Build branch main with version main (5fbd530)

Build pipeline: viash-hub.rnaseq.main-rfpzb Source commit: 5fbd530a7c Source message: add arguments to skip qc components
2024-11-13 10:26:31 +00:00
parent fe41adb0c7
commit bc17b94cd5
228 changed files with 846 additions and 656 deletions
--- a/src/deseq2_qc/config.vsh.yaml
+++ b/src/deseq2_qc/config.vsh.yaml
@@ -71,9 +71,8 @@ engines:
    image: rocker/r2u:22.04
    setup:
      - type: r
-        cran: [ optparse, ggplot2, RColorBrewer, pheatmap, stringr ]
+        cran: [ optparse, ggplot2, RColorBrewer, pheatmap, stringr, matrixStats ]
        bioc: [ DESeq2 ]
-        url: https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz
 runners:
  - type: executable
  - type: nextflow
--- a/src/workflows/quality_control/config.vsh.yaml
+++ b/src/workflows/quality_control/config.vsh.yaml
@@ -77,6 +77,15 @@ argument_groups:
        default: false
      - name: "--skip_pseudo_align"
        type: boolean
+      - name: "--skip_dupradar"
+        type: boolean_true
+      - name: "--skip_qualimap"
+        type: boolean_true
+      - name: "--skip_rseqc"
+        type: boolean_true
+      - name: "--skip_multiqc"
+        type: boolean_true
+

      # Component specific options
      # preseq
--- a/src/workflows/quality_control/main.nf
+++ b/src/workflows/quality_control/main.nf
@@ -16,7 +16,7 @@ workflow run_wf {
        }

        | featurecounts.run (
-            runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf },
+            runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.biotype_in_gtf && !state.skip_align },
            fromState: [
                "paired": "paired",
                "strand": "strand", 
@@ -37,7 +37,7 @@ workflow run_wf {
        )

        | multiqc_custom_biotype.run (
-            runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts },
+            runIf: { id, state -> !state.skip_qc && !state.skip_biotype_qc && state.biotype && state.featurecounts && !state.skip_align },
            fromState: [
                "id": "id",
                "biocounts": "featurecounts", 
@@ -50,7 +50,7 @@ workflow run_wf {
        )
              
        | preseq_lcextrap.run (
-            runIf: { id, state -> !state.skip_qc && !state.skip_preseq },
+            runIf: { id, state -> !state.skip_qc && !state.skip_preseq && !state.skip_align },
            fromState: [
                "paired": "paired",
                "input": "genome_bam",
@@ -60,7 +60,7 @@ workflow run_wf {
        )
   
        | rseqc_bamstat.run (
-            runIf: { id, state -> "bam_stat" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "bam_stat" in state.rseqc_modules && !state.skip_align },
            fromState: [
                "input": "genome_bam",
                "map_qual": "map_qual"
@@ -68,7 +68,7 @@ workflow run_wf {
            toState: [ "bamstat_output": "output" ]
        )
        | rseqc_inferexperiment.run(
-            runIf: { id, state -> "infer_experiment" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "infer_experiment" in state.rseqc_modules && !state.skip_align },
            fromState: [
                "input": "genome_bam",
                "refgene": "gene_bed",
@@ -84,7 +84,7 @@ workflow run_wf {
            [ id, state + [ inferred_strand: inferred_strand, passed_strand_check: passed_strand_check ] ]
        }
        | rseqc_innerdistance.run(
-            runIf: { id, state -> state.paired && "inner_distance" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && state.paired && "inner_distance" in state.rseqc_modules && !state.skip_align },
            key: "inner_distance",
            fromState: [
                "input": "genome_bam",
@@ -104,7 +104,7 @@ workflow run_wf {
            ]
        )
        | rseqc_junctionannotation.run(
-            runIf: { id, state -> "junction_annotation" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_annotation" in state.rseqc_modules && !state.skip_align },
            fromState: [
                "input": "genome_bam",
                "refgene": "gene_bed",
@@ -122,7 +122,7 @@ workflow run_wf {
            ]
        )
        | rseqc_junctionsaturation.run(
-            runIf: { id, state -> "junction_saturation" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "junction_saturation" in state.rseqc_modules && !state.skip_align },
            fromState: [
                "input": "genome_bam",
                "refgene": "gene_bed",
@@ -139,7 +139,7 @@ workflow run_wf {
            ]
        )
        | rseqc_readdistribution.run(
-            runIf: { id, state -> "read_distribution" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_distribution" in state.rseqc_modules && !state.skip_align },
            fromState: [
                "input": "genome_bam",
                "refgene": "gene_bed", 
@@ -147,7 +147,7 @@ workflow run_wf {
            toState: [ "read_distribution_output": "output" ]
        )                               
        | rseqc_readduplication.run(
-            runIf: { id, state -> "read_duplication" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "read_duplication" in state.rseqc_modules && !state.skip_align },
            fromState: [
                "input": "genome_bam",
                "read_count_upper_limit": "read_count_upper_limit",
@@ -161,7 +161,7 @@ workflow run_wf {
            ]
        )
        | rseqc_tin.run(
-            runIf: { id, state -> "tin" in state.rseqc_modules },
+            runIf: { id, state -> !state.skip_qc && !state.skip_rseqc && "tin" in state.rseqc_modules && !state.skip_align },
            fromState: [
                "bam_input": "genome_bam",
                "bai_input": "genome_bam_index",
@@ -177,6 +177,7 @@ workflow run_wf {
        )

        | dupradar.run(
+            runIf: { id, state -> !state.skip_qc && !state.skip_dupradar && !state.skip_align },
            fromState: [
                "id": "id",
                "input": "genome_bam",
@@ -196,6 +197,7 @@ workflow run_wf {
        )

        | qualimap.run(
+            runIf: { id, state -> !state.skip_qc && !state.skip_qualimap && !state.skip_align },
            fromState: [
                "input": "genome_bam",
                "gtf": "gtf",
@@ -216,7 +218,7 @@ workflow run_wf {
        
        | toSortedList
        | map { list -> 
-            def ids = list.collect { id, state -> state.id }
+            def ids = list.collect { id, state -> id }
            def strandedness = list.collect { id, state -> state.strandedness }
            def num_trimmed_reads = list.collect { id, state -> state.num_trimmed_reads }
            def passed_trimmed_reads = list.collect { id, state -> state.passed_trimmed_reads }
@@ -522,7 +524,7 @@ workflow run_wf {
        | deseq2_qc.run (
            runIf: { id, state -> !state.skip_qc && !state.skip_deseq2_qc && !state.skip_pseudo_align },
            fromState: [
-                "counts": "counts",
+                "counts": "pseudo_counts_gene_length_scaled",
                "vst": "deseq2_vst", 
                "label": "pseudo_aligner" 
            ],
@@ -534,7 +536,7 @@ workflow run_wf {
            ],
            key: "deseq2_qc_pseuso_align_quant"
        )
-
+        | niceView()
        // Get list of samples that failed trimming, mapping, and strand check for MultiQC report
        | map { id, state -> 
            def fail_trimming_header = ["Sample", "Reads after trimming"]
@@ -557,7 +559,7 @@ workflow run_wf {
                        fail_mapping_multiqc += tsv_data.join('\n')
                    }
                    if (!state.passed_strand_check[i]) {
-                        tsv_data = ([ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\t')
+                        tsv_data = ([state.ids[i], state.strandedness[i]] + state.inferred_strand[i]).join('\t')
                        fail_strand_multiqc += tsv_data.join('\n')
                    }
                }
@@ -577,6 +579,7 @@ workflow run_wf {
        }

        | prepare_multiqc_input.run(
+            runIf: { id, state -> !state.skip_qc && !state.skip_multiqc },
            fromState: [
                "fail_trimming_multiqc": "fail_trimming_multiqc", 
                "fail_mapping_multiqc": "fail_mapping_multiqc", 
@@ -617,6 +620,7 @@ workflow run_wf {
        )

        | multiqc.run (
+            runIf: { id, state -> !state.skip_qc && !state.skip_multiqc },
            fromState: [
                "title": "multiqc_title", 
                "input": "multiqc_input", 
--- a/src/workflows/rnaseq/config.vsh.yaml
+++ b/src/workflows/rnaseq/config.vsh.yaml
@@ -276,13 +276,16 @@ argument_groups:
      - name: "--skip_deseq2_qc"
        type: boolean_true
        description: Skip DESeq2 PCA and heatmap plotting.
-      - name: skip_dupradar
+      - name: --skip_dupradar
        type: boolean_true
        description: Skip dupRadar.
-      - name: skip_rseqc
+      - name: --skip_qualimap
+        type: boolean_true
+        description: Skip Qualimap.
+      - name: --skip_rseqc
        type: boolean_true
        description: Skip RSeQC.
-      - name: skip_multiqc
+      - name: --skip_multiqc
        type: boolean_true
        description: Skip MultiQC.

--- a/src/workflows/rnaseq/main.nf
+++ b/src/workflows/rnaseq/main.nf
@@ -241,7 +241,7 @@ workflow run_wf {

    // Filter channels to get samples that passed STAR minimum mapping percentage
    | map { id, state -> 
-      def percent_mapped = getStarPercentMapped(state.star_multiqc) 
+      def percent_mapped = (!state.skip_alignment) ? getStarPercentMapped(state.star_multiqc) : 0.0
      def passed_mapping = (percent_mapped >= state.min_mapped_reads) ? true : false
      [ id, state + [percent_mapped: percent_mapped, passed_mapping: passed_mapping] ]
    }
@@ -336,6 +336,11 @@ workflow run_wf {
          "strandedness": "strandedness", 
          "skip_align": "skip_alignment",
          "skip_pseudo_align": "skip_pseudo_alignment",
+          "skip_dupradar": "skip_dupradar",
+          "skip_qualimap": "skip_qualimap",
+          "skip_rseqc": "skip_rseqc",
+          "skip_multiqc": "skip_multiqc",
+          "skip_preseq": "skip_preseq",
          "gtf": "gtf", 
          "num_trimmed_reads": "num_trimmed_reads",
          "passed_trimmed_reads": "passed_trimmed_reads",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/.config.vsh.yaml
@@ -1083,9 +1083,9 @@ build_info:
  output: "target/nextflow/fastp"
  executable: "target/nextflow/fastp/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/fastp/main.nf
@@ -4023,9 +4023,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/fastp",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/.config.vsh.yaml
@@ -645,9 +645,9 @@ build_info:
  output: "target/nextflow/featurecounts"
  executable: "target/nextflow/featurecounts/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/featurecounts/main.nf
@@ -3549,9 +3549,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/featurecounts",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/.config.vsh.yaml
@@ -685,9 +685,9 @@ build_info:
  output: "target/nextflow/gffread"
  executable: "target/nextflow/gffread/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/gffread/main.nf
@@ -3606,9 +3606,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/gffread",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/.config.vsh.yaml
@@ -456,9 +456,9 @@ build_info:
  output: "target/nextflow/multiqc"
  executable: "target/nextflow/multiqc/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/multiqc/main.nf
@@ -3366,9 +3366,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/multiqc",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/.config.vsh.yaml
@@ -416,9 +416,9 @@ build_info:
  output: "target/nextflow/rsem/rsem_prepare_reference"
  executable: "target/nextflow/rsem/rsem_prepare_reference/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/rsem/rsem_prepare_reference/main.nf
@@ -3245,9 +3245,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/rsem/rsem_prepare_reference",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/.config.vsh.yaml
@@ -277,9 +277,9 @@ build_info:
  output: "target/nextflow/salmon/salmon_index"
  executable: "target/nextflow/salmon/salmon_index/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_index/main.nf
@@ -3129,9 +3129,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/salmon/salmon_index",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/.config.vsh.yaml
@@ -1173,9 +1173,9 @@ build_info:
  output: "target/nextflow/salmon/salmon_quant"
  executable: "target/nextflow/salmon/salmon_quant/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/salmon/salmon_quant/main.nf
@@ -3964,9 +3964,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/salmon/salmon_quant",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/.config.vsh.yaml
@@ -173,9 +173,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_flagstat"
  executable: "target/nextflow/samtools/samtools_flagstat/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_flagstat/main.nf
@@ -3028,9 +3028,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_flagstat",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/.config.vsh.yaml
@@ -183,9 +183,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_idxstats"
  executable: "target/nextflow/samtools/samtools_idxstats/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_idxstats/main.nf
@@ -3040,9 +3040,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_idxstats",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/.config.vsh.yaml
@@ -189,9 +189,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_index"
  executable: "target/nextflow/samtools/samtools_index/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_index/main.nf
@@ -3053,9 +3053,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_index",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/.config.vsh.yaml
@@ -332,9 +332,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_sort"
  executable: "target/nextflow/samtools/samtools_sort/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_sort/main.nf
@@ -3225,9 +3225,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_sort",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/.config.vsh.yaml
@@ -401,9 +401,9 @@ build_info:
  output: "target/nextflow/samtools/samtools_stats"
  executable: "target/nextflow/samtools/samtools_stats/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/samtools/samtools_stats/main.nf
@@ -3295,9 +3295,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/samtools/samtools_stats",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/.config.vsh.yaml
@@ -2663,9 +2663,9 @@ build_info:
  output: "target/nextflow/star/star_align_reads"
  executable: "target/nextflow/star/star_align_reads/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_align_reads/main.nf
@@ -5943,9 +5943,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/star/star_align_reads",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/.config.vsh.yaml
@@ -333,9 +333,9 @@ build_info:
  output: "target/nextflow/star/star_genome_generate"
  executable: "target/nextflow/star/star_genome_generate/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/star/star_genome_generate/main.nf
@@ -3195,9 +3195,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/star/star_genome_generate",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/.config.vsh.yaml
@@ -228,21 +228,6 @@ argument_groups:
    direction: "input"
    multiple: false
    multiple_sep: ";"
-  - type: "integer"
-    name: "--umi_discard_read"
-    description: "After UMI barcode extraction discard either R1 or R2 by setting\
-      \ this parameter to 1 or 2, respectively. Default: `0`\n"
-    info: null
-    example:
-    - 0
-    required: false
-    choices:
-    - 0
-    - 1
-    - 2
-    direction: "input"
-    multiple: false
-    multiple_sep: ";"
 - name: "Common Options"
  arguments:
  - type: "file"
@@ -259,7 +244,7 @@ argument_groups:
    name: "--log2stderr"
    description: "Send logging information to stderr."
    info: null
-    direction: "output"
+    direction: "input"
  - type: "integer"
    name: "--verbose"
    description: "Log level. The higher, the more output."
@@ -449,9 +434,9 @@ build_info:
  output: "target/nextflow/umi_tools/umi_tools_extract"
  executable: "target/nextflow/umi_tools/umi_tools_extract/main.nf"
  viash_version: "0.9.0"
-  git_commit: "7fb67a98539868b9af788338fb5f46d34ab742f7"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
  name: "biobox"
  version: "main"
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/main.nf
@@ -3050,23 +3050,6 @@ meta = [
          "direction" : "input",
          "multiple" : false,
          "multiple_sep" : ";"
-        },
-        {
-          "type" : "integer",
-          "name" : "--umi_discard_read",
-          "description" : "After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively. Default: `0`\n",
-          "example" : [
-            0
-          ],
-          "required" : false,
-          "choices" : [
-            0,
-            1,
-            2
-          ],
-          "direction" : "input",
-          "multiple" : false,
-          "multiple_sep" : ";"
        }
      ]
    },
@@ -3088,7 +3071,7 @@ meta = [
          "type" : "boolean_true",
          "name" : "--log2stderr",
          "description" : "Send logging information to stderr.",
-          "direction" : "output"
+          "direction" : "input"
        },
        {
          "type" : "integer",
@@ -3316,9 +3299,9 @@ meta = [
    "engine" : "docker|native",
    "output" : "target/nextflow/umi_tools/umi_tools_extract",
    "viash_version" : "0.9.0",
-    "git_commit" : "7fb67a98539868b9af788338fb5f46d34ab742f7",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
+    "git_tag" : "v0.2.0-24-g1d17ce0"
  },
  "package_config" : {
    "name" : "biobox",
@@ -3382,8 +3365,8 @@ $( if [ ! -z ${VIASH_PAR_THREE_PRIME+x} ]; then echo "${VIASH_PAR_THREE_PRIME}"
 $( if [ ! -z ${VIASH_PAR_IGNORE_READ_PAIR_SUFFIXES+x} ]; then echo "${VIASH_PAR_IGNORE_READ_PAIR_SUFFIXES}" | sed "s#'#'\\"'\\"'#g;s#.*#par_ignore_read_pair_suffixes='&'#" ; else echo "# par_ignore_read_pair_suffixes="; fi )
 $( if [ ! -z ${VIASH_PAR_UMI_SEPARATOR+x} ]; then echo "${VIASH_PAR_UMI_SEPARATOR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_umi_separator='&'#" ; else echo "# par_umi_separator="; fi )
 $( if [ ! -z ${VIASH_PAR_GROUPING_METHOD+x} ]; then echo "${VIASH_PAR_GROUPING_METHOD}" | sed "s#'#'\\"'\\"'#g;s#.*#par_grouping_method='&'#" ; else echo "# par_grouping_method="; fi )
-$( if [ ! -z ${VIASH_PAR_UMI_DISCARD_READ+x} ]; then echo "${VIASH_PAR_UMI_DISCARD_READ}" | sed "s#'#'\\"'\\"'#g;s#.*#par_umi_discard_read='&'#" ; else echo "# par_umi_discard_read="; fi )
 $( if [ ! -z ${VIASH_PAR_LOG+x} ]; then echo "${VIASH_PAR_LOG}" | sed "s#'#'\\"'\\"'#g;s#.*#par_log='&'#" ; else echo "# par_log="; fi )
+$( if [ ! -z ${VIASH_PAR_LOG2STDERR+x} ]; then echo "${VIASH_PAR_LOG2STDERR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_log2stderr='&'#" ; else echo "# par_log2stderr="; fi )
 $( if [ ! -z ${VIASH_PAR_VERBOSE+x} ]; then echo "${VIASH_PAR_VERBOSE}" | sed "s#'#'\\"'\\"'#g;s#.*#par_verbose='&'#" ; else echo "# par_verbose="; fi )
 $( if [ ! -z ${VIASH_PAR_ERROR+x} ]; then echo "${VIASH_PAR_ERROR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_error='&'#" ; else echo "# par_error="; fi )
 $( if [ ! -z ${VIASH_PAR_TEMP_DIR+x} ]; then echo "${VIASH_PAR_TEMP_DIR}" | sed "s#'#'\\"'\\"'#g;s#.*#par_temp_dir='&'#" ; else echo "# par_temp_dir="; fi )
@@ -3492,15 +3475,6 @@ umi_tools extract \\\\
    \\${par_log2stderr:+--log2stderr} \\\\
    \\${par_verbose:+--verbose "\\$par_verbose"} \\\\
    \\${par_error:+--error "\\$par_error"}
-
-
-if [ "\\$par_umi_discard_read" == 1 ]; then
-    # discard read 1
-    rm "\\$par_read1_out"
-elif [ "\\$par_umi_discard_read" == 2 ]; then
-    # discard read 2 (-f to bypass file existence check)
-    rm -f "\\$par_read2_out"
-fi
 VIASHMAIN
 bash "$tempscript"
 '''
--- a/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json
+++ b/target/dependencies/vsh/vsh/biobox/main/nextflow/umi_tools/umi_tools_extract/nextflow_schema.json
@@ -255,18 +255,6 @@
            }
    

-        ,
-                "umi_discard_read": {
-                "type":
-                "integer",
-                "description": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively",
-                "help_text": "Type: `integer`, example: `0`, choices: ``0`, `1`, `2``. After UMI barcode extraction discard either R1 or R2 by setting this parameter to 1 or 2, respectively. Default: `0`\n",
-                "enum": [0, 1, 2]
-            
-            
-            }
-    
-
 }
 },
    
--- a/target/executable/bbmap_bbsplit/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:48Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/bedtools_genomecov/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:42Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:38Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/cat_fastq/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:43Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/deseq2_qc/.config.vsh.yaml
+++ b/target/executable/deseq2_qc/.config.vsh.yaml
@@ -222,10 +222,9 @@ engines:
    - "RColorBrewer"
    - "pheatmap"
    - "stringr"
+    - "matrixStats"
    bioc:
    - "DESeq2"
-    url:
-    - "https://cran.r-project.org/src/contrib/Archive/matrixStats/matrixStats_1.1.0.tar.gz"
    bioc_force_install: false
  entrypoint: []
  cmd: null
@@ -238,8 +237,8 @@ build_info:
  output: "target/executable/deseq2_qc"
  executable: "target/executable/deseq2_qc/deseq2_qc"
  viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/deseq2_qc/deseq2_qc
+++ b/target/executable/deseq2_qc/deseq2_qc
@@ -503,13 +503,12 @@ ENTRYPOINT []
 RUN Rscript -e 'if (!requireNamespace("remotes", quietly = TRUE)) install.packages("remotes")' && \
  Rscript -e 'if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager")' && \
  Rscript -e 'if (!requireNamespace("DESeq2", quietly = TRUE)) BiocManager::install("DESeq2")' && \
-  Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr"), repos = "https://cran.rstudio.com")' && \
-  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")'
+  Rscript -e 'remotes::install_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), repos = "https://cran.rstudio.com")'

 LABEL org.opencontainers.image.description="Companion container for running component deseq2_qc"
-LABEL org.opencontainers.image.created="2024-10-25T08:58:45Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/dupradar/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:45Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fastqc/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:41Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:22Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/fq_subsample/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:42Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:21Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/getchromsizes/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:40Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gtf2bed/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:39Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:20Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gtf_filter/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:45Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/gunzip/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:43Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:46Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:46Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:14Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -161,8 +161,8 @@ build_info:
  output: "target/executable/multiqc_custom_biotype"
  executable: "target/executable/multiqc_custom_biotype/multiqc_custom_biotype"
  viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
+++ b/target/executable/multiqc_custom_biotype/multiqc_custom_biotype
@@ -476,9 +476,9 @@ function ViashDockerfile {
 FROM python:latest
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component multiqc_custom_biotype"
-LABEL org.opencontainers.image.created="2024-10-25T08:58:43Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/picard_markduplicates/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:41Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:39Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:11Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:40Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/preseq_lcextrap/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:41Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:16Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/qualimap/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:44Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:13Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -299,8 +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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression
+++ b/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="2024-10-25T08:58:40Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:13Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/rsem/rsem_merge_counts/rsem_merge_counts
+++ b/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="2024-10-25T08:58:39Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:12Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:44Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:43Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:43Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:44Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:45Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:19Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:42Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:44Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:17Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 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
@@ -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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:43Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:18Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/sortmerna/.config.vsh.yaml
+++ b/target/executable/sortmerna/.config.vsh.yaml
@@ -192,8 +192,8 @@ build_info:
  output: "target/executable/sortmerna"
  executable: "target/executable/sortmerna/sortmerna"
  viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  version: "main"
--- a/target/executable/sortmerna/sortmerna
+++ b/target/executable/sortmerna/sortmerna
@@ -486,9 +486,9 @@ function ViashDockerfile {
 FROM quay.io/biocontainers/sortmerna:4.3.6--h9ee0642_0
 ENTRYPOINT []
 LABEL org.opencontainers.image.description="Companion container for running component sortmerna"
-LABEL org.opencontainers.image.created="2024-10-25T08:58:42Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:22Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/target/executable/stringtie/.config.vsh.yaml
+++ b/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: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
  name: "rnaseq"
  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="2024-10-25T08:58:44Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.created="2024-11-13T10:13:23Z"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"

 VIASHDOCKER
--- a/Show More
+++ b/Show More