Build branch v0.9 with version v0.9.1 (1bce00e)

Build pipeline: viash-hub.htrnaseq.v0.9-4v78w

Source commit: 1bce00e811

Source message: Bump version to v0.9.1

CHANGELOG.md

@@ -1,3 +1,11 @@
+# htrnaseq v0.9.1
+
+## Bug fixes
+
+* Reverted functionality to set `fastq_publish_dir` and `results_publish_dir` using fromState (PR #64).
+
+* `runner`: fix detection of FASTQ files with non-numerical characters in the sample name (PR #65).
+
 # htrnaseq v0.9.0
 
 ## Breaking changes

_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: |

src/utils/listInputDir/main.nf

@@ -18,7 +18,7 @@ workflow run_wf {
 
         println("Extracting information from fastq/fasta filenames")
         def processed_fastqs = allFastqs.collect { f ->
-          def regex = ~/^(\w+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/
+          def regex = ~/^(\S+)_S(\d+)_(L(\d+)_)?R(\d)_(\d+)\.fast[qa](\.gz)?$/
           def validFastq = f.name ==~ regex
 
           assert validFastq: "${f} does not match the regex ${regex}"

src/workflows/runner/config.vsh.yaml

@@ -60,6 +60,11 @@ resources:
     path: main.nf
     entrypoint: run_wf
 
+test_resources:
+  - type: nextflow_script
+    path: test.nf
+    entrypoint: test_wf
+
 dependencies:
   - name: utils/listInputDir
     repository: local

src/workflows/runner/integration_test.sh

@@ -0,0 +1,13 @@
+# get the root of the directory
+REPO_ROOT=$(git rev-parse --show-toplevel)
+
+# ensure that the command below is run from the root of the repository
+cd "$REPO_ROOT"
+
+nextflow \
+  run . \
+  -main-script src/workflows/runner/test.nf \
+  -config ./src/config/labels.config \
+  -entry test_wf \
+  -resume \
+  -profile docker,local

src/workflows/runner/main.nf

@@ -16,24 +16,6 @@ workflow run_wf {
         return [id, new_state]
       }
 
-
-    // When this workflow is being used as a subworkflow, the publish directories might be defined
-    // in the state and not in params. The following snippets make sure the values are copied from state to params.
-    set_publish_dirs_channel = raw_ch
-      | toSortedList()
-      | map {ids_and_states ->
-        def publish_dir_arguments = ["results_publish_dir", "fastq_publish_dir"]
-        for (publish_dir_arg in publish_dir_arguments) {
-          if (!params.containsKey(publish_dir_arg)) {
-              def state_items = ids_and_states.collect{it[1].get(publish_dir_arg)}
-              assert state_items.toSet().size() == state_items.size(), "Items for '${publish_dir_arg}' must be unique! Found ${state_items}"
-              params[publish_dir_arg] = state_items[0]
-          }
-        }
-        ids_and_states
-      }
-
-
     save_params_ch = input_ch
       | toSortedList()
       | map { states ->
@@ -172,11 +154,7 @@ workflow run_wf {
       
       }
 
-    // Use combine here in order to be sure tha the publish dirs are set in params
-    // set_publish_dirs_channel should contain 1 event; so the result of the combine
-    // contains the events from grouped_with_params_list_ch
-    results_publish_ch = grouped_with_params_list_ch.combine(set_publish_dirs_channel)
-      | map {event -> [event[0], event[1]]}
+    results_publish_ch = grouped_with_params_list_ch
       | publish_results.run(
         fromState: { id, state ->
           def output_dir = "${state.project_id}/${state.experiment_id}/data_processed/${date}_htrnaseq_${version}"
@@ -204,7 +182,7 @@ workflow run_wf {
         ]
       )
 
-    fastq_publish_split_ch = grouped_ch
+    fastq_publish_ch = grouped_ch
       | flatMap{id, state ->
         def new_states = state.fastq_output.collect{fastq_dir -> 
           def run_id = fastq_dir.name // The folder name corresponds to the run
@@ -220,9 +198,6 @@ workflow run_wf {
         }
         return new_states
       }
-
-    fastq_publish_ch = fastq_publish_split_ch.combine(set_publish_dirs_channel)
-      | map{event -> [event[0], event[1]]}
       | publish_fastqs.run(
         fromState: { id, state ->
           def output_dir = "${state.run_id}/${date}_htrnaseq_${version}/${state.sample_id}"
@@ -287,4 +262,4 @@ def reduce_paths(paths, offset = 0) {
   println("")
 
   return grouped_paths
-}
+}

src/workflows/runner/nextflow.config

@@ -2,6 +2,10 @@ manifest {
   nextflowVersion = '!>=20.12.1-edge'
 }
 
+params {
+  rootDir = java.nio.file.Paths.get("$projectDir/../../../").toAbsolutePath().normalize().toString()
+}
+
 process {
   withName: publishStatesProc {
     publishDir = [ enabled: false ]

src/workflows/runner/test.nf

@@ -0,0 +1,181 @@
+import java.nio.file.Files
+import nextflow.exception.WorkflowScriptErrorException
+
+def viash_config = java.nio.file.Paths.get("${params.rootDir}/target/nextflow/workflows/runner/_viash.yaml")
+
+def get_version(inputFile) {
+  def yamlSlurper = new groovy.yaml.YamlSlurper()
+  def loaded_viash_config = yamlSlurper.parse(file(inputFile))
+  def version = (loaded_viash_config.version) ? loaded_viash_config.version : "unknown_version"
+  println("HT-RNAseq version to be used: ${version}")
+  return version
+}
+
+// Create temporary directory for the publish_dir if it is not defined
+if (!params.containsKey("publish_dir") && params.containsKey("publishDir")) {
+    params.publish_dir = params.publishDir
+}
+
+if (!params.containsKey("publish_dir")) {
+    def tempDir = Files.createTempDirectory("demultiplex_runner_integration_test")
+    println "Created temp directory: $tempDir"
+    // Register shutdown hook to delete it on JVM exit
+    Runtime.runtime.addShutdownHook(new Thread({
+        try {
+            // Delete directory recursively
+            Files.walk(tempDir)
+                .sorted(Comparator.reverseOrder())
+                .forEach { Files.delete(it) }
+            println "Deleted temp directory: $tempDir"
+        } catch (Exception e) {
+            println "Failed to delete temp directory: $e"
+        }
+    }))
+    params.publish_dir = tempDir
+}
+
+params.fastq_publish_dir = (file(params.publish_dir) / "fastq").toUriString()
+params.results_publish_dir = (file(params.publish_dir) / "results").toUriString()
+
+
+// The module inherits the parameters defined before the include statement, 
+// therefore any parameters set afterwards will not be used by the module.
+
+include { runner } from params.rootDir + "/target/nextflow/workflows/runner/main.nf"
+params.resources_test = params.rootDir + "/resources_test"
+
+workflow test_wf {
+  pipeline_version = get_version(viash_config)
+  resources_test = file(params.resources_test)
+
+  // results_publish_dir and results_publish_dir are inherited using params
+  // but they must be defined in the state as well because viash will check
+  // if all arguments are present in the hashmap
+  output_ch = Channel.fromList([
+    [
+        id: "run_1",
+        input: resources_test.resolve("10k/SRR14730301"),
+        genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
+        barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
+        annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
+        project_id: "foo",
+        experiment_id: "bar",
+        fastq_publish_dir: params.fastq_publish_dir,
+        results_publish_dir: params.results_publish_dir,
+    ],
+    [
+        id: "run_2",
+        input:  resources_test.resolve("10k/SRR14730301"),
+        genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
+        barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
+        annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
+        project_id: "foo",
+        experiment_id: "bar",
+        fastq_publish_dir: params.fastq_publish_dir,
+        results_publish_dir: params.results_publish_dir,
+    ],
+    [
+        id: "run_3",
+        input:resources_test.resolve("10k/SRR14730302"),
+        genomeDir: resources_test.resolve("genomeDir/subset/Homo_sapiens/v0.0.3"),
+        barcodesFasta: resources_test.resolve("2-wells-with-ids.fasta"),
+        annotation: resources_test.resolve("genomeDir/gencode.v41.annotation.gtf.gz"),
+        project_id: "foo",
+        experiment_id: "bar",
+        fastq_publish_dir: params.fastq_publish_dir,
+        results_publish_dir: params.results_publish_dir,
+    ]
+  ])
+  | map { state -> [state.id, state]}
+  | runner.run(
+    toState: { id, output, state -> output + [orig_input: state.input] }
+  )
+  | view { output ->
+    assert output.size() == 2 : "outputs should contain two elements; [id, file]"
+    "Output: $output"
+  }
+
+  tosortedlistch = output_ch
+    | toSortedList()
+    | map {events ->
+        assert events.size() == 1, "Expected one events to be output, found ${events.size()}"
+    }
+
+
+    workflow.onComplete = {
+        try {
+            // Nexflow only allows exceptions generated using the 'error' function (which throws WorkflowScriptErrorException).
+            // So in order for the assert statement to work (or allow other errors to let the tests to fail)
+            // We need to wrap these in WorkflowScriptErrorException. See https://github.com/nextflow-io/nextflow/pull/4458/files
+            // The error message will show up in .nextflow.log
+            def fastq_subdir = file("${params.fastq_publish_dir}")
+            assert fastq_subdir.isDirectory()
+            def found_fastq_folders = fastq_subdir.listFiles().findAll{it.isDirectory()}.collect{it.name}.toSet()
+            def expected_run_folders = ["run_1", "run_2", "run_3"].toSet()
+            assert found_fastq_folders == expected_run_folders, "Expected correct run folders to be present. Found: ${found_fastq_folders}"
+            unique_dirs = [
+                "run1": files("${fastq_subdir.toUriString()}/run_1/*_htrnaseq_${pipeline_version}", type: 'any'),
+                "run2": files("${fastq_subdir.toUriString()}/run_2/*_htrnaseq_${pipeline_version}", type: 'any'), 
+                "run3": files("${fastq_subdir.toUriString()}/run_3/*_htrnaseq_${pipeline_version}", type: 'any'),  
+            ]
+            assert unique_dirs.every{it.value.size() == 1}
+            unique_dirs = unique_dirs.collectEntries{k, v -> [k, v[0]]}
+
+            assert unique_dirs.every{it.value.isDirectory()}
+            assert unique_dirs.collect{_key, _value -> _value.name}.toSet().size() == 1
+            def expected_samples = [
+                "run1": "VH02001612",
+                "run2": "VH02001612",
+                "run3": "VH02001614"
+            ]
+
+            unique_dirs.each{_key, _value ->
+                def expected_sample = expected_samples[_key]
+                def expected_sample_dir = _value.resolve(expected_sample)
+                assert expected_sample_dir.isDirectory(), "Expected ${expected_sample} to be present in ${_value}"
+                def expected_fastq_files = [
+                    "A1_R1_001.fastq", "A1_R2_001.fastq", 
+                    "B1_R1_001.fastq", "B1_R2_001.fastq",
+                    "unknown_R1_001.fastq", "unknown_R2_001.fastq"]
+                def found_files = files("${expected_sample_dir}/*.fastq", type: 'any')
+                assert found_files.every{it.isFile()}
+                assert found_files.collect{it.name}.toSet() == expected_fastq_files.toSet()
+            }
+
+            def results_subdir = file("${params.results_publish_dir}")
+            assert fastq_subdir.isDirectory()
+            def expected_subdir = file("${results_subdir}/foo/bar/data_processed", type: 'any')
+            assert expected_subdir.isDirectory()
+            def expected_result_dir = files("${expected_subdir}/*_htrnaseq_${pipeline_version}", type: 'any')
+            assert expected_result_dir.size() == 1
+            expected_result_dir = expected_result_dir[0]
+            assert expected_result_dir.isDirectory()
+            def expected_esets = ["VH02001612.rds", "VH02001614.rds"]
+            def found_esets = files("${expected_result_dir}/esets/*.rds", type: 'any')
+            assert found_esets.size() == 2
+            assert found_esets.collect{it.name}.toSet() == expected_esets.toSet()
+            expected_table_filenames = ["VH02001612.txt", "VH02001614.txt"]
+            def found_pdata = files("${expected_result_dir}/pData/*.txt", type: 'any')
+            assert found_pdata.size() == 2
+            assert found_pdata.collect{it.name}.toSet() == expected_table_filenames.toSet()
+            def found_nr_genes_nr_reads = files("${expected_result_dir}/nrReadsNrGenesPerChrom/*.txt", type: 'any')
+            assert found_nr_genes_nr_reads.size() == 2
+            assert found_nr_genes_nr_reads.collect{it.name}.toSet() == expected_table_filenames.toSet() 
+            def found_star_logs = files("${expected_result_dir}/starLogs/*.txt", type: 'any')
+            assert found_star_logs.size() == 2
+            assert found_star_logs.collect{it.name}.toSet() == expected_table_filenames.toSet()
+            def star_output = file("${expected_result_dir}/star_output", type: 'any')
+            assert star_output.isDirectory()
+            
+            assert files("${star_output}/*", type: 'any').collect{it.name}.toSet() == ["VH02001612", "VH02001614"].toSet()
+            assert files("${star_output}/VH02001612/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+            assert files("${star_output}/VH02001614/*", type: 'any').collect{it.name}.toSet() == ["ACACCGAATT", "GGCTATTGAT"].toSet()
+            assert file("${expected_result_dir}/report.html").isFile()
+            assert file("${expected_result_dir}/params.yaml").isFile()
+            assert file("${expected_result_dir}/fData.gencode.v41.annotation.gtf.gz.txt").isFile()
+
+        } catch (Exception e) {
+            throw new WorkflowScriptErrorException("Integration test failed!", e)
+        }
+    }
+}

target/executable/eset/create_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -206,12 +206,12 @@ build_info:
   output: "target/executable/eset/create_eset"
   executable: "target/executable/eset/create_eset/create_eset"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -243,7 +243,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/eset/create_eset/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/eset/create_eset/create_eset

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_eset v0.9.0
+# create_eset v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -456,10 +456,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_eset"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:41Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -576,7 +576,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_eset v0.9.0"
+  echo "create_eset v0.9.1"
   echo ""
   echo "Arguments:"
   echo "    --pDataFile"
@@ -642,7 +642,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_eset v0.9.0"
+            echo "create_eset v0.9.1"
             exit
             ;;
         --pDataFile)
@@ -794,7 +794,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_eset:v0.9.1'
   fi
 
   # print dockerfile

target/executable/eset/create_fdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -154,7 +154,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -183,12 +183,12 @@ build_info:
   output: "target/executable/eset/create_fdata"
   executable: "target/executable/eset/create_fdata/create_fdata"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -220,7 +220,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/eset/create_fdata/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/eset/create_fdata/create_fdata

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_fdata v0.9.0
+# create_fdata v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_fdata"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_fdata v0.9.0"
+  echo "create_fdata v0.9.1"
   echo ""
   echo "Create a fdata file"
   echo ""
@@ -643,7 +643,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_fdata v0.9.0"
+            echo "create_fdata v0.9.1"
             exit
             ;;
         --gtf)
@@ -756,7 +756,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_fdata:v0.9.1'
   fi
 
   # print dockerfile

target/executable/eset/create_pdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -168,7 +168,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -197,12 +197,12 @@ build_info:
   output: "target/executable/eset/create_pdata"
   executable: "target/executable/eset/create_pdata/create_pdata"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -234,7 +234,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/eset/create_pdata/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/eset/create_pdata/create_pdata

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_pdata v0.9.0
+# create_pdata v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component eset create_pdata"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:41Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_pdata v0.9.0"
+  echo "create_pdata v0.9.1"
   echo ""
   echo "Create a pdata file by combining the mapping statistics"
   echo ""
@@ -653,7 +653,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_pdata v0.9.0"
+            echo "create_pdata v0.9.1"
             exit
             ;;
         --star_stats_file)
@@ -777,7 +777,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/eset/create_pdata:v0.9.1'
   fi
 
   # print dockerfile

target/executable/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -134,7 +134,7 @@ engines:
   id: "docker"
   image: "bioconductor/bioconductor_docker:3.19"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -155,12 +155,12 @@ build_info:
   output: "target/executable/integration_test_components/htrnaseq/check_eset"
   executable: "target/executable/integration_test_components/htrnaseq/check_eset/check_eset"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -192,7 +192,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/integration_test_components/htrnaseq/check_eset/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/integration_test_components/htrnaseq/check_eset/check_eset

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# check_eset v0.9.0
+# check_eset v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -455,10 +455,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/htrnaseq check_eset"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:41Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -575,7 +575,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_eset v0.9.0"
+  echo "check_eset v0.9.1"
   echo ""
   echo "This component test the ExpressionSet object as output by the main pipeline."
   echo ""
@@ -635,7 +635,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "check_eset v0.9.0"
+            echo "check_eset v0.9.1"
             exit
             ;;
         --eset)
@@ -754,7 +754,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/htrnaseq/check_eset:v0.9.1'
   fi
 
   # print dockerfile

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -141,7 +141,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -164,12 +164,12 @@ build_info:
   output: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -201,7 +201,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/integration_test_components/well_demultiplexing/check_cutadapt_output/check_cutadapt_output

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# check_cutadapt_output v0.9.0
+# check_cutadapt_output v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component integration_test_components/well_demultiplexing check_cutadapt_output"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:41Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "check_cutadapt_output v0.9.0"
+  echo "check_cutadapt_output v0.9.1"
   echo ""
   echo "This component test the cutadapt output from the well_demultiplex subworkflow."
   echo ""
@@ -641,7 +641,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "check_cutadapt_output v0.9.0"
+            echo "check_cutadapt_output v0.9.1"
             exit
             ;;
         --fastq_r1)
@@ -783,7 +783,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output:v0.9.1'
   fi
 
   # print dockerfile

target/executable/io/publish_fastqs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.9.0"
+version: "v0.9.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -121,7 +121,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -139,12 +139,12 @@ build_info:
   output: "target/executable/io/publish_fastqs"
   executable: "target/executable/io/publish_fastqs/publish_fastqs"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -176,7 +176,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/io/publish_fastqs/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/io/publish_fastqs/publish_fastqs

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish_fastqs v0.9.0
+# publish_fastqs v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_fastqs"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:41Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_fastqs v0.9.0"
+  echo "publish_fastqs v0.9.1"
   echo ""
   echo "Publish the fastq files per well"
   echo ""
@@ -631,7 +631,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish_fastqs v0.9.0"
+            echo "publish_fastqs v0.9.1"
             exit
             ;;
         --input)
@@ -750,7 +750,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_fastqs:v0.9.1'
   fi
 
   # print dockerfile

target/executable/io/publish_results/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.9.0"
+version: "v0.9.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -184,7 +184,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -202,12 +202,12 @@ build_info:
   output: "target/executable/io/publish_results"
   executable: "target/executable/io/publish_results/publish_results"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -239,7 +239,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/io/publish_results/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/io/publish_results/publish_results

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# publish_results v0.9.0
+# publish_results v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -450,10 +450,10 @@ RUN apt-get update && \
   rm -rf /var/lib/apt/lists/*
 
 LABEL org.opencontainers.image.description="Companion container for running component io publish_results"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -570,7 +570,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "publish_results v0.9.0"
+  echo "publish_results v0.9.1"
   echo ""
   echo "Publish the results"
   echo ""
@@ -652,7 +652,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "publish_results v0.9.0"
+            echo "publish_results v0.9.1"
             exit
             ;;
         --star_output)
@@ -878,7 +878,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/io/publish_results:v0.9.1'
   fi
 
   # print dockerfile

target/executable/parallel_map/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -248,7 +248,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -285,12 +285,12 @@ build_info:
   output: "target/executable/parallel_map"
   executable: "target/executable/parallel_map/parallel_map"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -322,7 +322,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/parallel_map/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/parallel_map/parallel_map

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# parallel_map v0.9.0
+# parallel_map v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -461,10 +461,10 @@ ENV STAR_BINARY=STAR
 COPY STAR /usr/local/bin/$STAR_BINARY
 LABEL org.opencontainers.image.authors="Dries Schaumont, Toni Verbeiren"
 LABEL org.opencontainers.image.description="Companion container for running component parallel_map"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:42Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "parallel_map v0.9.0"
+  echo "parallel_map v0.9.1"
   echo ""
   echo "Map wells in batch, using STAR"
   echo "Spliced Transcripts Alignment to a Reference (C) Alexander Dobin"
@@ -705,7 +705,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "parallel_map v0.9.0"
+            echo "parallel_map v0.9.1"
             exit
             ;;
         --input_r1)
@@ -907,7 +907,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/parallel_map:v0.9.1'
   fi
 
   # print dockerfile

target/executable/report/create_report/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -215,12 +215,12 @@ build_info:
   output: "target/executable/report/create_report"
   executable: "target/executable/report/create_report/create_report"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -252,7 +252,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/report/create_report/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/report/create_report/create_report

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# create_report v0.9.0
+# create_report v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -465,10 +465,10 @@ RUN Rscript -e 'options(warn = 2); if (!requireNamespace("remotes", quietly = TR
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component report create_report"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -585,7 +585,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "create_report v0.9.0"
+  echo "create_report v0.9.1"
   echo ""
   echo "Create a basic QC report in HTML format based on a number of esets."
   echo ""
@@ -644,7 +644,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "create_report v0.9.0"
+            echo "create_report v0.9.1"
             exit
             ;;
         --eset)
@@ -763,7 +763,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/report/create_report:v0.9.1'
   fi
 
   # print dockerfile

target/executable/stats/combine_star_logs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -175,7 +175,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -204,12 +204,12 @@ build_info:
   output: "target/executable/stats/combine_star_logs"
   executable: "target/executable/stats/combine_star_logs/combine_star_logs"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -241,7 +241,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/stats/combine_star_logs/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/stats/combine_star_logs/combine_star_logs

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# combine_star_logs v0.9.0
+# combine_star_logs v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -457,10 +457,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont"
 LABEL org.opencontainers.image.description="Companion container for running component stats combine_star_logs"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -577,7 +577,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "combine_star_logs v0.9.0"
+  echo "combine_star_logs v0.9.1"
   echo ""
   echo "Arguments:"
   echo "    --barcodes"
@@ -655,7 +655,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "combine_star_logs v0.9.0"
+            echo "combine_star_logs v0.9.1"
             exit
             ;;
         --barcodes)
@@ -825,7 +825,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/combine_star_logs:v0.9.1'
   fi
 
   # print dockerfile

target/executable/stats/generate_pool_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -188,12 +188,12 @@ build_info:
   output: "target/executable/stats/generate_pool_statistics"
   executable: "target/executable/stats/generate_pool_statistics/generate_pool_statistics"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -225,7 +225,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/stats/generate_pool_statistics/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/stats/generate_pool_statistics/generate_pool_statistics

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# generate_pool_statistics v0.9.0
+# generate_pool_statistics v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -458,10 +458,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_pool_statistics"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:39Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:32Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -578,7 +578,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_pool_statistics v0.9.0"
+  echo "generate_pool_statistics v0.9.1"
   echo ""
   echo "Arguments:"
   echo "    --nrReadsNrGenesPerChrom"
@@ -648,7 +648,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "generate_pool_statistics v0.9.0"
+            echo "generate_pool_statistics v0.9.1"
             exit
             ;;
         --nrReadsNrGenesPerChrom)
@@ -767,7 +767,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_pool_statistics:v0.9.1'
   fi
 
   # print dockerfile

target/executable/stats/generate_well_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -230,7 +230,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -270,12 +270,12 @@ build_info:
   output: "target/executable/stats/generate_well_statistics"
   executable: "target/executable/stats/generate_well_statistics/generate_well_statistics"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -307,7 +307,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/stats/generate_well_statistics/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/stats/generate_well_statistics/generate_well_statistics

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# generate_well_statistics v0.9.0
+# generate_well_statistics v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -461,10 +461,10 @@ RUN pip install --upgrade pip && \
 
 LABEL org.opencontainers.image.authors="Dries Schaumont, Marijke Van Moerbeke"
 LABEL org.opencontainers.image.description="Companion container for running component stats generate_well_statistics"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:30Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -581,7 +581,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "generate_well_statistics v0.9.0"
+  echo "generate_well_statistics v0.9.1"
   echo ""
   echo "Generate summary statistics from BAM files generated by STAR solo."
   echo ""
@@ -685,7 +685,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "generate_well_statistics v0.9.0"
+            echo "generate_well_statistics v0.9.1"
             exit
             ;;
         --input)
@@ -864,7 +864,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/stats/generate_well_statistics:v0.9.1'
   fi
 
   # print dockerfile

target/executable/utils/save_params/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "save_params"
 namespace: "utils"
-version: "v0.9.0"
+version: "v0.9.1"
 argument_groups:
 - name: "Inputs"
   arguments:
@@ -128,7 +128,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -151,12 +151,12 @@ build_info:
   output: "target/executable/utils/save_params"
   executable: "target/executable/utils/save_params/save_params"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -188,7 +188,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/executable/utils/save_params/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/executable/utils/save_params/save_params

@@ -1,6 +1,6 @@
 #!/usr/bin/env bash
 
-# save_params v0.9.0
+# save_params v0.9.1
 # 
 # This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 # work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -453,10 +453,10 @@ RUN pip install --upgrade pip && \
   pip install --upgrade --no-cache-dir "pyyaml"
 
 LABEL org.opencontainers.image.description="Companion container for running component utils save_params"
-LABEL org.opencontainers.image.created="2025-07-30T14:40:40Z"
+LABEL org.opencontainers.image.created="2025-08-01T11:03:31Z"
 LABEL org.opencontainers.image.source="https://github.com/viash-hub/htrnaseq"
-LABEL org.opencontainers.image.revision="8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
-LABEL org.opencontainers.image.version="v0.9.0"
+LABEL org.opencontainers.image.revision="1bce00e81124868b9dce7df10f3aa090ea38af22"
+LABEL org.opencontainers.image.version="v0.9.1"
 
 VIASHDOCKER
   fi
@@ -573,7 +573,7 @@ VIASH_DOCKER_RUN_ARGS=(-i --rm)
 
 # ViashHelp: Display helpful explanation about this executable
 function ViashHelp {
-  echo "save_params v0.9.0"
+  echo "save_params v0.9.1"
   echo ""
   echo "Save parameters to a YAML file"
   echo ""
@@ -639,7 +639,7 @@ while [[ $# -gt 0 ]]; do
             shift 1
             ;;
         --version)
-            echo "save_params v0.9.0"
+            echo "save_params v0.9.1"
             exit
             ;;
         --id)
@@ -763,7 +763,7 @@ if [[ "$VIASH_ENGINE_TYPE" == "docker" ]]; then
 
   # determine docker image id
   if [[ "$VIASH_ENGINE_ID" == 'docker' ]]; then
-    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.9.0'
+    VIASH_DOCKER_IMAGE_ID='images.viash-hub.com/vsh/htrnaseq/utils/save_params:v0.9.1'
   fi
 
   # print dockerfile

target/nextflow/eset/create_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_eset"
 namespace: "eset"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -178,7 +178,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -206,12 +206,12 @@ build_info:
   output: "target/nextflow/eset/create_eset"
   executable: "target/nextflow/eset/create_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -243,7 +243,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/eset/create_eset/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/eset/create_eset/main.nf

@@ -1,4 +1,4 @@
-// create_eset v0.9.0
+// create_eset v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_eset",
   "namespace" : "eset",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3271,7 +3271,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3309,13 +3309,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3333,7 +3333,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -4208,7 +4208,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_eset",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_eset/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_eset'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
 

target/nextflow/eset/create_fdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_fdata"
 namespace: "eset"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -154,7 +154,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -183,12 +183,12 @@ build_info:
   output: "target/nextflow/eset/create_fdata"
   executable: "target/nextflow/eset/create_fdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -220,7 +220,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/eset/create_fdata/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/eset/create_fdata/main.nf

@@ -1,4 +1,4 @@
-// create_fdata v0.9.0
+// create_fdata v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_fdata",
   "namespace" : "eset",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3279,13 +3279,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_fdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3303,7 +3303,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3873,7 +3873,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_fdata",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_fdata/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_fdata'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'Create a fdata file\n'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/eset/create_pdata/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_pdata"
 namespace: "eset"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -168,7 +168,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -197,12 +197,12 @@ build_info:
   output: "target/nextflow/eset/create_pdata"
   executable: "target/nextflow/eset/create_pdata/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -234,7 +234,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/eset/create_pdata/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/eset/create_pdata/main.nf

@@ -1,4 +1,4 @@
-// create_pdata v0.9.0
+// create_pdata v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_pdata",
   "namespace" : "eset",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3252,7 +3252,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3293,13 +3293,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/eset/create_pdata",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3317,7 +3317,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3813,7 +3813,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/eset/create_pdata",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/eset/create_pdata/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'eset/create_pdata'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'Create a pdata file by combining the mapping statistics \n'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/integration_test_components/htrnaseq/check_eset/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_eset"
 namespace: "integration_test_components/htrnaseq"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -134,7 +134,7 @@ engines:
   id: "docker"
   image: "bioconductor/bioconductor_docker:3.19"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "r"
@@ -155,12 +155,12 @@ build_info:
   output: "target/nextflow/integration_test_components/htrnaseq/check_eset"
   executable: "target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -192,7 +192,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/integration_test_components/htrnaseq/check_eset/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/integration_test_components/htrnaseq/check_eset/main.nf

@@ -1,4 +1,4 @@
-// check_eset v0.9.0
+// check_eset v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "check_eset",
   "namespace" : "integration_test_components/htrnaseq",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3206,7 +3206,7 @@ meta = [
       "id" : "docker",
       "image" : "bioconductor/bioconductor_docker:3.19",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3233,13 +3233,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/htrnaseq/check_eset",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3257,7 +3257,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3907,7 +3907,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/integration_test_components/htrnaseq/check_eset",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/integration_test_components/htrnaseq/check_eset/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'integration_test_components/htrnaseq/check_eset'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'This component test the ExpressionSet object as output by the main pipeline.'
   author = 'Dries Schaumont'
 }

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "check_cutadapt_output"
 namespace: "integration_test_components/well_demultiplexing"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -141,7 +141,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -164,12 +164,12 @@ build_info:
   output: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output"
   executable: "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -201,7 +201,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/main.nf

@@ -1,4 +1,4 @@
-// check_cutadapt_output v0.9.0
+// check_cutadapt_output v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "check_cutadapt_output",
   "namespace" : "integration_test_components/well_demultiplexing",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3213,7 +3213,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3244,13 +3244,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3268,7 +3268,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3787,7 +3787,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/integration_test_components/well_demultiplexing/check_cutadapt_output",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/integration_test_components/well_demultiplexing/check_cutadapt_output/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'integration_test_components/well_demultiplexing/check_cutadapt_output'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'This component test the cutadapt output from the well_demultiplex subworkflow.'
   author = 'Dries Schaumont'
 }

target/nextflow/io/publish_fastqs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_fastqs"
 namespace: "io"
-version: "v0.9.0"
+version: "v0.9.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -121,7 +121,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -139,12 +139,12 @@ build_info:
   output: "target/nextflow/io/publish_fastqs"
   executable: "target/nextflow/io/publish_fastqs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -176,7 +176,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/io/publish_fastqs/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/io/publish_fastqs/main.nf

@@ -1,4 +1,4 @@
-// publish_fastqs v0.9.0
+// publish_fastqs v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish_fastqs",
   "namespace" : "io",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3184,7 +3184,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3207,13 +3207,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_fastqs",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3231,7 +3231,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3683,7 +3683,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/io/publish_fastqs",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish_fastqs/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish_fastqs'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'Publish the fastq files per well'
 }
 

target/nextflow/io/publish_results/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "publish_results"
 namespace: "io"
-version: "v0.9.0"
+version: "v0.9.1"
 argument_groups:
 - name: "Input arguments"
   arguments:
@@ -184,7 +184,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -202,12 +202,12 @@ build_info:
   output: "target/nextflow/io/publish_results"
   executable: "target/nextflow/io/publish_results/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -239,7 +239,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/io/publish_results/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/io/publish_results/main.nf

@@ -1,4 +1,4 @@
-// publish_results v0.9.0
+// publish_results v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "publish_results",
   "namespace" : "io",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "argument_groups" : [
     {
       "name" : "Input arguments",
@@ -3254,7 +3254,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3277,13 +3277,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/io/publish_results",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3301,7 +3301,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3789,7 +3789,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/io/publish_results",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/io/publish_results/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'io/publish_results'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'Publish the results'
 }
 

target/nextflow/parallel_map/.config.vsh.yaml

@@ -1,5 +1,5 @@
 name: "parallel_map"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -248,7 +248,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -285,12 +285,12 @@ build_info:
   output: "target/nextflow/parallel_map"
   executable: "target/nextflow/parallel_map/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -322,7 +322,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/parallel_map/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/parallel_map/main.nf

@@ -1,4 +1,4 @@
-// parallel_map v0.9.0
+// parallel_map v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "resources_dir": moduleDir.toRealPath().normalize(),
   "config": processConfig(readJsonBlob('''{
   "name" : "parallel_map",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3332,7 +3332,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3379,13 +3379,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/parallel_map",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3403,7 +3403,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -4172,7 +4172,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/parallel_map",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/parallel_map/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'parallel_map'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'Map wells in batch, using STAR\nSpliced Transcripts Alignment to a Reference (C) Alexander Dobin\nhttps://github.com/alexdobin/STAR\n'
   author = 'Dries Schaumont, Toni Verbeiren'
 }

target/nextflow/report/create_report/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "create_report"
 namespace: "report"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "rocker/r2u:24.04"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -215,12 +215,12 @@ build_info:
   output: "target/nextflow/report/create_report"
   executable: "target/nextflow/report/create_report/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -252,7 +252,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/report/create_report/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/report/create_report/main.nf

@@ -1,4 +1,4 @@
-// create_report v0.9.0
+// create_report v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "create_report",
   "namespace" : "report",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3251,7 +3251,7 @@ meta = [
       "id" : "docker",
       "image" : "rocker/r2u:24.04",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3323,13 +3323,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/report/create_report",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3347,7 +3347,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3832,7 +3832,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/report/create_report",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/report/create_report/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'report/create_report'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'Create a basic QC report in HTML format based on a number of esets.\n'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/stats/combine_star_logs/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "combine_star_logs"
 namespace: "stats"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -175,7 +175,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -204,12 +204,12 @@ build_info:
   output: "target/nextflow/stats/combine_star_logs"
   executable: "target/nextflow/stats/combine_star_logs/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -241,7 +241,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/stats/combine_star_logs/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/stats/combine_star_logs/main.nf

@@ -1,4 +1,4 @@
-// combine_star_logs v0.9.0
+// combine_star_logs v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3035,7 +3035,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "combine_star_logs",
   "namespace" : "stats",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3254,7 +3254,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3295,13 +3295,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/combine_star_logs",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3319,7 +3319,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3978,7 +3978,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/stats/combine_star_logs",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/stats/combine_star_logs/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'stats/combine_star_logs'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   author = 'Dries Schaumont'
 }
 

target/nextflow/stats/generate_pool_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_pool_statistics"
 namespace: "stats"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -159,7 +159,7 @@ engines:
   id: "docker"
   image: "python:3.12-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "apt"
@@ -188,12 +188,12 @@ build_info:
   output: "target/nextflow/stats/generate_pool_statistics"
   executable: "target/nextflow/stats/generate_pool_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -225,7 +225,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/stats/generate_pool_statistics/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/stats/generate_pool_statistics/main.nf

@@ -1,4 +1,4 @@
-// generate_pool_statistics v0.9.0
+// generate_pool_statistics v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "generate_pool_statistics",
   "namespace" : "stats",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3238,7 +3238,7 @@ meta = [
       "id" : "docker",
       "image" : "python:3.12-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3279,13 +3279,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_pool_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3303,7 +3303,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3833,7 +3833,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/stats/generate_pool_statistics",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/stats/generate_pool_statistics/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'stats/generate_pool_statistics'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }
 

target/nextflow/stats/generate_well_statistics/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "generate_well_statistics"
 namespace: "stats"
-version: "v0.9.0"
+version: "v0.9.1"
 authors:
 - name: "Dries Schaumont"
   roles:
@@ -230,7 +230,7 @@ engines:
   id: "docker"
   image: "debian:stable-slim"
   target_registry: "images.viash-hub.com"
-  target_tag: "v0.9.0"
+  target_tag: "v0.9.1"
   namespace_separator: "/"
   setup:
   - type: "docker"
@@ -270,12 +270,12 @@ build_info:
   output: "target/nextflow/stats/generate_well_statistics"
   executable: "target/nextflow/stats/generate_well_statistics/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -307,7 +307,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/stats/generate_well_statistics/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/stats/generate_well_statistics/main.nf

@@ -1,4 +1,4 @@
-// generate_well_statistics v0.9.0
+// generate_well_statistics v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3036,7 +3036,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "generate_well_statistics",
   "namespace" : "stats",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "authors" : [
     {
       "name" : "Dries Schaumont",
@@ -3319,7 +3319,7 @@ meta = [
       "id" : "docker",
       "image" : "debian:stable-slim",
       "target_registry" : "images.viash-hub.com",
-      "target_tag" : "v0.9.0",
+      "target_tag" : "v0.9.1",
       "namespace_separator" : "/",
       "setup" : [
         {
@@ -3374,13 +3374,13 @@ meta = [
     "engine" : "docker|native",
     "output" : "target/nextflow/stats/generate_well_statistics",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3398,7 +3398,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",
@@ -3919,7 +3919,7 @@ meta["defaults"] = [
   "container" : {
     "registry" : "images.viash-hub.com",
     "image" : "vsh/htrnaseq/stats/generate_well_statistics",
-    "tag" : "v0.9.0"
+    "tag" : "v0.9.1"
   },
   "tag" : "$id"
 }'''),

target/nextflow/stats/generate_well_statistics/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'stats/generate_well_statistics'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'Generate summary statistics from BAM files generated by STAR solo.'
   author = 'Dries Schaumont, Marijke Van Moerbeke'
 }

target/nextflow/utils/concatRuns/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "concatRuns"
 namespace: "utils"
-version: "v0.9.0"
+version: "v0.9.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -160,14 +160,14 @@ build_info:
   output: "target/nextflow/utils/concatRuns"
   executable: "target/nextflow/utils/concatRuns/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
   dependencies:
   - "target/dependencies/vsh/vsh/craftbox/v0.2.0/nextflow/concat_text"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -199,7 +199,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"

target/nextflow/utils/concatRuns/_viash.yaml

@@ -1,5 +1,5 @@
 name: htrnaseq
-version: v0.9.0
+version: v0.9.1
 summary: |
   A workflow for high-throughput RNA-seq data analyses.
 description: "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n"

target/nextflow/utils/concatRuns/main.nf

@@ -1,4 +1,4 @@
-// concatRuns v0.9.0
+// concatRuns v0.9.1
 // 
 // This wrapper script is auto-generated by viash 0.9.4 and is thus a derivative
 // work thereof. This software comes with ABSOLUTELY NO WARRANTY from Data
@@ -3032,7 +3032,7 @@ meta = [
   "config": processConfig(readJsonBlob('''{
   "name" : "concatRuns",
   "namespace" : "utils",
-  "version" : "v0.9.0",
+  "version" : "v0.9.1",
   "argument_groups" : [
     {
       "name" : "Arguments",
@@ -3229,13 +3229,13 @@ meta = [
     "engine" : "native|native",
     "output" : "target/nextflow/utils/concatRuns",
     "viash_version" : "0.9.4",
-    "git_commit" : "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a",
+    "git_commit" : "1bce00e81124868b9dce7df10f3aa090ea38af22",
     "git_remote" : "https://github.com/viash-hub/htrnaseq",
-    "git_tag" : "v0.7.2-11-g8afa5dc"
+    "git_tag" : "v0.9.0-3-g1bce00e"
   },
   "package_config" : {
     "name" : "htrnaseq",
-    "version" : "v0.9.0",
+    "version" : "v0.9.1",
     "summary" : "A workflow for high-throughput RNA-seq data analyses.\n",
     "description" : "This workflow is designed to process high-throughput RNA-seq data, where every\nwell of a microarray plate is a sample. A fasta file provided as input\ndefines the mapping between sample barcodes and wells.\n\nThe workflow is built in a modular fashion, where most of the base functionality\nis provided by components from [`biobox`](https://www.viash-hub.com/packages/biobox/latest)\nsupplemented by custom base components and workflow components in this package.\n\nThe full workflow is split in two major subworkflows that can be run independently:\n\n* **Well-demultiplexing:** Split the input (plate/pool level) fastq files per well.\n* **Mapping, counting and QC:** Run per-well mapping, counting and generate QC reports.\n\nEach of those can be started individually, or the full workflow can be run in two ways:\n\n1. Run the [main workflow](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/htrnaseq) \ncontaining the main functionality.\n2. Run the [(opinionated) `runner`](https://www.viash-hub.com/packages/htrnaseq/v0.3.0/components/workflows/runner) where a\nnumber of choices (input/output structure and location) have been made.\n\nInput for the workflow has to be `fastq` files (zipped or not). For bcl or other formats, please consider running\n[demultiplex](https://www.viash-hub.com/packages/demultiplex) first.\n",
     "info" : {
@@ -3253,7 +3253,7 @@ meta = [
       ".requirements.commands := ['ps']\n.runners[.type == 'nextflow'].config.script := 'includeConfig(\\"nextflow_labels.config\\")'\n.resources += {path: '/src/config/labels.config', dest: 'nextflow_labels.config'}\n.resources += {path: '/_viash.yaml', dest: '_viash.yaml'}\n",
       ".engines += { type: \\"native\\" }",
       ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'",
-      ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+      ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
     ],
     "keywords" : [
       "bioinformatics",

target/nextflow/utils/concatRuns/nextflow.config

@@ -2,7 +2,7 @@ manifest {
   name = 'utils/concatRuns'
   mainScript = 'main.nf'
   nextflowVersion = '!>=20.12.1-edge'
-  version = 'v0.9.0'
+  version = 'v0.9.1'
   description = 'Concatenate well FASTQ files from different runs in order to increase sequencing depth.\n'
 }
 

target/nextflow/utils/listInputDir/.config.vsh.yaml

@@ -1,6 +1,6 @@
 name: "listInputDir"
 namespace: "utils"
-version: "v0.9.0"
+version: "v0.9.1"
 argument_groups:
 - name: "Arguments"
   arguments:
@@ -171,12 +171,12 @@ build_info:
   output: "target/nextflow/utils/listInputDir"
   executable: "target/nextflow/utils/listInputDir/main.nf"
   viash_version: "0.9.4"
-  git_commit: "8afa5dc946e4f01a5e38a787c8304a9e2b1d4c8a"
+  git_commit: "1bce00e81124868b9dce7df10f3aa090ea38af22"
   git_remote: "https://github.com/viash-hub/htrnaseq"
-  git_tag: "v0.7.2-11-g8afa5dc"
+  git_tag: "v0.9.0-3-g1bce00e"
 package_config:
   name: "htrnaseq"
-  version: "v0.9.0"
+  version: "v0.9.1"
   summary: "A workflow for high-throughput RNA-seq data analyses.\n"
   description: "This workflow is designed to process high-throughput RNA-seq data,\
     \ where every\nwell of a microarray plate is a sample. A fasta file provided as\
@@ -208,7 +208,7 @@ package_config:
     \ '_viash.yaml'}\n"
   - ".engines += { type: \"native\" }"
   - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
-  - ".engines[.type == 'docker'].target_tag := 'v0.9.0'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.9.1'"
   keywords:
   - "bioinformatics"
   - "sequencing"