Build branch main with version main (cb9b328)

Build pipeline: viash-hub.rnaseq.main-mf5kg Source commit: cb9b328834 Source message: Update pointers to biobox and craftbox
2024-09-13 11:32:59 +00:00
parent 1ebb61f1e8
commit 92b5a42360
284 changed files with 1310 additions and 29225 deletions
--- a/target/executable/bbmap_bbsplit/.config.vsh.yaml
+++ b/target/executable/bbmap_bbsplit/.config.vsh.yaml
@@ -229,7 +229,7 @@ build_info:
  output: "target/executable/bbmap_bbsplit"
  executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/bbmap_bbsplit/bbmap_bbsplit
+++ b/target/executable/bbmap_bbsplit/bbmap_bbsplit
@@ -506,9 +506,9 @@ tar xzf BBMap_39.01.tar.gz && \
 cp -r bbmap/* /usr/local/bin

 LABEL org.opencontainers.image.description="Companion container for running component bbmap_bbsplit"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:49Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:10Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools_genomecov/.config.vsh.yaml
+++ b/target/executable/bedtools_genomecov/.config.vsh.yaml
@@ -169,7 +169,7 @@ build_info:
  output: "target/executable/bedtools_genomecov"
  executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/bedtools_genomecov/bedtools_genomecov
+++ b/target/executable/bedtools_genomecov/bedtools_genomecov
@@ -481,9 +481,9 @@ mv bedtools.static /usr/local/bin/bedtools && \
 chmod a+x /usr/local/bin/bedtools

 LABEL org.opencontainers.image.description="Companion container for running component bedtools_genomecov"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:49Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cat_additional_fasta/.config.vsh.yaml
+++ b/target/executable/cat_additional_fasta/.config.vsh.yaml
@@ -173,7 +173,7 @@ build_info:
  output: "target/executable/cat_additional_fasta"
  executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/cat_additional_fasta/cat_additional_fasta
+++ b/target/executable/cat_additional_fasta/cat_additional_fasta
@@ -480,9 +480,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_additional_fasta"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:57Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cat_fastq/.config.vsh.yaml
+++ b/target/executable/cat_fastq/.config.vsh.yaml
@@ -160,7 +160,7 @@ build_info:
  output: "target/executable/cat_fastq"
  executable: "target/executable/cat_fastq/cat_fastq"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/cat_fastq/cat_fastq
+++ b/target/executable/cat_fastq/cat_fastq
@@ -472,9 +472,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component cat_fastq"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:57Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/deseq2_qc/.config.vsh.yaml
+++ b/target/executable/deseq2_qc/.config.vsh.yaml
@@ -228,7 +228,7 @@ build_info:
  output: "target/executable/deseq2_qc"
  executable: "target/executable/deseq2_qc/deseq2_qc"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/deseq2_qc/deseq2_qc
+++ b/target/executable/deseq2_qc/deseq2_qc
@@ -502,9 +502,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
  Rscript -e 'remotes::install_url(c("https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:07Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/dupradar/.config.vsh.yaml
+++ b/target/executable/dupradar/.config.vsh.yaml
@@ -257,7 +257,7 @@ build_info:
  output: "target/executable/dupradar"
  executable: "target/executable/dupradar/dupradar"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/dupradar/dupradar
+++ b/target/executable/dupradar/dupradar
@@ -520,9 +520,9 @@ RUN Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.pa
  Rscript -e 'if (!requireNamespace("dupRadar", quietly = TRUE)) BiocManager::install("dupRadar")'

 LABEL org.opencontainers.image.description="Companion container for running component dupradar"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:58Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:19Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/target/executable/fastqc/.config.vsh.yaml
@@ -189,7 +189,7 @@ build_info:
  output: "target/executable/fastqc"
  executable: "target/executable/fastqc/fastqc"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/fastqc/fastqc
+++ b/target/executable/fastqc/fastqc
@@ -490,9 +490,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component fastqc"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:50Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/target/executable/fq_subsample/.config.vsh.yaml
@@ -168,7 +168,7 @@ build_info:
  output: "target/executable/fq_subsample"
  executable: "target/executable/fq_subsample/fq_subsample"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/fq_subsample/fq_subsample
+++ b/target/executable/fq_subsample/fq_subsample
@@ -485,9 +485,9 @@ cargo install --locked --path . && \
 mv /usr/local/fq/target/release/fq /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:50Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/getchromsizes/.config.vsh.yaml
+++ b/target/executable/getchromsizes/.config.vsh.yaml
@@ -158,7 +158,7 @@ build_info:
  output: "target/executable/getchromsizes"
  executable: "target/executable/getchromsizes/getchromsizes"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/getchromsizes/getchromsizes
+++ b/target/executable/getchromsizes/getchromsizes
@@ -480,9 +480,9 @@ make && \
 make install

 LABEL org.opencontainers.image.description="Companion container for running component getchromsizes"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:51Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gtf2bed/.config.vsh.yaml
+++ b/target/executable/gtf2bed/.config.vsh.yaml
@@ -136,7 +136,7 @@ build_info:
  output: "target/executable/gtf2bed"
  executable: "target/executable/gtf2bed/gtf2bed"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/gtf2bed/gtf2bed
+++ b/target/executable/gtf2bed/gtf2bed
@@ -466,9 +466,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component gtf2bed"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:02Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gtf_filter/.config.vsh.yaml
+++ b/target/executable/gtf_filter/.config.vsh.yaml
@@ -146,7 +146,7 @@ build_info:
  output: "target/executable/gtf_filter"
  executable: "target/executable/gtf_filter/gtf_filter"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/gtf_filter/gtf_filter
+++ b/target/executable/gtf_filter/gtf_filter
@@ -470,9 +470,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component gtf_filter"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:05Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gunzip/.config.vsh.yaml
+++ b/target/executable/gunzip/.config.vsh.yaml
@@ -135,7 +135,7 @@ build_info:
  output: "target/executable/gunzip"
  executable: "target/executable/gunzip/gunzip"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/gunzip/gunzip
+++ b/target/executable/gunzip/gunzip
@@ -466,9 +466,9 @@ RUN apt-get update && \
  rm -rf /var/lib/apt/lists/*

 LABEL org.opencontainers.image.description="Companion container for running component gunzip"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:51Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_index/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_index/.config.vsh.yaml
@@ -146,7 +146,7 @@ build_info:
  output: "target/executable/kallisto/kallisto_index"
  executable: "target/executable/kallisto/kallisto_index/kallisto_index"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/kallisto/kallisto_index/kallisto_index
+++ b/target/executable/kallisto/kallisto_index/kallisto_index
@@ -471,9 +471,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_index"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:04Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
+++ b/target/executable/kallisto/kallisto_quant/.config.vsh.yaml
@@ -244,7 +244,7 @@ build_info:
  output: "target/executable/kallisto/kallisto_quant"
  executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/kallisto/kallisto_quant/kallisto_quant
+++ b/target/executable/kallisto/kallisto_quant/kallisto_quant
@@ -515,9 +515,9 @@ tar -xzf kallisto_linux-v0.50.1.tar.gz && \
 mv kallisto/kallisto /usr/local/bin/

 LABEL org.opencontainers.image.description="Companion container for running component kallisto kallisto_quant"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:03Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/multiqc_custom_biotype/.config.vsh.yaml
+++ b/target/executable/multiqc_custom_biotype/.config.vsh.yaml
@@ -161,7 +161,7 @@ build_info:
  output: "target/executable/multiqc_custom_biotype"
  executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
+++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
@@ -481,9 +481,9 @@ RUN apt-get update && \
 RUN pip install --upgrade pip

 LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:58Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/picard_markduplicates/.config.vsh.yaml
+++ b/target/executable/picard_markduplicates/.config.vsh.yaml
@@ -198,7 +198,7 @@ build_info:
  output: "target/executable/picard_markduplicates"
  executable: "target/executable/picard_markduplicates/picard_markduplicates"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/picard_markduplicates/picard_markduplicates
+++ b/target/executable/picard_markduplicates/picard_markduplicates
@@ -494,9 +494,9 @@ wget --no-check-certificate https://github.com/broadinstitute/picard/releases/do
 mv picard.jar /usr/local/bin 

 LABEL org.opencontainers.image.description="Companion container for running component picard_markduplicates"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:06Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/prepare_multiqc_input/.config.vsh.yaml
+++ b/target/executable/prepare_multiqc_input/.config.vsh.yaml
@@ -400,7 +400,7 @@ build_info:
  output: "target/executable/prepare_multiqc_input"
  executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/prepare_multiqc_input/prepare_multiqc_input
+++ b/target/executable/prepare_multiqc_input/prepare_multiqc_input
@@ -557,9 +557,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component prepare_multiqc_input"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:01Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
+++ b/target/executable/preprocess_transcripts_fasta/.config.vsh.yaml
@@ -129,7 +129,7 @@ build_info:
  output: "target/executable/preprocess_transcripts_fasta"
  executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
+++ b/target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta
@@ -462,9 +462,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component preprocess_transcripts_fasta"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:01Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/preseq_lcextrap/.config.vsh.yaml
+++ b/target/executable/preseq_lcextrap/.config.vsh.yaml
@@ -182,7 +182,7 @@ build_info:
  output: "target/executable/preseq_lcextrap"
  executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/preseq_lcextrap/preseq_lcextrap
+++ b/target/executable/preseq_lcextrap/preseq_lcextrap
@@ -495,9 +495,9 @@ mkdir build && cd build && \
 make && make install && make HAVE_HTSLIB=1 all 

 LABEL org.opencontainers.image.description="Companion container for running component preseq_lcextrap"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:52Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:12Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/.config.vsh.yaml
+++ b/target/executable/qualimap/.config.vsh.yaml
@@ -262,7 +262,7 @@ build_info:
  output: "target/executable/qualimap"
  executable: "target/executable/qualimap/qualimap"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/qualimap/qualimap
+++ b/target/executable/qualimap/qualimap
@@ -537,9 +537,9 @@ RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packag
  Rscript -e 'remotes::install_cran(c("optparse"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component qualimap"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:50Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:11Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml
@@ -299,7 +299,7 @@ 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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
@@ -545,9 +545,9 @@ echo 'export PATH=$PATH:/usr/local/bin' >> ~/.bashrc && \
 /bin/bash -c "source /etc/profile && source ~/.bashrc && echo $PATH && which STAR"

 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_calculate_expression"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:03Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
+++ b/target/executable/rsem/rsem_merge_counts/.config.vsh.yaml
@@ -193,7 +193,7 @@ 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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
+++ b/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
@@ -490,9 +490,9 @@ function ViashDockerfile {
 FROM ubuntu:22.04
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component rsem rsem_merge_counts"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:03Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:26Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml
@@ -154,7 +154,7 @@ build_info:
  output: "target/executable/rseqc/rseqc_bamstat"
  executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
+++ b/target/executable/rseqc/rseqc_bamstat/rseqc_bamstat
@@ -477,9 +477,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_bamstat"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:01Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml
@@ -177,7 +177,7 @@ build_info:
  output: "target/executable/rseqc/rseqc_inferexperiment"
  executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
+++ b/target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment
@@ -487,9 +487,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_inferexperiment"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:59Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml
@@ -263,7 +263,7 @@ build_info:
  output: "target/executable/rseqc/rseqc_innerdistance"
  executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
+++ b/target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance
@@ -529,9 +529,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_innerdistance"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:00Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:22Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml
@@ -251,7 +251,7 @@ build_info:
  output: "target/executable/rseqc/rseqc_junctionannotation"
  executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
+++ b/target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation
@@ -519,9 +519,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionannotation"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:00Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:22Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml
@@ -240,7 +240,7 @@ build_info:
  output: "target/executable/rseqc/rseqc_junctionsaturation"
  executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
+++ b/target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation
@@ -522,9 +522,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_junctionsaturation"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:00Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:21Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml
@@ -153,7 +153,7 @@ build_info:
  output: "target/executable/rseqc/rseqc_readdistribution"
  executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
+++ b/target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution
@@ -474,9 +474,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readdistribution"
-LABEL org.opencontainers.image.created="2024-09-13T06:50:01Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:23Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml
@@ -202,7 +202,7 @@ build_info:
  output: "target/executable/rseqc/rseqc_readduplication"
  executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
+++ b/target/executable/rseqc/rseqc_readduplication/rseqc_readduplication
@@ -499,9 +499,9 @@ RUN pip install --upgrade pip && \
  pip install --upgrade --no-cache-dir "RSeQC"

 LABEL org.opencontainers.image.description="Companion container for running component rseqc rseqc_readduplication"
-LABEL org.opencontainers.image.created="2024-09-13T06:49:59Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:20Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/rseqc/rseqc_tin/.config.vsh.yaml
+++ b/target/executable/rseqc/rseqc_tin/.config.vsh.yaml
@@ -205,7 +205,7 @@ build_info:
  output: "target/executable/rseqc/rseqc_tin"
  executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/rseqc/rseqc_tin/rseqc_tin
+++ b/target/executable/rseqc/rseqc_tin/rseqc_tin
@@ -501,9 +501,9 @@ 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="2024-09-13T06:49:59Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:21Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/sortmerna/.config.vsh.yaml
+++ b/target/executable/sortmerna/.config.vsh.yaml
@@ -189,7 +189,7 @@ build_info:
  output: "target/executable/sortmerna"
  executable: "target/executable/sortmerna/sortmerna"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/sortmerna/sortmerna
+++ b/target/executable/sortmerna/sortmerna
@@ -492,9 +492,9 @@ 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="2024-09-13T06:50:05Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stringtie/.config.vsh.yaml
+++ b/target/executable/stringtie/.config.vsh.yaml
@@ -207,7 +207,7 @@ build_info:
  output: "target/executable/stringtie"
  executable: "target/executable/stringtie/stringtie"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/stringtie/stringtie
+++ b/target/executable/stringtie/stringtie
@@ -496,9 +496,9 @@ 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="2024-09-13T06:50:02Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:25Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/summarizedexperiment/.config.vsh.yaml
+++ b/target/executable/summarizedexperiment/.config.vsh.yaml
@@ -190,7 +190,7 @@ build_info:
  output: "target/executable/summarizedexperiment"
  executable: "target/executable/summarizedexperiment/summarizedexperiment"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/summarizedexperiment/summarizedexperiment
+++ b/target/executable/summarizedexperiment/summarizedexperiment
@@ -487,9 +487,9 @@ 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="2024-09-13T06:50:06Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/trimgalore/.config.vsh.yaml
+++ b/target/executable/trimgalore/.config.vsh.yaml
@@ -779,7 +779,7 @@ build_info:
  output: "target/executable/trimgalore"
  executable: "target/executable/trimgalore/trimgalore"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/trimgalore/trimgalore
+++ b/target/executable/trimgalore/trimgalore
@@ -858,9 +858,9 @@ 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="2024-09-13T06:50:05Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:28Z"
 LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/tx2gene/.config.vsh.yaml
+++ b/target/executable/tx2gene/.config.vsh.yaml
@@ -183,7 +183,7 @@ build_info:
  output: "target/executable/tx2gene"
  executable: "target/executable/tx2gene/tx2gene"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/tx2gene/tx2gene
+++ b/target/executable/tx2gene/tx2gene
@@ -487,9 +487,9 @@ 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="2024-09-13T06:50:02Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:24Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/tximport/.config.vsh.yaml
+++ b/target/executable/tximport/.config.vsh.yaml
@@ -238,7 +238,7 @@ build_info:
  output: "target/executable/tximport"
  executable: "target/executable/tximport/tximport"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/tximport/tximport
+++ b/target/executable/tximport/tximport
@@ -508,9 +508,9 @@ 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="2024-09-13T06:49:57Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:17Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/ucsc/bedclip/.config.vsh.yaml
+++ b/target/executable/ucsc/bedclip/.config.vsh.yaml
@@ -155,7 +155,7 @@ build_info:
  output: "target/executable/ucsc/bedclip"
  executable: "target/executable/ucsc/bedclip/bedclip"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/ucsc/bedclip/bedclip
+++ b/target/executable/ucsc/bedclip/bedclip
@@ -473,9 +473,9 @@ 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="2024-09-13T06:49:57Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
+++ b/target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml
@@ -155,7 +155,7 @@ build_info:
  output: "target/executable/ucsc/bedgraphtobigwig"
  executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
+++ b/target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig
@@ -473,9 +473,9 @@ 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="2024-09-13T06:49:58Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:18Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/umitools/umitools_dedup/.config.vsh.yaml
+++ b/target/executable/umitools/umitools_dedup/.config.vsh.yaml
@@ -186,7 +186,7 @@ build_info:
  output: "target/executable/umitools/umitools_dedup"
  executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/umitools/umitools_dedup/umitools_dedup
+++ b/target/executable/umitools/umitools_dedup/umitools_dedup
@@ -489,9 +489,9 @@ 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="2024-09-13T06:50:04Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/umitools/umitools_extract/.config.vsh.yaml
+++ b/target/executable/umitools/umitools_extract/.config.vsh.yaml
@@ -244,7 +244,7 @@ build_info:
  output: "target/executable/umitools/umitools_extract"
  executable: "target/executable/umitools/umitools_extract/umitools_extract"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/umitools/umitools_extract/umitools_extract
+++ b/target/executable/umitools/umitools_extract/umitools_extract
@@ -521,9 +521,9 @@ 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="2024-09-13T06:50:04Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:27Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/umitools_prepareforquant/.config.vsh.yaml
+++ b/target/executable/umitools_prepareforquant/.config.vsh.yaml
@@ -147,7 +147,7 @@ build_info:
  output: "target/executable/umitools_prepareforquant"
  executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
 package_config:
  version: "main"
--- a/target/executable/umitools_prepareforquant/umitools_prepareforquant
+++ b/target/executable/umitools_prepareforquant/umitools_prepareforquant
@@ -473,9 +473,9 @@ 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="2024-09-13T06:50:06Z"
+LABEL org.opencontainers.image.created="2024-09-13T10:19:29Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+LABEL org.opencontainers.image.revision="cb9b32883494c48f394213551a82e9103f2e620c"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
+++ b/target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml
@@ -398,26 +398,32 @@ dependencies:
  repository:
    type: "vsh"
    repo: "vsh/biobox"
+    tag: "v0.2.0"
 - name: "samtools/samtools_sort"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
+    tag: "v0.2.0"
 - name: "samtools/samtools_index"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
+    tag: "v0.2.0"
 - name: "samtools/samtools_stats"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
+    tag: "v0.2.0"
 - name: "samtools/samtools_flagstat"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
+    tag: "v0.2.0"
 - name: "samtools/samtools_idxstats"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
+    tag: "v0.2.0"
 - name: "umitools/umitools_dedup"
  repository:
    type: "local"
@@ -428,6 +434,7 @@ dependencies:
  repository:
    type: "vsh"
    repo: "vsh/biobox"
+    tag: "v0.2.0"
 - name: "rsem/rsem_calculate_expression"
  repository:
    type: "local"
@@ -435,6 +442,7 @@ repositories:
 - type: "vsh"
  name: "biobox"
  repo: "vsh/biobox"
+  tag: "v0.2.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -510,18 +518,18 @@ 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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
-  - "target/dependencies/vsh/vsh/biobox/nextflow/star/star_align_reads"
-  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_sort"
-  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_index"
-  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_stats"
-  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_flagstat"
-  - "target/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_idxstats"
+  - "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"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats"
  - "target/nextflow/umitools/umitools_dedup"
  - "target/nextflow/umitools_prepareforquant"
-  - "target/dependencies/vsh/vsh/biobox/nextflow/salmon/salmon_quant"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
  - "target/nextflow/rsem/rsem_calculate_expression"
 package_config:
  version: "main"
--- a/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
+++ b/target/executable/workflows/genome_alignment_and_quant/genome_alignment_and_quant
@@ -1169,13 +1169,13 @@ fi
 VIASH_DEP_UMITOOLS_UMITOOLS_DEDUP="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools/umitools_dedup/main.nf"
 VIASH_DEP_UMITOOLS_PREPAREFORQUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/umitools_prepareforquant/main.nf"
 VIASH_DEP_RSEM_RSEM_CALCULATE_EXPRESSION="$VIASH_META_RESOURCES_DIR/../../../nextflow/rsem/rsem_calculate_expression/main.nf"
-VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/star/star_align_reads/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_sort/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_index/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_stats/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_flagstat/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/samtools/samtools_idxstats/main.nf"
-VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/nextflow/salmon/salmon_quant/main.nf"
+VIASH_DEP_STAR_STAR_ALIGN_READS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_align_reads/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"
+VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"

 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD
--- a/target/executable/workflows/merge_quant_results/.config.vsh.yaml
+++ b/target/executable/workflows/merge_quant_results/.config.vsh.yaml
@@ -269,7 +269,7 @@ 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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/tx2gene"
--- a/target/executable/workflows/post_processing/.config.vsh.yaml
+++ b/target/executable/workflows/post_processing/.config.vsh.yaml
@@ -369,27 +369,27 @@ dependencies:
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "samtools/samtools_index"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "samtools/samtools_stats"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "samtools/samtools_flagstat"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "samtools/samtools_idxstats"
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "stringtie"
  repository:
    type: "local"
@@ -406,7 +406,7 @@ repositories:
 - type: "vsh"
  name: "biobox"
  repo: "vsh/biobox"
-  tag: "v0.1"
+  tag: "v0.2.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -482,15 +482,15 @@ build_info:
  output: "target/executable/workflows/post_processing"
  executable: "target/executable/workflows/post_processing/post_processing"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/picard_markduplicates"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_sort"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_index"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_stats"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_flagstat"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_idxstats"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats"
  - "target/nextflow/stringtie"
  - "target/nextflow/bedtools_genomecov"
  - "target/nextflow/ucsc/bedclip"
--- a/target/executable/workflows/post_processing/post_processing
+++ b/target/executable/workflows/post_processing/post_processing
@@ -1143,11 +1143,11 @@ VIASH_DEP_STRINGTIE="$VIASH_META_RESOURCES_DIR/../../../nextflow/stringtie/main.
 VIASH_DEP_BEDTOOLS_GENOMECOV="$VIASH_META_RESOURCES_DIR/../../../nextflow/bedtools_genomecov/main.nf"
 VIASH_DEP_UCSC_BEDCLIP="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedclip/main.nf"
 VIASH_DEP_UCSC_BEDGRAPHTOBIGWIG="$VIASH_META_RESOURCES_DIR/../../../nextflow/ucsc/bedgraphtobigwig/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_sort/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_index/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_stats/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_flagstat/main.nf"
-VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/samtools/samtools_idxstats/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_SORT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_index/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_STATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_stats/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_FLAGSTAT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_flagstat/main.nf"
+VIASH_DEP_SAMTOOLS_SAMTOOLS_IDXSTATS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_idxstats/main.nf"

 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD
--- a/target/executable/workflows/pre_processing/.config.vsh.yaml
+++ b/target/executable/workflows/pre_processing/.config.vsh.yaml
@@ -551,7 +551,7 @@ dependencies:
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "fq_subsample"
  repository:
    type: "local"
@@ -559,12 +559,12 @@ dependencies:
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 repositories:
 - type: "vsh"
  name: "biobox"
  repo: "vsh/biobox"
-  tag: "v0.1"
+  tag: "v0.2.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -640,7 +640,7 @@ build_info:
  output: "target/executable/workflows/pre_processing"
  executable: "target/executable/workflows/pre_processing/pre_processing"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/fastqc"
@@ -648,9 +648,9 @@ build_info:
  - "target/nextflow/trimgalore"
  - "target/nextflow/bbmap_bbsplit"
  - "target/nextflow/sortmerna"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/fastp"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp"
  - "target/nextflow/fq_subsample"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
 package_config:
  version: "main"
  info:
--- a/target/executable/workflows/pre_processing/pre_processing
+++ b/target/executable/workflows/pre_processing/pre_processing
@@ -1462,8 +1462,8 @@ VIASH_DEP_TRIMGALORE="$VIASH_META_RESOURCES_DIR/../../../nextflow/trimgalore/mai
 VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
 VIASH_DEP_SORTMERNA="$VIASH_META_RESOURCES_DIR/../../../nextflow/sortmerna/main.nf"
 VIASH_DEP_FQ_SUBSAMPLE="$VIASH_META_RESOURCES_DIR/../../../nextflow/fq_subsample/main.nf"
-VIASH_DEP_FASTP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/fastp/main.nf"
-VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant/main.nf"
+VIASH_DEP_FASTP="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/fastp/main.nf"
+VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"

 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD
--- a/target/executable/workflows/prepare_genome/.config.vsh.yaml
+++ b/target/executable/workflows/prepare_genome/.config.vsh.yaml
@@ -370,7 +370,7 @@ dependencies:
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "main"
+    tag: "v0.2.0"
 - name: "cat_additional_fasta"
  repository:
    type: "local"
@@ -387,7 +387,7 @@ dependencies:
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "main"
+    tag: "v0.2.0"
 - name: "getchromsizes"
  repository:
    type: "local"
@@ -395,12 +395,12 @@ dependencies:
  repository:
    type: "vsh"
    repo: "craftbox"
-    tag: "main"
+    tag: "v0.1.0"
 - name: "star/star_genome_generate"
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "main"
+    tag: "v0.2.0"
 - name: "bbmap_bbsplit"
  repository:
    type: "local"
@@ -408,7 +408,7 @@ dependencies:
  repository:
    type: "vsh"
    repo: "biobox"
-    tag: "main"
+    tag: "v0.2.0"
 - name: "kallisto/kallisto_index"
  repository:
    type: "local"
@@ -416,11 +416,11 @@ repositories:
 - type: "vsh"
  name: "biobox"
  repo: "biobox"
-  tag: "main"
+  tag: "v0.2.0"
 - type: "vsh"
  name: "craftbox"
  repo: "craftbox"
-  tag: "main"
+  tag: "v0.1.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -496,21 +496,21 @@ build_info:
  output: "target/executable/workflows/prepare_genome"
  executable: "target/executable/workflows/prepare_genome/prepare_genome"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/gunzip"
-  - "target/dependencies/vsh/vsh/biobox/main/nextflow/gffread"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread"
  - "target/nextflow/cat_additional_fasta"
  - "target/nextflow/gtf2bed"
  - "target/nextflow/preprocess_transcripts_fasta"
  - "target/nextflow/gtf_filter"
-  - "target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference"
  - "target/nextflow/getchromsizes"
-  - "target/dependencies/vsh/vsh/craftbox/main/nextflow/untar"
-  - "target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate"
+  - "target/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate"
  - "target/nextflow/bbmap_bbsplit"
-  - "target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index"
  - "target/nextflow/kallisto/kallisto_index"
 package_config:
  version: "main"
--- a/target/executable/workflows/prepare_genome/prepare_genome
+++ b/target/executable/workflows/prepare_genome/prepare_genome
@@ -1111,11 +1111,11 @@ VIASH_DEP_GTF_FILTER="$VIASH_META_RESOURCES_DIR/../../../nextflow/gtf_filter/mai
 VIASH_DEP_GETCHROMSIZES="$VIASH_META_RESOURCES_DIR/../../../nextflow/getchromsizes/main.nf"
 VIASH_DEP_BBMAP_BBSPLIT="$VIASH_META_RESOURCES_DIR/../../../nextflow/bbmap_bbsplit/main.nf"
 VIASH_DEP_KALLISTO_KALLISTO_INDEX="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_index/main.nf"
-VIASH_DEP_GFFREAD="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf"
-VIASH_DEP_RSEM_RSEM_PREPARE_REFERENCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf"
-VIASH_DEP_UNTAR="$VIASH_TARGET_DIR/dependencies/vsh/vsh/craftbox/main/nextflow/untar/main.nf"
-VIASH_DEP_STAR_STAR_GENOME_GENERATE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf"
-VIASH_DEP_SALMON_SALMON_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf"
+VIASH_DEP_GFFREAD="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/gffread/main.nf"
+VIASH_DEP_RSEM_RSEM_PREPARE_REFERENCE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/rsem/rsem_prepare_reference/main.nf"
+VIASH_DEP_UNTAR="$VIASH_TARGET_DIR/dependencies/vsh/vsh/craftbox/v0.1.0/nextflow/untar/main.nf"
+VIASH_DEP_STAR_STAR_GENOME_GENERATE="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/star/star_genome_generate/main.nf"
+VIASH_DEP_SALMON_SALMON_INDEX="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_index/main.nf"

 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD
--- a/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
+++ b/target/executable/workflows/pseudo_alignment_and_quant/.config.vsh.yaml
@@ -197,7 +197,7 @@ dependencies:
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "kallisto/kallisto_quant"
  repository:
    type: "local"
@@ -205,7 +205,7 @@ repositories:
 - type: "vsh"
  name: "biobox"
  repo: "vsh/biobox"
-  tag: "v0.1"
+  tag: "v0.2.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -281,10 +281,10 @@ 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: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant"
  - "target/nextflow/kallisto/kallisto_quant"
 package_config:
  version: "main"
--- a/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant
+++ b/target/executable/workflows/pseudo_alignment_and_quant/pseudo_alignment_and_quant
@@ -784,7 +784,7 @@ fi

 # set dependency paths
 VIASH_DEP_KALLISTO_KALLISTO_QUANT="$VIASH_META_RESOURCES_DIR/../../../nextflow/kallisto/kallisto_quant/main.nf"
-VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/salmon/salmon_quant/main.nf"
+VIASH_DEP_SALMON_SALMON_QUANT="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/salmon/salmon_quant/main.nf"

 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD
--- a/target/executable/workflows/quality_control/.config.vsh.yaml
+++ b/target/executable/workflows/quality_control/.config.vsh.yaml
@@ -1490,7 +1490,7 @@ dependencies:
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "multiqc_custom_biotype"
  repository:
    type: "local"
@@ -1504,7 +1504,7 @@ dependencies:
  repository:
    type: "vsh"
    repo: "vsh/biobox"
-    tag: "v0.1"
+    tag: "v0.2.0"
 - name: "workflows/merge_quant_results"
  repository:
    type: "local"
@@ -1512,7 +1512,7 @@ repositories:
 - type: "vsh"
  name: "biobox"
  repo: "vsh/biobox"
-  tag: "v0.1"
+  tag: "v0.2.0"
 runners:
 - type: "executable"
  id: "executable"
@@ -1588,7 +1588,7 @@ build_info:
  output: "target/executable/workflows/quality_control"
  executable: "target/executable/workflows/quality_control/quality_control"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/rseqc/rseqc_bamstat"
@@ -1602,11 +1602,11 @@ build_info:
  - "target/nextflow/dupradar"
  - "target/nextflow/qualimap"
  - "target/nextflow/preseq_lcextrap"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/featurecounts"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts"
  - "target/nextflow/multiqc_custom_biotype"
  - "target/nextflow/deseq2_qc"
  - "target/nextflow/prepare_multiqc_input"
-  - "target/dependencies/vsh/vsh/biobox/v0.1/nextflow/multiqc"
+  - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc"
  - "target/nextflow/workflows/merge_quant_results"
 package_config:
  version: "main"
--- a/target/executable/workflows/quality_control/quality_control
+++ b/target/executable/workflows/quality_control/quality_control
@@ -3343,8 +3343,8 @@ VIASH_DEP_MULTIQC_CUSTOM_BIOTYPE="$VIASH_META_RESOURCES_DIR/../../../nextflow/mu
 VIASH_DEP_DESEQ2_QC="$VIASH_META_RESOURCES_DIR/../../../nextflow/deseq2_qc/main.nf"
 VIASH_DEP_PREPARE_MULTIQC_INPUT="$VIASH_META_RESOURCES_DIR/../../../nextflow/prepare_multiqc_input/main.nf"
 VIASH_DEP_WORKFLOWS_MERGE_QUANT_RESULTS="$VIASH_META_RESOURCES_DIR/../../../nextflow/workflows/merge_quant_results/main.nf"
-VIASH_DEP_FEATURECOUNTS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/featurecounts/main.nf"
-VIASH_DEP_MULTIQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.1/nextflow/multiqc/main.nf"
+VIASH_DEP_FEATURECOUNTS="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/featurecounts/main.nf"
+VIASH_DEP_MULTIQC="$VIASH_TARGET_DIR/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/multiqc/main.nf"

 ViashDebug "Running command: $(echo $VIASH_CMD)"
 cat << VIASHEOF | eval $VIASH_CMD
--- a/target/executable/workflows/rnaseq/.config.vsh.yaml
+++ b/target/executable/workflows/rnaseq/.config.vsh.yaml
@@ -1956,7 +1956,7 @@ build_info:
  output: "target/executable/workflows/rnaseq"
  executable: "target/executable/workflows/rnaseq/rnaseq"
  viash_version: "0.9.0"
-  git_commit: "1e1ffb315fefec05db2ee0c62e1c98ce4b49929c"
+  git_commit: "cb9b32883494c48f394213551a82e9103f2e620c"
  git_remote: "https://github.com/viash-hub/rnaseq"
  dependencies:
  - "target/nextflow/workflows/prepare_genome"