Build branch main with version main (fd0354d)

Build pipeline: viash-hub.rnaseq.main-kqfj7

Source commit: fd0354dae8

Source message: Point to new assets dir

src/deseq2_qc/config.vsh.yaml

@@ -5,14 +5,14 @@ info:
     paths: [modules/local/deseq2_qc.nf]
     last_sha: 92b2a7857de1dda9d1c19a088941fc81e2976ff7
 description: | 
-  Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples in the counts files
+  run deseq2, perform pca, generate heatmaps and scatterplots for samples in the counts files
 
 argument_groups: 
-- name: "Input"
+- name: "input"
   arguments: 
   - name: "--counts"
     type: file
-    description: Count file matrix where rows are genes and columns are samples
+    description: count file matrix where rows are genes and columns are samples
   - name: "--pca_header_multiqc"
     type: file
     default: assets/multiqc/deseq2_pca_header.txt
@@ -50,13 +50,16 @@ resources:
     path: script.sh
   # copied from https://github.com/nf-core/rnaseq/blob/3.12.0/bin/deseq2_qc.r
   - path: deseq2_qc.r
+  # Add proper default headers as part of the component
+  - path: /src/assets/multiqc/deseq2_pca_header.txt
+    dest: assets/multiqc/deseq2_pca_header.txt
+  - path: /src/assets/multiqc/deseq2_clustering_header.txt
+    dest: assets/multiqc/deseq2_clustering_header.txt
 
 test_resources:
   - type: bash_script
     path: test.sh
   - path: /testData/unit_test_resources/counts.tsv
-  - path: /assets/multiqc/deseq2_pca_header.txt
-  - path: /assets/multiqc/deseq2_clustering_header.txt
 
 engines: 
   - type: docker
@@ -70,4 +73,4 @@ engines:
         url: https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz
 runners:
   - type: executable
-  - type: nextflow
+  - type: nextflow

src/deseq2_qc/test.sh

@@ -5,8 +5,6 @@ echo "> Running $meta_functionality_name"
 
 "$meta_executable" \
     --counts $meta_resources_dir/counts.tsv \
-    --pca_header_multiqc $meta_resources_dir/deseq2_pca_header.txt \
-    --clustering_header_multiqc $meta_resources_dir/deseq2_clustering_header.txt \
     --extra_args "--id_col 1 --sample_suffix '' --outprefix deseq2 --count_col 2" \
     --extra_args2 "test" \
     --deseq2_output "deseq2/" \
@@ -25,4 +23,4 @@ echo ">> Check whether output exists"
 [ ! -f "sample.dists_mqc.tsv" ] && echo "sample.dists_mqc.tsv was not created" && exit 1
 [ ! -s "sample.dists_mqc.tsv" ] && echo "sample.dists_mqc.tsv is empty" && exit 1
 
-exit 0
+exit 0

src/multiqc_custom_biotype/config.vsh.yaml

@@ -33,6 +33,9 @@ resources:
     path: script.sh
   # Copied from https://github.com/nf-core/rnaseq/blob/3.12.0/bin/mqc_features_stat.py
   - path: mqc_features_stat.py
+  # Include the header for the biotypes in the component
+  - path: /src/assets/multiqc/biotypes_header.txt
+    dest: assets/multiqc/biotypes_header.txt
 
 engines:
   - type: docker
@@ -43,4 +46,4 @@ engines:
       - type: python
 runners: 
   - type: executable
-  - type: nextflow
+  - type: nextflow

src/workflows/quality_control/config.vsh.yaml

@@ -101,7 +101,7 @@ argument_groups:
         description: Specify if the GTF annotation is in GENCODE format.
       - name: "--biotypes_header"
         type: file
-        default: assets/multiqc/biotypes_header.txt
+        default: src/assets/multiqc/biotypes_header.txt
       - name: "--biotype"
         type: string
         description: Biotype value to use while appending entries to GTF file when additional fasta file is provided.
@@ -243,10 +243,10 @@ argument_groups:
         type: boolean
       - name: "--pca_header_multiqc"
         type: file
-        default: assets/multiqc/deseq2_pca_header.txt
+        default: src/assets/multiqc/deseq2_pca_header.txt
       - name: "--clustering_header_multiqc"
         type: file
-        default: assets/multiqc/deseq2_clustering_header.txt
+        default: src/assets/multiqc/deseq2_clustering_header.txt
       - name: "--deseq2_vst"
         type: boolean
         description: Use vst transformation instead of rlog with DESeq2

src/workflows/rnaseq/config.vsh.yaml

@@ -129,7 +129,7 @@ argument_groups:
       - name: "--ribo_database_manifest"
         type: file
         description: Text file containing paths to fasta files (one per line) that will be used to create the database for SortMeRNA.
-        default: assets/rrna-db-defaults.txt
+        default: src/assets/rrna-db-defaults.txt
 
   - name: UMI options
     arguments:
@@ -310,10 +310,10 @@ argument_groups:
         default: '-verbose -seed 1 -seg_len 100000000'
       - name: "--pca_header_multiqc"
         type: file
-        default: assets/multiqc/deseq2_pca_header.txt
+        default: src/assets/multiqc/deseq2_pca_header.txt
       - name: "--clustering_header_multiqc"
         type: file
-        default: assets/multiqc/deseq2_clustering_header.txt
+        default: src/assets/multiqc/deseq2_clustering_header.txt
       - name: "--deseq2_vst"
         type: boolean
         default: true
@@ -336,12 +336,12 @@ argument_groups:
     arguments:
       - name: "--multiqc_custom_config"
         type: file
-        default: assets/multiqc_config.yml
+        default: src/assets/multiqc_config.yml
       - name: "--multiqc_title"
         type: string
       - name: "--multiqc_methods_description"
         type: file
-        default: assets/methods_description_template.yml
+        default: src/assets/methods_description_template.yml
     
   - name: Output
     arguments:

target/executable/bbmap_bbsplit/.config.vsh.yaml

@@ -238,8 +238,8 @@ build_info:
   output: "target/executable/bbmap_bbsplit"
   executable: "target/executable/bbmap_bbsplit/bbmap_bbsplit"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:50Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:05Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/bedtools_genomecov/.config.vsh.yaml

@@ -178,8 +178,8 @@ build_info:
   output: "target/executable/bedtools_genomecov"
   executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:51Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:05Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/cat_additional_fasta/.config.vsh.yaml

@@ -182,8 +182,8 @@ build_info:
   output: "target/executable/cat_additional_fasta"
   executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:59Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/cat_fastq/.config.vsh.yaml

@@ -169,8 +169,8 @@ build_info:
   output: "target/executable/cat_fastq"
   executable: "target/executable/cat_fastq/cat_fastq"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:59Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/deseq2_qc/.config.vsh.yaml

@@ -1,11 +1,11 @@
 name: "deseq2_qc"
 version: "main"
 argument_groups:
-- name: "Input"
+- name: "input"
   arguments:
   - type: "file"
     name: "--counts"
-    description: "Count file matrix where rows are genes and columns are samples"
+    description: "count file matrix where rows are genes and columns are samples"
     info: null
     must_exist: true
     create_parent: true
@@ -104,7 +104,13 @@ resources:
   is_executable: true
 - type: "file"
   path: "deseq2_qc.r"
-description: "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples\
+- type: "file"
+  path: "assets/multiqc/deseq2_pca_header.txt"
+  dest: "assets/multiqc/deseq2_pca_header.txt"
+- type: "file"
+  path: "assets/multiqc/deseq2_clustering_header.txt"
+  dest: "assets/multiqc/deseq2_clustering_header.txt"
+description: "run deseq2, perform pca, generate heatmaps and scatterplots for samples\
   \ in the counts files\n"
 test_resources:
 - type: "bash_script"
@@ -112,10 +118,6 @@ test_resources:
   is_executable: true
 - type: "file"
   path: "counts.tsv"
-- type: "file"
-  path: "deseq2_pca_header.txt"
-- type: "file"
-  path: "deseq2_clustering_header.txt"
 info:
   migration_info:
     git_repo: "https://github.com/nf-core/rnaseq.git"
@@ -237,8 +239,8 @@ build_info:
   output: "target/executable/deseq2_qc"
   executable: "target/executable/deseq2_qc/deseq2_qc"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/deseq2_qc/assets/multiqc/deseq2_clustering_header.txt

@@ -0,0 +1,12 @@
+#id: 'deseq2_clustering'
+#section_name: 'DESeq2 sample similarity'
+#description: "is generated from clustering by Euclidean distances between
+#	       <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html' target='_blank'>DESeq2</a>
+#              rlog values for each sample
+#              in the <a href='https://github.com/nf-core/rnaseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
+#plot_type: 'heatmap'
+#anchor: 'deseq2_clustering'
+#pconfig:
+#    title: 'DESeq2: Heatmap of the sample-to-sample distances'
+#    xlab: True
+#    reverseColors: True

target/executable/deseq2_qc/assets/multiqc/deseq2_pca_header.txt

@@ -0,0 +1,11 @@
+#id: 'deseq2_pca'
+#section_name: 'DESeq2 PCA plot'
+#description: "PCA plot between samples in the experiment.
+#              These values are calculated using <a href='https://bioconductor.org/packages/release/bioc/html/DESeq2.html'>DESeq2</a>
+#              in the <a href='https://github.com/nf-core/atacseq/blob/master/bin/deseq2_qc.r'><code>deseq2_qc.r</code></a> script."
+#plot_type: 'scatter'
+#anchor: 'deseq2_pca'
+#pconfig:
+#    title: 'DESeq2: Principal component plot'
+#    xlab: PC1
+#    ylab: PC2

target/executable/deseq2_qc/deseq2_qc

@@ -173,13 +173,13 @@ VIASH_META_TEMP_DIR="$VIASH_TEMP"
 function ViashHelp {
   echo "deseq2_qc main"
   echo ""
-  echo "Run DESeq2, perform PCA, generate heatmaps and scatterplots for samples in the"
+  echo "run deseq2, perform pca, generate heatmaps and scatterplots for samples in the"
   echo "counts files"
   echo ""
-  echo "Input:"
+  echo "input:"
   echo "    --counts"
   echo "        type: file, file must exist"
-  echo "        Count file matrix where rows are genes and columns are samples"
+  echo "        count file matrix where rows are genes and columns are samples"
   echo ""
   echo "    --pca_header_multiqc"
   echo "        type: file, file must exist"
@@ -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="2024-10-01T10:02:10Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:25Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/dupradar/.config.vsh.yaml

@@ -266,8 +266,8 @@ build_info:
   output: "target/executable/dupradar"
   executable: "target/executable/dupradar/dupradar"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:01Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:14Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/fastqc/.config.vsh.yaml

@@ -198,8 +198,8 @@ build_info:
   output: "target/executable/fastqc"
   executable: "target/executable/fastqc/fastqc"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:52Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/fq_subsample/.config.vsh.yaml

@@ -177,8 +177,8 @@ build_info:
   output: "target/executable/fq_subsample"
   executable: "target/executable/fq_subsample/fq_subsample"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:51Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/getchromsizes/.config.vsh.yaml

@@ -167,8 +167,8 @@ build_info:
   output: "target/executable/getchromsizes"
   executable: "target/executable/getchromsizes/getchromsizes"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:52Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/gtf2bed/.config.vsh.yaml

@@ -145,8 +145,8 @@ build_info:
   output: "target/executable/gtf2bed"
   executable: "target/executable/gtf2bed/gtf2bed"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:06Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/gtf_filter/.config.vsh.yaml

@@ -155,8 +155,8 @@ build_info:
   output: "target/executable/gtf_filter"
   executable: "target/executable/gtf_filter/gtf_filter"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:09Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/gunzip/.config.vsh.yaml

@@ -144,8 +144,8 @@ build_info:
   output: "target/executable/gunzip"
   executable: "target/executable/gunzip/gunzip"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:52Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/kallisto/kallisto_index/.config.vsh.yaml

@@ -155,8 +155,8 @@ build_info:
   output: "target/executable/kallisto/kallisto_index"
   executable: "target/executable/kallisto/kallisto_index/kallisto_index"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:07Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/kallisto/kallisto_quant/.config.vsh.yaml

@@ -253,8 +253,8 @@ build_info:
   output: "target/executable/kallisto/kallisto_quant"
   executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:07Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/multiqc_custom_biotype/.config.vsh.yaml

@@ -64,6 +64,9 @@ resources:
   is_executable: true
 - type: "file"
   path: "mqc_features_stat.py"
+- type: "file"
+  path: "assets/multiqc/biotypes_header.txt"
+  dest: "assets/multiqc/biotypes_header.txt"
 description: "Calculate features percentage for biotype counts"
 info: null
 status: "enabled"
@@ -170,8 +173,8 @@ build_info:
   output: "target/executable/multiqc_custom_biotype"
   executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/multiqc_custom_biotype/assets/multiqc/biotypes_header.txt

@@ -0,0 +1,11 @@
+# id: 'biotype_counts'
+# section_name: 'Biotype Counts'
+# description: "shows reads overlapping genomic features of different biotypes,
+#     counted by <a href='http://bioinf.wehi.edu.au/featureCounts'>featureCounts</a>."
+# plot_type: 'bargraph'
+# anchor: 'featurecounts_biotype'
+# pconfig:
+#     id: "featurecounts_biotype_plot"
+#     title: "featureCounts: Biotypes"
+#     xlab: "# Reads"
+#     cpswitch_counts_label: "Number of Reads"

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="2024-10-01T10:02:01Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:15Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/picard_markduplicates/.config.vsh.yaml

@@ -207,8 +207,8 @@ build_info:
   output: "target/executable/picard_markduplicates"
   executable: "target/executable/picard_markduplicates/picard_markduplicates"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:09Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/prepare_multiqc_input/.config.vsh.yaml

@@ -409,8 +409,8 @@ build_info:
   output: "target/executable/prepare_multiqc_input"
   executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:05Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/preprocess_transcripts_fasta/.config.vsh.yaml

@@ -138,8 +138,8 @@ build_info:
   output: "target/executable/preprocess_transcripts_fasta"
   executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:04Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/preseq_lcextrap/.config.vsh.yaml

@@ -191,8 +191,8 @@ build_info:
   output: "target/executable/preseq_lcextrap"
   executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:53Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:07Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/qualimap/.config.vsh.yaml

@@ -271,8 +271,8 @@ build_info:
   output: "target/executable/qualimap"
   executable: "target/executable/qualimap/qualimap"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:51Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:06Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rsem/rsem_calculate_expression/.config.vsh.yaml

@@ -299,8 +299,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression

@@ -542,9 +542,9 @@ 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="2024-10-01T10:02:06Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rsem/rsem_merge_counts/.config.vsh.yaml

@@ -182,8 +182,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

target/executable/rsem/rsem_merge_counts/rsem_merge_counts

@@ -483,9 +483,9 @@ 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="2024-10-01T10:02:06Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:21Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_bamstat/.config.vsh.yaml

@@ -163,8 +163,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_bamstat"
   executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:04Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_inferexperiment/.config.vsh.yaml

@@ -186,8 +186,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_inferexperiment"
   executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:01Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:15Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_innerdistance/.config.vsh.yaml

@@ -272,8 +272,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_innerdistance"
   executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:03Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_junctionannotation/.config.vsh.yaml

@@ -260,8 +260,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_junctionannotation"
   executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:03Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_junctionsaturation/.config.vsh.yaml

@@ -249,8 +249,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_junctionsaturation"
   executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:03Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_readdistribution/.config.vsh.yaml

@@ -162,8 +162,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_readdistribution"
   executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:04Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_readduplication/.config.vsh.yaml

@@ -211,8 +211,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_readduplication"
   executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:02Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/rseqc/rseqc_tin/.config.vsh.yaml

@@ -214,8 +214,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_tin"
   executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:02Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/sortmerna/.config.vsh.yaml

@@ -198,8 +198,8 @@ build_info:
   output: "target/executable/sortmerna"
   executable: "target/executable/sortmerna/sortmerna"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:09Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/stringtie/.config.vsh.yaml

@@ -216,8 +216,8 @@ build_info:
   output: "target/executable/stringtie"
   executable: "target/executable/stringtie/stringtie"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:06Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/summarizedexperiment/.config.vsh.yaml

@@ -199,8 +199,8 @@ build_info:
   output: "target/executable/summarizedexperiment"
   executable: "target/executable/summarizedexperiment/summarizedexperiment"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:10Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/trimgalore/.config.vsh.yaml

@@ -788,8 +788,8 @@ build_info:
   output: "target/executable/trimgalore"
   executable: "target/executable/trimgalore/trimgalore"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:08Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:23Z"
 LABEL org.opencontainers.image.source="https://github.com/FelixKrueger/TrimGalore"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/tx2gene/.config.vsh.yaml

@@ -192,8 +192,8 @@ build_info:
   output: "target/executable/tx2gene"
   executable: "target/executable/tx2gene/tx2gene"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:05Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:20Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/tximport/.config.vsh.yaml

@@ -247,8 +247,8 @@ build_info:
   output: "target/executable/tximport"
   executable: "target/executable/tximport/tximport"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:01:59Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:12Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/ucsc/bedclip/.config.vsh.yaml

@@ -164,8 +164,8 @@ build_info:
   output: "target/executable/ucsc/bedclip"
   executable: "target/executable/ucsc/bedclip/bedclip"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:00Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:13Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/ucsc/bedgraphtobigwig/.config.vsh.yaml

@@ -164,8 +164,8 @@ build_info:
   output: "target/executable/ucsc/bedgraphtobigwig"
   executable: "target/executable/ucsc/bedgraphtobigwig/bedgraphtobigwig"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:00Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:14Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/umitools/umitools_dedup/.config.vsh.yaml

@@ -195,8 +195,8 @@ build_info:
   output: "target/executable/umitools/umitools_dedup"
   executable: "target/executable/umitools/umitools_dedup/umitools_dedup"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:07Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/umitools/umitools_extract/.config.vsh.yaml

@@ -253,8 +253,8 @@ build_info:
   output: "target/executable/umitools/umitools_extract"
   executable: "target/executable/umitools/umitools_extract/umitools_extract"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:08Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:22Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/umitools_prepareforquant/.config.vsh.yaml

@@ -156,8 +156,8 @@ build_info:
   output: "target/executable/umitools_prepareforquant"
   executable: "target/executable/umitools_prepareforquant/umitools_prepareforquant"
   viash_version: "0.9.0"
-  git_commit: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
 package_config:
   version: "main"
   info:

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="2024-10-01T10:02:10Z"
+LABEL org.opencontainers.image.created="2024-10-03T15:52:24Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+LABEL org.opencontainers.image.revision="fd0354dae813d953b107e8fa856f3cd4e7939f2b"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

target/executable/workflows/genome_alignment_and_quant/.config.vsh.yaml

@@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@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"

target/executable/workflows/merge_quant_results/.config.vsh.yaml

@@ -278,8 +278,8 @@ 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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/tx2gene"
   - "target/nextflow/tximport"

target/executable/workflows/post_processing/.config.vsh.yaml

@@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/picard_markduplicates"
   - "target/dependencies/vsh/vsh/biobox/v0.2.0/nextflow/samtools/samtools_sort"

target/executable/workflows/pre_processing/.config.vsh.yaml

@@ -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: "1d87dc7c24f540c96460e69322f06d4be0bb7be8"
+  git_commit: "fd0354dae813d953b107e8fa856f3cd4e7939f2b"
-  git_remote: "https://x-access-token:ghs_vs3fpTo1mWGISEIj2mqOUQA3IRBYZ30EQLHG@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_PTWjrDyiP6F8xJddYWNdkyLhIv0ZGM1AEXAG@github.com/viash-hub/rnaseq"
   dependencies:
   - "target/nextflow/fastqc"
   - "target/nextflow/umitools/umitools_extract"