0"
+  echo "qualimap v0.1.1"
  echo ""
  echo "RNA-seq QC analysis using the qualimap"
  echo ""
@@ -537,10 +537,10 @@ 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="2024-10-04T11:21:40Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -676,7 +676,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "qualimap v0.1.0"
+            echo "qualimap v0.1.1"
            exit
            ;;
        --input)
@@ -887,7 +887,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/qualimap:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/qualimap:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rsem_calculate_expression"
 namespace: "rsem"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -251,7 +251,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -299,10 +299,11 @@ 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: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -324,5 +325,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rsem_calculate_expression v0.1.0
+# rsem_calculate_expression v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rsem_calculate_expression v0.1.0"
+  echo "rsem_calculate_expression v0.1.1"
  echo ""
  echo "Calculate expression with RSEM."
  echo ""
@@ -542,10 +542,10 @@ 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="2024-10-04T11:21:55Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -681,7 +681,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rsem_calculate_expression v0.1.0"
+            echo "rsem_calculate_expression v0.1.1"
            exit
            ;;
        --id)
@@ -921,7 +921,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rsem/rsem_calculate_expression:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rsem/rsem_calculate_expression:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rsem_merge_counts"
 namespace: "rsem"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -169,7 +169,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  entrypoint: []
  cmd: null
@@ -182,10 +182,11 @@ 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: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -207,5 +208,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
+++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rsem_merge_counts v0.1.0
+# rsem_merge_counts v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rsem_merge_counts v0.1.0"
+  echo "rsem_merge_counts v0.1.1"
  echo ""
  echo "Merge the transcript quantification results obtained from rsem"
  echo "calculate-expression across all samples."
@@ -483,10 +483,10 @@ 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="2024-10-04T11:21:54Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -622,7 +622,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rsem_merge_counts v0.1.0"
+            echo "rsem_merge_counts v0.1.1"
            exit
            ;;
        --counts_gene)
@@ -779,7 +779,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rsem/rsem_merge_counts:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rsem/rsem_merge_counts:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rseqc_bamstat"
 namespace: "rseqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -140,7 +140,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -163,10 +163,11 @@ build_info:
  output: "target/executable/rseqc/rseqc_bamstat"
  executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -188,5 +189,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
+++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rseqc_bamstat v0.1.0
+# rseqc_bamstat v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rseqc_bamstat v0.1.0"
+  echo "rseqc_bamstat v0.1.1"
  echo ""
  echo "Generate statistics from a bam file."
  echo ""
@@ -477,10 +477,10 @@ 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="2024-10-04T11:21:52Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -616,7 +616,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rseqc_bamstat v0.1.0"
+            echo "rseqc_bamstat v0.1.1"
            exit
            ;;
        --input)
@@ -740,7 +740,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_bamstat:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_bamstat:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rseqc_inferexperiment"
 namespace: "rseqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -163,7 +163,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -186,10 +186,11 @@ build_info:
  output: "target/executable/rseqc/rseqc_inferexperiment"
  executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -211,5 +212,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
+++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rseqc_inferexperiment v0.1.0
+# rseqc_inferexperiment v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rseqc_inferexperiment v0.1.0"
+  echo "rseqc_inferexperiment v0.1.1"
  echo ""
  echo "Infer strandedness from sequencing reads"
  echo ""
@@ -487,10 +487,10 @@ 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="2024-10-04T11:21:50Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rseqc_inferexperiment v0.1.0"
+            echo "rseqc_inferexperiment v0.1.1"
            exit
            ;;
        --input)
@@ -772,7 +772,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_inferexperiment:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_inferexperiment:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rseqc_innerdistance"
 namespace: "rseqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -248,7 +248,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -272,10 +272,11 @@ build_info:
  output: "target/executable/rseqc/rseqc_innerdistance"
  executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -297,5 +298,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
+++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rseqc_innerdistance v0.1.0
+# rseqc_innerdistance v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rseqc_innerdistance v0.1.0"
+  echo "rseqc_innerdistance v0.1.1"
  echo ""
  echo "Calculate inner distance between read pairs."
  echo ""
@@ -529,10 +529,10 @@ 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="2024-10-04T11:21:52Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -668,7 +668,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rseqc_innerdistance v0.1.0"
+            echo "rseqc_innerdistance v0.1.1"
            exit
            ;;
        --input)
@@ -891,7 +891,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_innerdistance:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_innerdistance:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rseqc_junctionannotation"
 namespace: "rseqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -236,7 +236,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -260,10 +260,11 @@ build_info:
  output: "target/executable/rseqc/rseqc_junctionannotation"
  executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -285,5 +286,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
+++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rseqc_junctionannotation v0.1.0
+# rseqc_junctionannotation v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rseqc_junctionannotation v0.1.0"
+  echo "rseqc_junctionannotation v0.1.1"
  echo ""
  echo "Compare detected splice junctions to reference gene model."
  echo ""
@@ -519,10 +519,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:51Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:30Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -658,7 +658,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rseqc_junctionannotation v0.1.0"
+            echo "rseqc_junctionannotation v0.1.1"
            exit
            ;;
        --input)
@@ -870,7 +870,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_junctionannotation:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_junctionannotation:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rseqc_junctionsaturation"
 namespace: "rseqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -225,7 +225,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -249,10 +249,11 @@ build_info:
  output: "target/executable/rseqc/rseqc_junctionsaturation"
  executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -274,5 +275,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
+++ b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rseqc_junctionsaturation v0.1.0
+# rseqc_junctionsaturation v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rseqc_junctionsaturation v0.1.0"
+  echo "rseqc_junctionsaturation v0.1.1"
  echo ""
  echo "Compare detected splice junctions to reference gene model."
  echo ""
@@ -522,10 +522,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:51Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -661,7 +661,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rseqc_junctionsaturation v0.1.0"
+            echo "rseqc_junctionsaturation v0.1.1"
            exit
            ;;
        --input)
@@ -862,7 +862,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_junctionsaturation:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_junctionsaturation:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rseqc_readdistribution"
 namespace: "rseqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -139,7 +139,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -162,10 +162,11 @@ build_info:
  output: "target/executable/rseqc/rseqc_readdistribution"
  executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -187,5 +188,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
+++ b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rseqc_readdistribution v0.1.0
+# rseqc_readdistribution v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rseqc_readdistribution v0.1.0"
+  echo "rseqc_readdistribution v0.1.1"
  echo ""
  echo "Calculate how mapped reads are distributed over genomic features."
  echo ""
@@ -474,10 +474,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:52Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -613,7 +613,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rseqc_readdistribution v0.1.0"
+            echo "rseqc_readdistribution v0.1.1"
            exit
            ;;
        --input)
@@ -737,7 +737,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_readdistribution:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_readdistribution:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rseqc_readduplication"
 namespace: "rseqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -187,7 +187,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -211,10 +211,11 @@ build_info:
  output: "target/executable/rseqc/rseqc_readduplication"
  executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -236,5 +237,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
+++ b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rseqc_readduplication v0.1.0
+# rseqc_readduplication v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rseqc_readduplication v0.1.0"
+  echo "rseqc_readduplication v0.1.1"
  echo ""
  echo "Calculate read duplication rate."
  echo ""
@@ -499,10 +499,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:50Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -638,7 +638,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rseqc_readduplication v0.1.0"
+            echo "rseqc_readduplication v0.1.1"
            exit
            ;;
        --input)
@@ -806,7 +806,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_readduplication:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_readduplication:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rseqc_tin"
 namespace: "rseqc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -193,7 +193,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -214,10 +214,11 @@ build_info:
  output: "target/executable/rseqc/rseqc_tin"
  executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -239,5 +240,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/rseqc/rseqc_tin/rseqc_tin
+++ b/target/executable/rseqc/rseqc_tin/rseqc_tin
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rseqc_tin v0.1.0
+# rseqc_tin v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rseqc_tin v0.1.0"
+  echo "rseqc_tin v0.1.1"
  echo ""
  echo "Calculte TIN (transcript integrity number) from RNA-seq reads"
  echo ""
@@ -501,10 +501,10 @@ RUN apt-get update && \
 RUN pip3 install RSeQC

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_tin"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:50Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -640,7 +640,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rseqc_tin v0.1.0"
+            echo "rseqc_tin v0.1.1"
            exit
            ;;
        --bam_input)
@@ -813,7 +813,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rseqc/rseqc_tin:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/rseqc/rseqc_tin:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/sortmerna/.config.vsh.yaml
+++ b/target/executable/sortmerna/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "sortmerna"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -179,7 +179,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -198,10 +198,11 @@ build_info:
  output: "target/executable/sortmerna"
  executable: "target/executable/sortmerna/sortmerna"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -223,5 +224,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/sortmerna/sortmerna
+++ b/target/executable/sortmerna/sortmerna
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# sortmerna v0.1.0
+# sortmerna v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "sortmerna v0.1.0"
+  echo "sortmerna v0.1.1"
  echo ""
  echo "Local sequence alignment tool for filtering, mapping and clustering. The main"
  echo "application of SortMeRNA is filtering rRNA from metatranscriptomic data."
@@ -492,10 +492,10 @@ wget --no-check-certificate https://github.com/sortmerna/sortmerna/releases/down
 bash sortmerna-4.3.6-Linux.sh --skip-license

 LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:57Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:25Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "sortmerna v0.1.0"
+            echo "sortmerna v0.1.1"
            exit
            ;;
        --paired)
@@ -794,7 +794,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/sortmerna:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/sortmerna:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/stringtie/.config.vsh.yaml
+++ b/target/executable/stringtie/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "stringtie"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -196,7 +196,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -216,10 +216,11 @@ build_info:
  output: "target/executable/stringtie"
  executable: "target/executable/stringtie/stringtie"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -241,5 +242,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/stringtie/stringtie
+++ b/target/executable/stringtie/stringtie
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# stringtie v0.1.0
+# stringtie v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "stringtie v0.1.0"
+  echo "stringtie v0.1.1"
  echo ""
  echo "Transcript assembly and quantification for RNA-Seq"
  echo ""
@@ -496,10 +496,10 @@ tar -xzf stringtie-2.2.1.Linux_x86_64.tar.gz && \
 cp stringtie-2.2.1.Linux_x86_64/stringtie /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component stringtie"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:54Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "stringtie v0.1.0"
+            echo "stringtie v0.1.1"
            exit
            ;;
        --strandedness)
@@ -825,7 +825,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/stringtie:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/stringtie:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/summarizedexperiment/.config.vsh.yaml
+++ b/target/executable/summarizedexperiment/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "summarizedexperiment"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -175,7 +175,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -199,10 +199,11 @@ build_info:
  output: "target/executable/summarizedexperiment"
  executable: "target/executable/summarizedexperiment/summarizedexperiment"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -224,5 +225,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/summarizedexperiment/summarizedexperiment
+++ b/target/executable/summarizedexperiment/summarizedexperiment
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# summarizedexperiment v0.1.0
+# summarizedexperiment v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "summarizedexperiment v0.1.0"
+  echo "summarizedexperiment v0.1.1"
  echo ""
  echo "Create SummarizedExperiment object from Salmon counts"
  echo ""
@@ -487,10 +487,10 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
  Rscript -e 'if (!requireNamespace("tximeta", quietly = TRUE)) BiocManager::install("tximeta")'

 LABEL org.opencontainers.image.description="Companion container for running component summarizedexperiment"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:58Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "summarizedexperiment v0.1.0"
+            echo "summarizedexperiment v0.1.1"
            exit
            ;;
        --tpm_gene)
@@ -805,7 +805,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/summarizedexperiment:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/summarizedexperiment:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/trimgalore/.config.vsh.yaml
+++ b/target/executable/trimgalore/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "trimgalore"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -770,7 +770,7 @@ engines:
  id: "docker"
  image: "quay.io/biocontainers/trim-galore:0.6.9--hdfd78af_0"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -788,10 +788,11 @@ build_info:
  output: "target/executable/trimgalore"
  executable: "target/executable/trimgalore/trimgalore"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -813,5 +814,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/trimgalore/trimgalore
+++ b/target/executable/trimgalore/trimgalore
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# trimgalore v0.1.0
+# trimgalore v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "trimgalore v0.1.0"
+  echo "trimgalore v0.1.1"
  echo ""
  echo "A wrapper tool around Cutadapt and FastQC to consistently apply quality and"
  echo "adapter trimming to FastQ files."
@@ -858,10 +858,10 @@ ENTRYPOINT []
 RUN echo "TrimGalore: `trim_galore --version | sed -n 's/.*version\s\+\([0-9]\+\.[0-9]\+\.[0-9]\+\).*/\1/p'`" > /var/software_versions.txt

 LABEL org.opencontainers.image.description="Companion container for running component trimgalore"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:56Z"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
 LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -997,7 +997,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "trimgalore v0.1.0"
+            echo "trimgalore v0.1.1"
            exit
            ;;
        --input)
@@ -1725,7 +1725,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/trimgalore:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/trimgalore:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/tx2gene/.config.vsh.yaml
+++ b/target/executable/tx2gene/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "tx2gene"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -170,7 +170,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -192,10 +192,11 @@ build_info:
  output: "target/executable/tx2gene"
  executable: "target/executable/tx2gene/tx2gene"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -217,5 +218,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/tx2gene/tx2gene
+++ b/target/executable/tx2gene/tx2gene
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# tx2gene v0.1.0
+# tx2gene v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "tx2gene v0.1.0"
+  echo "tx2gene v0.1.1"
  echo ""
  echo "Get transcript id (tx) to gene names for tximport"
  echo ""
@@ -487,10 +487,10 @@ RUN apt-get update && \
 RUN pip install --upgrade pip

 LABEL org.opencontainers.image.description="Companion container for running component tx2gene"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:53Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:26Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -626,7 +626,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "tx2gene v0.1.0"
+            echo "tx2gene v0.1.1"
            exit
            ;;
        --quant_results)
@@ -800,7 +800,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/tx2gene:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/tx2gene:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/tximport/.config.vsh.yaml
+++ b/target/executable/tximport/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "tximport"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -218,7 +218,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -247,10 +247,11 @@ build_info:
  output: "target/executable/tximport"
  executable: "target/executable/tximport/tximport"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -272,5 +273,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/tximport/tximport
+++ b/target/executable/tximport/tximport
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# tximport v0.1.0
+# tximport v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "tximport v0.1.0"
+  echo "tximport v0.1.1"
  echo ""
  echo "Get dataframe linking transcript ID, gene ID, and gene name"
  echo ""
@@ -508,10 +508,10 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
  Rscript -e 'remotes::install_cran(c("jsonlite"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component tximport"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:48Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:24Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -647,7 +647,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "tximport v0.1.0"
+            echo "tximport v0.1.1"
            exit
            ;;
        --quant_results)
@@ -865,7 +865,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/tximport:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/tximport:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/ucsc/bedclip/.config.vsh.yaml
+++ b/target/executable/ucsc/bedclip/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bedclip"
 namespace: "ucsc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -141,7 +141,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -164,10 +164,11 @@ build_info:
  output: "target/executable/ucsc/bedclip"
  executable: "target/executable/ucsc/bedclip/bedclip"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -189,5 +190,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/ucsc/bedclip/bedclip
+++ b/target/executable/ucsc/bedclip/bedclip
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# bedclip v0.1.0
+# bedclip v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bedclip v0.1.0"
+  echo "bedclip v0.1.1"
  echo ""
  echo "Remove lines from bed file that refer to off-chromosome locations"
  echo ""
@@ -473,10 +473,10 @@ RUN apt-get update && \
 RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedClip /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component ucsc bedclip"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:49Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "bedclip v0.1.0"
+            echo "bedclip v0.1.1"
            exit
            ;;
        --input_bedgraph)
@@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/ucsc/bedclip:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/ucsc/bedclip:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
+++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "bedgraphtobigwig"
 namespace: "ucsc"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -141,7 +141,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -164,10 +164,11 @@ build_info:
  output: "target/executable/ucsc/bedgraphtobigwig"
  executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -189,5 +190,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
+++ b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# bedgraphtobigwig v0.1.0
+# bedgraphtobigwig v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "bedgraphtobigwig v0.1.0"
+  echo "bedgraphtobigwig v0.1.1"
  echo ""
  echo "Convert a bedGraph file to bigWig format"
  echo ""
@@ -473,10 +473,10 @@ RUN apt-get update && \
 RUN rsync -aP rsync://hgdownload.soe.ucsc.edu/genome/admin/exe/linux.x86_64/bedGraphToBigWig /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component ucsc bedgraphtobigwig"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:49Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:29Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "bedgraphtobigwig v0.1.0"
+            echo "bedgraphtobigwig v0.1.1"
            exit
            ;;
        --bedgraph)
@@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/ucsc/bedgraphtobigwig:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/ucsc/bedgraphtobigwig:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml
+++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "umitools_dedup"
 namespace: "umitools"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -172,7 +172,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -195,10 +195,11 @@ build_info:
  output: "target/executable/umitools/umitools_dedup"
  executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -220,5 +221,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/umitools/umitools_dedup/umitools_dedup
+++ b/target/executable/umitools/umitools_dedup/umitools_dedup
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# umitools_dedup v0.1.0
+# umitools_dedup v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "umitools_dedup v0.1.0"
+  echo "umitools_dedup v0.1.1"
  echo ""
  echo "Deduplicate reads based on the mapping co-ordinate and the UMI attached to the"
  echo "read."
@@ -489,10 +489,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "umi_tools"

 LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_dedup"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:56Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -628,7 +628,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "umitools_dedup v0.1.0"
+            echo "umitools_dedup v0.1.1"
            exit
            ;;
        --paired)
@@ -785,7 +785,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools/umitools_dedup:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools/umitools_dedup:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/umitools/umitools_extract/.config.vsh.yaml
+++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "umitools_extract"
 namespace: "umitools"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -230,7 +230,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -253,10 +253,11 @@ build_info:
  output: "target/executable/umitools/umitools_extract"
  executable: "target/executable/umitools/umitools_extract/umitools_extract"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -278,5 +279,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/umitools/umitools_extract/umitools_extract
+++ b/target/executable/umitools/umitools_extract/umitools_extract
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# umitools_extract v0.1.0
+# umitools_extract v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "umitools_extract v0.1.0"
+  echo "umitools_extract v0.1.1"
  echo ""
  echo "UMI-tools contains tools for dealing with Unique Molecular Identifiers"
  echo "(UMIs)/Random Molecular Tags (RMTs) and single cell RNA-Seq cell barcodes. See"
@@ -521,10 +521,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "umi_tools"

 LABEL org.opencontainers.image.description="Companion container for running component umitools umitools_extract"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:56Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:28Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -660,7 +660,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "umitools_extract v0.1.0"
+            echo "umitools_extract v0.1.1"
            exit
            ;;
        --paired)
@@ -862,7 +862,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools/umitools_extract:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools/umitools_extract:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/umitools_prepareforquant/.config.vsh.yaml
+++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "umitools_prepareforquant"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -132,7 +132,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "apt"
@@ -156,10 +156,11 @@ build_info:
  output: "target/executable/umitools_prepareforquant"
  executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -181,5 +182,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/umitools_prepareforquant/umitools_prepareforquant
+++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# umitools_prepareforquant v0.1.0
+# umitools_prepareforquant v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "umitools_prepareforquant v0.1.0"
+  echo "umitools_prepareforquant v0.1.1"
  echo ""
  echo "Fix paired-end reads in name sorted BAM file to prepare for salmon"
  echo "quantification"
@@ -473,10 +473,10 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "umi_tools" "pysam"

 LABEL org.opencontainers.image.description="Companion container for running component umitools_prepareforquant"
-LABEL org.opencontainers.image.created="2024-10-04T11:21:58Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-LABEL org.opencontainers.image.version="v0.1.0"
+LABEL org.opencontainers.image.created="2024-10-17T16:18:27Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="0f49a3ff62687a68af3e43608224d922a5fad518"
+LABEL org.opencontainers.image.version="v0.1.1"

 VIASHDOCKER
  fi
@@ -612,7 +612,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "umitools_prepareforquant v0.1.0"
+            echo "umitools_prepareforquant v0.1.1"
            exit
            ;;
        --bam)
@@ -736,7 +736,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then

  # determine docker image id
  if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/umitools_prepareforquant:v0.1.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/rnaseq/umitools_prepareforquant:v0.1.1'
  fi

  # print dockerfile
--- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
+++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "genome_alignment_and_quant"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -603,8 +603,8 @@ build_info:
  output: "target/executable/workflows/genome_alignment_and_quant"
  executable: "target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads"
  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
@@ -617,7 +617,8 @@ build_info:
  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
  - "target/nextflow/rsem/rsem_calculate_expression"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -639,5 +640,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
+++ b/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# genome_alignment_and_quant v0.1.0
+# genome_alignment_and_quant v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "genome_alignment_and_quant v0.1.0"
+  echo "genome_alignment_and_quant v0.1.1"
  echo ""
  echo "A viash sub-workflow for genome alignment and quantification stage of"
  echo "nf-core/rnaseq pipeline."
@@ -401,7 +401,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "genome_alignment_and_quant v0.1.0"
+            echo "genome_alignment_and_quant v0.1.1"
            exit
            ;;
        --id)
--- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml
+++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "merge_quant_results"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -278,14 +278,15 @@ build_info:
  output: "target/executable/workflows/merge_quant_results"
  executable: "target/executable/workflows/merge_quant_results/merge_quant_results"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/tx2gene"
  - "target/nextflow/tximport"
  - "target/nextflow/summarizedexperiment"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -307,5 +308,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/workflows/merge_quant_results/merge_quant_results
+++ b/target/executable/workflows/merge_quant_results/merge_quant_results
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# merge_quant_results v0.1.0
+# merge_quant_results v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "merge_quant_results v0.1.0"
+  echo "merge_quant_results v0.1.1"
  echo ""
  echo "A sub-workflow to merge the counts obtained from salmon quant across all"
  echo "samples."
@@ -267,7 +267,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "merge_quant_results v0.1.0"
+            echo "merge_quant_results v0.1.1"
            exit
            ;;
        --salmon_quant_results)
--- a/target/executable/workflows/post_processing/.config.vsh.yaml
+++ b/target/executable/workflows/post_processing/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "post_processing"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -486,8 +486,8 @@ build_info:
  output: "target/executable/workflows/post_processing"
  executable: "target/executable/workflows/post_processing/post_processing"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/picard_markduplicates"
  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
@@ -500,7 +500,8 @@ build_info:
  - "target/nextflow/ucsc/bedclip"
  - "target/nextflow/ucsc/bedgraphtobigwig"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -522,5 +523,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/workflows/post_processing/post_processing
+++ b/target/executable/workflows/post_processing/post_processing
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# post_processing v0.1.0
+# post_processing v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "post_processing v0.1.0"
+  echo "post_processing v0.1.1"
  echo ""
  echo "A viash sub-workflow for the post-processing stage of nf-core/rnaseq pipeline."
  echo ""
@@ -350,7 +350,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "post_processing v0.1.0"
+            echo "post_processing v0.1.1"
            exit
            ;;
        --id)
--- a/target/executable/workflows/pre_processing/.config.vsh.yaml
+++ b/target/executable/workflows/pre_processing/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "pre_processing"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Inputs"
  arguments:
@@ -673,8 +673,8 @@ build_info:
  output: "target/executable/workflows/pre_processing"
  executable: "target/executable/workflows/pre_processing/pre_processing"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/fastqc"
  - "target/nextflow/umitools/umitools_extract"
@@ -686,7 +686,8 @@ build_info:
  - "target/nextflow/fq_subsample"
  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -708,5 +709,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/workflows/pre_processing/pre_processing
+++ b/target/executable/workflows/pre_processing/pre_processing
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# pre_processing v0.1.0
+# pre_processing v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "pre_processing v0.1.0"
+  echo "pre_processing v0.1.1"
  echo ""
  echo "A subworkflow for the pre-processing stage of the nf-core/rnaseq pipeline."
  echo ""
@@ -453,7 +453,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "pre_processing v0.1.0"
+            echo "pre_processing v0.1.1"
            exit
            ;;
        --id)
--- a/target/executable/workflows/prepare_genome/.config.vsh.yaml
+++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "prepare_genome"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -496,8 +496,8 @@ build_info:
  output: "target/executable/workflows/prepare_genome"
  executable: "target/executable/workflows/prepare_genome/prepare_genome"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/gunzip"
  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"
@@ -513,7 +513,8 @@ build_info:
  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index"
  - "target/nextflow/kallisto/kallisto_index"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -535,5 +536,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/workflows/prepare_genome/prepare_genome
+++ b/target/executable/workflows/prepare_genome/prepare_genome
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# prepare_genome v0.1.0
+# prepare_genome v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "prepare_genome v0.1.0"
+  echo "prepare_genome v0.1.1"
  echo ""
  echo "A subworkflow for preparing all the required genome references"
  echo ""
@@ -354,7 +354,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "prepare_genome v0.1.0"
+            echo "prepare_genome v0.1.1"
            exit
            ;;
        --fasta)
--- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
+++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "pseudo_alignment_and_quant"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -283,13 +283,14 @@ build_info:
  output: "target/executable/workflows/pseudo_alignment_and_quant"
  executable: "target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
  - "target/nextflow/kallisto/kallisto_quant"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -311,5 +312,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant
+++ b/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# pseudo_alignment_and_quant v0.1.0
+# pseudo_alignment_and_quant v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "pseudo_alignment_and_quant v0.1.0"
+  echo "pseudo_alignment_and_quant v0.1.1"
  echo ""
  echo "A viash sub-workflow for pseudo alignment and quantification stage of"
  echo "nf-core/rnaseq pipeline."
@@ -279,7 +279,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "pseudo_alignment_and_quant v0.1.0"
+            echo "pseudo_alignment_and_quant v0.1.1"
            exit
            ;;
        --id)
--- a/target/executable/workflows/quality_control/.config.vsh.yaml
+++ b/target/executable/workflows/quality_control/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "quality_control"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -1596,8 +1596,8 @@ build_info:
  output: "target/executable/workflows/quality_control"
  executable: "target/executable/workflows/quality_control/quality_control"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/rseqc/rseqc_bamstat"
  - "target/nextflow/rseqc/rseqc_inferexperiment"
@@ -1618,7 +1618,8 @@ build_info:
  - "target/nextflow/rsem/rsem_merge_counts"
  - "target/nextflow/workflows/merge_quant_results"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -1640,5 +1641,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/workflows/quality_control/quality_control
+++ b/target/executable/workflows/quality_control/quality_control
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# quality_control v0.1.0
+# quality_control v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "quality_control v0.1.0"
+  echo "quality_control v0.1.1"
  echo ""
  echo "A subworkflow for the final quality control stage of the nf-core/rnaseq"
  echo "pipeline."
@@ -834,7 +834,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "quality_control v0.1.0"
+            echo "quality_control v0.1.1"
            exit
            ;;
        --id)
--- a/target/executable/workflows/rnaseq/.config.vsh.yaml
+++ b/target/executable/workflows/rnaseq/.config.vsh.yaml
@@ -1,6 +1,6 @@
 name: "rnaseq"
 namespace: "workflows"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -2117,8 +2117,8 @@ build_info:
  output: "target/executable/workflows/rnaseq"
  executable: "target/executable/workflows/rnaseq/rnaseq"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/workflows/prepare_genome"
  - "target/nextflow/cat_fastq"
@@ -2128,7 +2128,8 @@ build_info:
  - "target/nextflow/workflows/post_processing"
  - "target/nextflow/workflows/quality_control"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -2150,5 +2151,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/target/executable/workflows/rnaseq/rnaseq
+++ b/target/executable/workflows/rnaseq/rnaseq
@@ -1,6 +1,6 @@
 #!/usr/bin/env bash

-# rnaseq v0.1.0
+# rnaseq v0.1.1
 # 
 # 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
@@ -171,7 +171,7 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"

 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "rnaseq v0.1.0"
+  echo "rnaseq v0.1.1"
  echo ""
  echo "A viash workflow for the nf-core/rnaseq pipeline."
  echo ""
@@ -1093,7 +1093,7 @@ while [[ $# -gt 0 ]]; do
            shift 1
            ;;
        --version)
-            echo "rnaseq v0.1.0"
+            echo "rnaseq v0.1.1"
            exit
            ;;
        --id)
--- a/target/nextflow/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/nextflow/bbmap_bbsplit/.config.vsh.yaml
@@ -1,5 +1,5 @@
 name: "bbmap_bbsplit"
-version: "v0.1.0"
+version: "v0.1.1"
 argument_groups:
 - name: "Input"
  arguments:
@@ -219,7 +219,7 @@ engines:
  id: "docker"
  image: "ubuntu:22.04"
  target_registry: "images.viash-hub.com"
-  target_tag: "v0.1.0"
+  target_tag: "v0.1.1"
  namespace_separator: "/"
  setup:
  - type: "docker"
@@ -238,10 +238,11 @@ build_info:
  output: "target/nextflow/bbmap_bbsplit"
  executable: "target/nextflow/bbmap_bbsplit/main.nf"
  viash_version: "0.9.0"
-  git_commit: "ed1f6955d07b7dc1f4a606fc35a1176f7d70a6fa"
-  git_remote: "https://x-access-token:ghs_tXtyBoqiv8A2hCsnUFe4lEgzrzh9764dBmxo@github.com/viash-hub/rnaseq"
+  git_commit: "0f49a3ff62687a68af3e43608224d922a5fad518"
+  git_remote: "https://x-access-token:ghs_uqSddS0Zy4kGjO3RZOSoZ4S61aL57936NNSr@github.com/viash-hub/rnaseq"
 package_config:
-  version: "v0.1.0"
+  name: "rnaseq"
+  version: "v0.1.1"
  info:
    test_resources:
    - path: "gs://viash-hub-test-data/rnaseq/v1"
@@ -263,5 +264,5 @@ package_config:
    \ := '$id'\n"
  - ".engines += { type: \"native\" }"
  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.1'"
  organization: "vsh"
--- a/Show More
+++ b/Show More