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

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

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

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", 

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.
 

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",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "git_tag" : "v0.2.0-24-g1d17ce0"
   },
   "package_config" : {
     "name" : "biobox",

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_commit: "1d17ce01e25569c8e898b8160af1480ad22fc986"
-  git_remote: "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox"
+  git_remote: "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox"
-  git_tag: "v0.2.0-11-g7fb67a9"
+  git_tag: "v0.2.0-24-g1d17ce0"
 package_config:
   name: "biobox"
   version: "main"

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_commit" : "1d17ce01e25569c8e898b8160af1480ad22fc986",
-    "git_remote" : "https://x-access-token:ghs_lv5GvifOUhTQDSxrDFIWt5FoCBy00e2Tt6iO@github.com/viash-hub/biobox",
+    "git_remote" : "https://x-access-token:ghs_6YTGQkPF5IMZyp8fS3YMcIBjhXPmep1DKcNC@github.com/viash-hub/biobox",
-    "git_tag" : "v0.2.0-11-g7fb67a9"
+    "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"
 '''

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]
-            
-            
-            }
-    
-
 }
 },
     

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_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:21Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -178,8 +178,8 @@ build_info:
   output: "target/executable/bedtools_genomecov"
   executable: "target/executable/bedtools_genomecov/bedtools_genomecov"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -182,8 +182,8 @@ build_info:
   output: "target/executable/cat_additional_fasta"
   executable: "target/executable/cat_additional_fasta/cat_additional_fasta"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -169,8 +169,8 @@ build_info:
   output: "target/executable/cat_fastq"
   executable: "target/executable/cat_fastq/cat_fastq"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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_cran(c("optparse", "ggplot2", "RColorBrewer", "pheatmap", "stringr", "matrixStats"), 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")'
 
 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.created="2024-11-13T10:13:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -266,8 +266,8 @@ build_info:
   output: "target/executable/dupradar"
   executable: "target/executable/dupradar/dupradar"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:20Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -198,8 +198,8 @@ build_info:
   output: "target/executable/fastqc"
   executable: "target/executable/fastqc/fastqc"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:22Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -177,8 +177,8 @@ build_info:
   output: "target/executable/fq_subsample"
   executable: "target/executable/fq_subsample/fq_subsample"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:21Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -167,8 +167,8 @@ build_info:
   output: "target/executable/getchromsizes"
   executable: "target/executable/getchromsizes/getchromsizes"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -145,8 +145,8 @@ build_info:
   output: "target/executable/gtf2bed"
   executable: "target/executable/gtf2bed/gtf2bed"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:20Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -155,8 +155,8 @@ build_info:
   output: "target/executable/gtf_filter"
   executable: "target/executable/gtf_filter/gtf_filter"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -144,8 +144,8 @@ build_info:
   output: "target/executable/gunzip"
   executable: "target/executable/gunzip/gunzip"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:14Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -155,8 +155,8 @@ build_info:
   output: "target/executable/kallisto/kallisto_index"
   executable: "target/executable/kallisto/kallisto_index/kallisto_index"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:14Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -253,8 +253,8 @@ build_info:
   output: "target/executable/kallisto/kallisto_quant"
   executable: "target/executable/kallisto/kallisto_quant/kallisto_quant"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:14Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -207,8 +207,8 @@ build_info:
   output: "target/executable/picard_markduplicates"
   executable: "target/executable/picard_markduplicates/picard_markduplicates"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -409,8 +409,8 @@ build_info:
   output: "target/executable/prepare_multiqc_input"
   executable: "target/executable/prepare_multiqc_input/prepare_multiqc_input"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:11Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -138,8 +138,8 @@ build_info:
   output: "target/executable/preprocess_transcripts_fasta"
   executable: "target/executable/preprocess_transcripts_fasta/preprocess_transcripts_fasta"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -191,8 +191,8 @@ build_info:
   output: "target/executable/preseq_lcextrap"
   executable: "target/executable/preseq_lcextrap/preseq_lcextrap"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:16Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -271,8 +271,8 @@ build_info:
   output: "target/executable/qualimap"
   executable: "target/executable/qualimap/qualimap"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:13Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -299,8 +299,8 @@ build_info:
   output: "target/executable/rsem/rsem_calculate_expression"
   executable: "target/executable/rsem/rsem_calculate_expression/rsem_calculate_expression"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:13Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -182,8 +182,8 @@ build_info:
   output: "target/executable/rsem/rsem_merge_counts"
   executable: "target/executable/rsem/rsem_merge_counts/rsem_merge_counts"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:12Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -163,8 +163,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_bamstat"
   executable: "target/executable/rseqc/rseqc_bamstat/rseqc_bamstat"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -186,8 +186,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_inferexperiment"
   executable: "target/executable/rseqc/rseqc_inferexperiment/rseqc_inferexperiment"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -272,8 +272,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_innerdistance"
   executable: "target/executable/rseqc/rseqc_innerdistance/rseqc_innerdistance"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -260,8 +260,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_junctionannotation"
   executable: "target/executable/rseqc/rseqc_junctionannotation/rseqc_junctionannotation"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -249,8 +249,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_junctionsaturation"
   executable: "target/executable/rseqc/rseqc_junctionsaturation/rseqc_junctionsaturation"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:19Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -162,8 +162,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_readdistribution"
   executable: "target/executable/rseqc/rseqc_readdistribution/rseqc_readdistribution"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -211,8 +211,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_readduplication"
   executable: "target/executable/rseqc/rseqc_readduplication/rseqc_readduplication"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:17Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -214,8 +214,8 @@ build_info:
   output: "target/executable/rseqc/rseqc_tin"
   executable: "target/executable/rseqc/rseqc_tin/rseqc_tin"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:18Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:22Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER

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

@@ -216,8 +216,8 @@ build_info:
   output: "target/executable/stringtie"
   executable: "target/executable/stringtie/stringtie"
   viash_version: "0.9.0"
-  git_commit: "05d48ac2f802e6510893b0966727b56adf2d5bf7"
+  git_commit: "5fbd530a7cf631bcc2930747d4712993ee19f07a"
-  git_remote: "https://x-access-token:ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+  git_remote: "https://x-access-token:ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
 package_config:
   name: "rnaseq"
   version: "main"

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.created="2024-11-13T10:13:23Z"
-LABEL org.opencontainers.image.source="https://x-access-token/ghs_Z6NU8I659v7MJh9nvPEvAbNENWdyYA3AOdw4@github.com/viash-hub/rnaseq"
+LABEL org.opencontainers.image.source="https://x-access-token/ghs_2KJ9dSEPJriSLryPjkD8jGq8HeUsFi4f32RI@github.com/viash-hub/rnaseq"
-LABEL org.opencontainers.image.revision="05d48ac2f802e6510893b0966727b56adf2d5bf7"
+LABEL org.opencontainers.image.revision="5fbd530a7cf631bcc2930747d4712993ee19f07a"
 LABEL org.opencontainers.image.version="main"
 
 VIASHDOCKER