Build branch main with version main (ed860be)

Build pipeline: vsh-ci-template-hp9jh

Source commit: ed860bed30

Source message: BUG: Wrong pointer to biobox dependency (#15)

* Fix pointer to biobox

* Add PR number

.gitignore

@@ -0,0 +1,7 @@
+target
+testData
+
+# Nextflow related files
+.nextflow
+.nextflow.log*
+work

CHANGELOG.md

@@ -0,0 +1,17 @@
+# 0.1.2
+
+## NEW FEATURES
+
+* Renamed `biobase` repository to `biobox` (PR #13 and PR #15).
+
+* Bump viash to 0.9.0-RC6 (PR #14).
+
+# v0.1.1
+
+## NEW FEATURES
+
+* `demultiplex` workflow: use `v0.1.0` release instead of `main` branch for `biobase` dependencies (PR #11).
+
+# v0.1.0
+
+Initial release

_viash.yaml

@@ -0,0 +1,17 @@
+name: demultiplex
+description: |
+  Demultiplexing pipeline
+license: MIT
+keywords: [bioinformatics, sequence, demultiplexing, pipeline]
+links:
+  issue_tracker: https://github.com/viash-hub/demultiplex/issues
+  repository: https://github.com/viash-hub/demultiplex
+info:
+  test_resources:
+    - path: https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz
+      dest: test_resources
+
+viash_version: 0.9.0-RC6
+
+config_mods: |
+  .requirements.commands := ['ps']

main.nf

@@ -0,0 +1,3 @@
+workflow {
+    print("This is a dummy placeholder for pipeline execution. Please use the corresponding nf files for running pipelines.")
+}

nextflow.config

@@ -0,0 +1,6 @@
+manifest {
+  name = "demultiplex"
+  version = "main"
+  defaultBranch = "main"
+  nextflowVersion = "!>=20.12.1-edge"
+}

src/config/labels.config

@@ -0,0 +1,43 @@
+process {
+  // Default resources for components that hardly do any processing
+  memory = { 2.GB * task.attempt }
+  cpus = 1
+
+  // Retry for exit codes that have something to do with memory issues
+  errorStrategy = { task.exitStatus in 137..140 ? 'retry' : 'terminate' }
+  maxRetries = 3
+  maxMemory = null
+
+  // Resource labels
+  withLabel: singlecpu { cpus = 1 }
+  withLabel: lowcpu { cpus = 4 }
+  withLabel: midcpu { cpus = 10 }
+  withLabel: highcpu { cpus = 20 }
+  
+  withLabel: lowmem { memory = { get_memory( 4.GB * task.attempt ) } }
+  withLabel: midmem { memory = { get_memory( 25.GB * task.attempt ) } }
+  withLabel: highmem { memory = { get_memory( 50.GB * task.attempt ) } }
+  withLabel: veryhighmem { memory = { get_memory( 75.GB * task.attempt ) } }
+
+}
+
+def get_memory(to_compare) {
+    if (!process.containsKey("maxMemory") || !process.maxMemory) {
+      return to_compare
+    }
+
+    try {
+      if (process.containsKey("maxRetries") && process.maxRetries && task.attempt == (process.maxRetries as int)) {
+        return process.maxMemory
+      }
+      else if (to_compare.compareTo(process.maxMemory as nextflow.util.MemoryUnit) == 1) {
+        return max_memory as nextflow.util.MemoryUnit
+      }
+      else {
+        return to_compare
+      }  
+    } catch (all) {
+          println "Error processing memory resources. Please check that process.maxMemory '${process.maxMemory}' and process.maxRetries '${process.maxRetries}' are valid!"
+          System.exit(1)
+    }
+  }

src/config/tests.config

@@ -0,0 +1,38 @@
+
+process.container = 'nextflow/bash:latest'
+profiles {
+  // detect tempdir
+  tempDir = java.nio.file.Paths.get(
+    System.getenv('NXF_TEMP') ?:
+      System.getenv('VIASH_TEMP') ?: 
+      System.getenv('TEMPDIR') ?: 
+      System.getenv('TMPDIR') ?: 
+      '/tmp'
+  ).toAbsolutePath()
+
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+
+  docker {
+    docker.fixOwnership    = true
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+}

src/dataflow/combine_samples/config.vsh.yaml

@@ -0,0 +1,38 @@
+name: combine_samples
+namespace: dataflow
+description: Combine fastq files from across samples into one event with a list of fastq files per orientation.
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: "--id"
+        description: "ID of the new event"
+        type: string
+        required: true
+      - name: --forward_input
+        type: file
+        required: true
+      - name: --reverse_input
+        type: file
+        required: false
+  - name: Output arguments
+    arguments:
+      - name: --output_forward
+        type: file
+        direction: output
+        multiple: true
+        required: true
+      - name: --output_reverse
+        type: file
+        direction: output
+        multiple: true
+        required: false
+resources:
+  - type: nextflow_script
+    path: main.nf
+    entrypoint: run_wf
+
+runners:
+  - type: nextflow
+
+engines:
+  - type: native

src/dataflow/combine_samples/main.nf

@@ -0,0 +1,28 @@
+workflow run_wf {
+  take:
+    input_ch
+
+  main:
+    output_ch = input_ch
+      | map { id, state ->
+        def newEvent = [state.id, state + ["_meta": ["join_id": id]]]
+        newEvent
+      }
+      | groupTuple(by: 0, sort: "hash")
+      | map {run_id, states ->
+        // Gather the following state for all samples
+        def forward_fastqs = states.collect{it.forward_input}
+        def reverse_fastqs = states.collect{it.reverse_input}.findAll{it != null}
+        
+        def resultState = [
+          "output_forward": forward_fastqs,
+          "output_reverse": reverse_fastqs,
+          // The join ID is the same across all samples from the same run
+          "_meta": ["join_id": states[0]._meta.join_id]
+        ]
+        return [run_id, resultState]
+      }
+  
+  emit:
+    output_ch
+}

src/dataflow/gather_fastqs_and_validate/config.vsh.yaml

@@ -0,0 +1,36 @@
+name: gather_fastqs_and_validate
+namespace: dataflow
+description: |
+  From a directory containing fastq files, gather the files per sample 
+  and validate according to the contents of the sample sheet.
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        description: Directory containing .fastq files
+        type: file
+        required: true
+      - name: --sample_sheet
+        description: Sample sheet
+        type: file
+        required: true
+  - name: Output arguments
+    arguments:
+      - name: --fastq_forward
+        type: file
+        direction: output
+        required: true
+      - name: "--fastq_reverse"
+        type: file
+        direction: output
+        required: false
+resources:
+  - type: nextflow_script
+    path: main.nf
+    entrypoint: run_wf
+
+runners:
+  - type: nextflow
+
+engines:
+  - type: native

src/dataflow/gather_fastqs_and_validate/main.nf

@@ -0,0 +1,73 @@
+workflow run_wf {
+  take:
+    input_ch
+
+  main:
+    output_ch = input_ch
+      // Gather input files from BCL convert output folder
+      | flatMap { id, state ->
+        println "Processing sample sheet: $state.sample_sheet"
+        def sample_sheet = state.sample_sheet
+        def start_parsing = false
+        def sample_id_column_index = null
+        def samples = ["Undetermined"]
+        def original_id = id
+
+        // Parse sample sheet for sample IDs
+        csv_lines = sample_sheet.splitCsv(header: false, sep: ',')
+        csv_lines.any { csv_items ->
+          if (csv_items.isEmpty()) {
+            return
+          }
+          def possible_header = csv_items[0]
+          def header = possible_header.find(/\[(.*)\]/){fullmatch, header_name -> header_name}
+          if (header) {
+            if (start_parsing) {
+              // Stop parsing when encountering the next header
+              return true
+            }
+            if (header == "Data") {
+              start_parsing = true
+            }
+          }
+          if (start_parsing) {
+            if ( !sample_id_column_index ) {
+              sample_id_column_index = csv_items.findIndexValues{it == "Sample_ID"}
+              assert sample_id_column_index != -1:
+              "Could not find column 'Sample_ID' in sample sheet!"
+              return
+            }
+            samples += csv_items[sample_id_column_index]
+          }
+        }
+        println "Looking for fastq files in ${state.input}."
+        def allfastqs = state.input.listFiles().findAll{it.isFile() && it.name ==~ /^.+\.fastq.gz$/}
+        println "Found ${allfastqs.size()} fastq files, matching them to the following samples: ${samples}."
+        processed_samples = samples.collect { sample_id ->
+          def forward_regex = ~/^${sample_id}_S(\d+)_(L(\d+)_)?R1_(\d+)\.fastq\.gz$/
+          def reverse_regex = ~/^${sample_id}_S(\d+)_(L(\d+)_)?R2_(\d+)\.fastq\.gz$/
+          def forward_fastq = state.input.listFiles().findAll{it.isFile() && it.name ==~ forward_regex}
+          def reverse_fastq = state.input.listFiles().findAll{it.isFile() && it.name ==~ reverse_regex}
+          assert forward_fastq : "No forward fastq files were found for sample ${sample_id}"
+          assert forward_fastq.size() < 2:
+          "Found multiple forward fastq files corresponding to sample ${sample_id}: ${forward_fastq}"
+          assert reverse_fastq.size() < 2:
+          "Found multiple reverse fastq files corresponding to sample ${sample_id}: ${reverse_fastq}."
+          assert !forward_fastq.isEmpty():
+          "Expected a forward fastq file to have been created correspondig to sample ${sample_id}."
+          // TODO: if one sample had reverse reads, the others must as well.
+          reverse_fastq = !reverse_fastq.isEmpty() ? reverse_fastq[0] : null
+          def fastqs_state = [
+            "fastq_forward": forward_fastq[0],
+            "fastq_reverse": reverse_fastq,
+            "_meta": [ "join_id": original_id ],
+          ]
+          [sample_id, fastqs_state]
+        }
+        println "Finished processing sample sheet."
+        return processed_samples
+      }
+
+  emit:
+    output_ch
+}

src/demultiplex/config.vsh.yaml

@@ -0,0 +1,70 @@
+name: demultiplex
+description: Demultiplexing of raw sequencing data
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        description: Directory containing raw sequencing data
+        type: file
+        required: true
+      - name: --sample_sheet
+        description: |
+          Sample sheet as input for BCL Convert. If not specified,
+          will try to autodetect the sample sheet in the input directory
+        type: file
+        required: false
+  - name: Output arguments
+    arguments:
+      - name: --output
+        description: Directory to write fastq data to
+        type: file
+        direction: output
+        required: true
+      - name: "--output_falco"
+        description: Directory to write falco output to
+        type: file
+        direction: output
+        required: false
+        default: "$id/falco"
+      - name: "--output_multiqc"
+        description: Directory to write falco output to
+        type: file
+        direction: output
+        required: false
+        default: "$id/multiqc_report.html"
+resources:
+  - type: nextflow_script
+    path: main.nf
+    entrypoint: run_wf
+
+test_resources:
+  - type: nextflow_script
+    path: test.nf
+    entrypoint: test_wf
+
+dependencies:
+  - name: io/untar
+    repository: local
+  - name: dataflow/gather_fastqs_and_validate
+    repository: local
+  - name: io/interop_summary_to_csv
+    repository: local
+  - name: dataflow/combine_samples
+    repository: local
+  - name: bcl_convert
+    repository: bb
+  - name: falco
+    repository: bb
+  - name: multiqc
+    repository: bb
+repositories:
+  - name: bb
+    type: vsh
+    repo: biobox
+    tag: v0.1.0
+
+runners:
+  - type: nextflow
+
+engines:
+  - type: native

src/demultiplex/integration_tests.sh

@@ -0,0 +1,16 @@
+#!/usr/bin/env bash
+
+# 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"
+
+viash ns build --setup cb
+
+nextflow run . \
+  -main-script src/demultiplex/test.nf \
+  -profile docker,no_publish \
+  -entry test_wf \
+  -c src/config/tests.config \
+  -resume

src/demultiplex/main.nf

@@ -0,0 +1,132 @@
+workflow run_wf {
+  take:
+    input_ch
+
+  main:
+    samples_ch = input_ch
+      // untar input if needed
+      | untar.run(
+        runIf: {id, state ->
+          def inputStr = state.input.toString()
+          inputStr.endsWith(".tar.gz") || \
+          inputStr.endsWith(".tar") || \
+          inputStr.endsWith(".tgz") ? true : false
+        },
+        fromState: [
+          "input": "input",
+        ],
+        toState: { id, result, state ->
+          state + ["input": result.output]
+        },
+      )
+      // Gather input files from folder
+      | map {id, state ->
+        def newState = [:]
+        if (!state.sample_sheet) {
+          def sample_sheet = state.input.resolve("SampleSheet.csv")
+          assert (sample_sheet && sample_sheet.isFile()): "Could not find 'SampleSheet.csv' file in input directory."
+          newState["sample_sheet"] = sample_sheet
+        }
+
+        // Do not add InterOp to state because we generate the summary csv's in the next
+        // step based on the run dir, not the InterOp dir.
+        def interop_dir = state.input.resolve("InterOp")
+        assert interop_dir.isDirectory(): "Expected InterOp directory to be present."
+
+        def resultState = state + newState
+        [id, resultState]
+      }
+
+      | interop_summary_to_csv.run(
+        fromState: [
+          "input": "input", 
+        ],
+        toState: [
+          "interop_run_summary": "output_run_summary",
+          "interop_index_summary": "output_index_summary",
+        ]
+      )
+      // run bcl_convert
+      | bcl_convert.run(
+        fromState: [
+          "bcl_input_directory": "input",
+          "sample_sheet": "sample_sheet",
+          "output_directory": "output",
+        ],
+        toState: {id, result, state -> 
+          def toAdd = [
+            "output_bclconvert" : result.output_directory,
+            "bclconvert_reports": result.reports,
+            "run_id": id,
+          ]
+          def newState = state + toAdd
+          return newState
+        }
+      )
+      | gather_fastqs_and_validate.run(
+        fromState: [
+          "input": "output_bclconvert",
+          "sample_sheet": "sample_sheet",
+        ],
+        toState: [
+          "fastq_forward": "fastq_forward",
+          "fastq_reverse": "fastq_reverse",
+        ],
+      )
+
+    output_ch = samples_ch 
+      | combine_samples.run(
+        fromState: { id, state ->
+          [
+            "id": state.run_id,
+            "forward_input": state.fastq_forward,
+            "reverse_input": state.fastq_reverse, 
+          ]
+        },
+        toState: [
+          "forward_fastqs": "output_forward",
+          "reverse_fastqs": "output_reverse",
+        ]
+      )
+      | falco.run(
+        fromState: {id, state ->
+          reverse_fastqs_list = state.reverse_fastqs ? state.reverse_fastqs : []
+          [
+            "input": state.forward_fastqs + reverse_fastqs_list,
+            "outdir": "${state.output_falco}",
+            "summary_filename": null,
+            "report_filename": null,
+            "data_filename": null,
+          ]
+        },
+        toState: { id, result, state ->
+          state + [ "output_falco" : result.outdir ]
+        },
+      )
+      | multiqc.run(
+        fromState: {id, state ->
+          [
+            "input": [
+              state.output_falco,
+              state.interop_run_summary.getParent(),
+              state.interop_index_summary.getParent()
+            ],
+            "output_report": state.output_multiqc,
+            "cl_config": 'sp: {fastqc/data: {fn: "*_fastqc_data.txt"}}',
+          ]
+        },
+        toState: { id, result, state ->
+          state + [ "output_multiqc" : result.output_report ]
+        },
+      )
+      | setState(
+        [
+          "output": "output_bclconvert",
+          "output_falco": "output_falco",
+          "output_multiqc": "output_multiqc"
+        ]
+      )
+
+  emit:
+    output_ch
+}

src/demultiplex/nextflow.config

@@ -0,0 +1,10 @@
+manifest {
+  nextflowVersion = '!>=20.12.1-edge'
+}
+
+params {
+  rootDir = java.nio.file.Paths.get("$projectDir/../../").toAbsolutePath().normalize().toString()
+}
+
+// include common settings
+includeConfig("${params.rootDir}/src/config/labels.config")

src/demultiplex/test.nf

@@ -0,0 +1,29 @@
+nextflow.enable.dsl=2
+
+include { demultiplex } from params.rootDir + "/target/nextflow/demultiplex/main.nf"
+
+workflow test_wf {
+  output_ch = Channel.fromList([
+        [
+          // sample_sheet: resources_test.resolve("bcl_convert_samplesheet.csv"),
+          // input: resources_test.resolve("iseq-DI/"),
+          //sample_sheet: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/SampleSheet.csv",
+          input: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz",
+          publish_dir: "output_dir/",
+        ]
+      ])
+    | map { state -> [ "run", state ] }
+    | demultiplex.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"
+      }
+    | map {id, state ->
+      assert state.output.isDirectory(): "Expected bclconvert output to be a directory"
+      assert state.output_falco.isDirectory(): "Expected falco output to be a directory"
+      assert state.output_multiqc.isFile(): "Expected multiQC output to be a file"
+    }
+}

src/io/interop_summary_to_csv/config.vsh.yaml

@@ -0,0 +1,41 @@
+name: interop_summary_to_csv
+namespace: io
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        description: Sequencing run folder (*not* InterOp folder).
+        type: file
+        required: true
+  - name: Output arguments
+    arguments:
+      - name: --output_run_summary
+        type: file
+        direction: output
+        required: true
+      - name: --output_index_summary
+        type: file
+        direction: output
+        required: true
+requirements:
+  - commands: ["summary", "index-summary"]
+resources:
+  - type: bash_script
+    path: script.sh
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages:
+          - procps
+          - wget
+      - type: docker
+        run: |
+          wget https://github.com/Illumina/interop/releases/download/v1.3.1/interop-1.3.1-Linux-GNU.tar.gz -O /tmp/interop.tar.gz && \
+          tar -C /tmp/ --no-same-owner --no-same-permissions -xvf /tmp/interop.tar.gz && \
+          mv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/
+
+runners:
+  - type: executable
+  - type: nextflow

src/io/interop_summary_to_csv/script.sh

@@ -0,0 +1,10 @@
+#!/usr/bin/env bash
+
+set -eo pipefail
+
+if [ ! -d "$par_input" ]; then
+    echo "Input directory does not exist or is not a directory"
+    exit 1
+fi
+$(which summary) --csv=1 "$par_input" 1> "$par_output_run_summary"
+$(which index-summary) --csv=1 "$par_input" 1> "$par_output_index_summary"

src/io/untar/config.vsh.yaml

@@ -0,0 +1,44 @@
+name: untar
+namespace: io
+description: |
+  Unpack a .tar file. When the contents of the .tar file is just a single directory,
+  put the contents of the directory into the output folder instead of that directory.
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        description: Tarball file to be unpacked.
+        type: file
+        required: true
+  - name: Output arguments
+    arguments:
+      - name: --output
+        description: Directory to write the contents of the .tar file to.
+        type: file
+        direction: output
+        required: true
+  - name: "Other arguments"
+    arguments:
+      - name: "--exclude"
+        alternatives: ["-e"]
+        type: string
+        description: Prevents any file or member whose name matches the shell wildcard (pattern) from being extracted.
+        example: "docs/figures"
+        required: false
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+engines:
+  - type: docker
+    image: debian:stable-slim
+    setup:
+      - type: apt
+        packages:
+          - procps
+
+runners:
+  - type: executable
+  - type: nextflow

src/io/untar/script.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+set -eo pipefail
+
+extra_args=()
+
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Check if tarball contains 1 top-level directory. If so, extract the contents of the
+# directory to the output directory instead of the directory itself.
+echo "Directory contents:"
+tar -taf "${par_input}" > "$TMPDIR/tar_contents.txt"
+cat "$TMPDIR/tar_contents.txt"
+
+printf "Checking if tarball contains only a single top-level directory: "
+if [[ $(grep -o -E '^[./]*[^/]+/$' "$TMPDIR/tar_contents.txt" | uniq | wc -l) -eq 1 ]]; then
+    echo "It does."
+    echo "Extracting the contents of the top-level directory to the output directory instead of the directory itself."
+    # The directory can be both of the format './<directory>' (or ././<directory>) or just <directory>
+    # Adjust the number of stripped components accordingly by looking for './' at the beginning of the file.
+    starting_relative=$(grep -oP -m 1 '^(./)*' "$TMPDIR/tar_contents.txt" | tr -d '\n' | wc -c)
+    n_strips=$(( ($starting_relative / 2)+1 ))
+    extra_args+=("--strip-components=$n_strips")
+else
+    echo "It does not."
+fi
+
+if [ "$par_exclude" != "" ]; then
+    echo "Exclusion of files with wildcard '$par_exclude' requested."
+    extra_args+=("--exclude=$par_exclude")
+fi
+
+echo "Starting extraction of tarball '$par_input' to output directory '$par_output'."
+mkdir -p "$par_output"
+echo "executing 'tar --no-same-owner --no-same-permissions --directory=$par_output ${extra_args[@]} -xavf $par_input'"
+tar --no-same-owner --no-same-permissions --directory="$par_output" ${extra_args[@]} -xavf "$par_input"
+

src/io/untar/test.sh

@@ -0,0 +1,126 @@
+#!/usr/bin/env bash
+
+set -eo pipefail
+
+# create tempdir
+echo ">>> Creating temporary test directory."
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_functionality_name-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+echo ">>> Created temporary directory '$TMPDIR'."
+
+INPUT_FILE="$TMPDIR/test_file.txt"
+echo ">>> Creating test input file at '$TMPDIR/test_file.txt'."
+echo "foo" > "$INPUT_FILE"
+echo ">>> Created '$INPUT_FILE'."
+
+echo ">>> Creating tar.gz from '$INPUT_FILE'."
+TARFILE="${INPUT_FILE}.tar.gz"
+tar -C "$TMPDIR" -czvf ${INPUT_FILE}.tar.gz $(basename "$INPUT_FILE")
+[[ ! -f "$TARFILE" ]] && echo ">>> Test setup failed: could not create tarfile." && exit 1
+echo ">>> '$TARFILE' created."
+
+echo ">>> Check whether tar.gz can be extracted"
+echo ">>> Creating temporary output directory for test 1."
+OUTPUT_DIR_1="$TMPDIR/output_test_1/"
+mkdir "$OUTPUT_DIR_1"
+
+echo ">>> Extracting '$TARFILE' to '$OUTPUT_DIR_1'".
+./$meta_functionality_name \
+   --input "$TARFILE" \
+   --output "$OUTPUT_DIR_1"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_1/test_file.txt" ]] && echo "Output file could not be found. Output directory contents: " && ls "$OUTPUT_DIR_1" && exit 1
+
+echo ">>> Creating temporary output directory for test 2."
+OUTPUT_DIR_2="$TMPDIR/output_test_2/"
+mkdir "$OUTPUT_DIR_2"
+
+echo ">>> Extracting '$TARFILE' to '$OUTPUT_DIR_2', excluding '$test_file.txt'".
+./$meta_functionality_name \
+   --input "$TARFILE" \
+   --output "$OUTPUT_DIR_2" \
+   --exclude 'test_file.txt'
+
+echo ">>> Check whether excluded file was not extracted"
+[[ -f "$OUTPUT_DIR_2/test_file.txt" ]] && echo "File should have been excluded! Output directory contents:" && ls "$OUTPUT_DIR_2" && exit 1
+
+echo ">>> Creating test tarball containing only 1 top-level directory."
+mkdir "$TMPDIR/input_test_3/"
+cp "$INPUT_FILE" "$TMPDIR/input_test_3/"
+tar -C "$TMPDIR" -czvf "$TMPDIR/input_test_3.tar.gz" $(basename "$TMPDIR/input_test_3")
+TARFILE_3="$TMPDIR/input_test_3.tar.gz"
+
+echo ">>> Creating temporary output directory for test 3."
+OUTPUT_DIR_3="$TMPDIR/output_test_3/"
+mkdir "$OUTPUT_DIR_3"
+
+echo "Extracting '$TARFILE_3' to '$OUTPUT_DIR_3'".
+./$meta_functionality_name \
+   --input "$TARFILE_3" \
+   --output "$OUTPUT_DIR_3"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_3/test_file.txt" ]] && echo "Output file could not be found!" && exit 1
+
+echo ">>> Check for tar archive that contains a single directory starting with './'."
+mkdir "$TMPDIR/input_test_4/"
+cp "$INPUT_FILE" "$TMPDIR/input_test_4/"
+
+pushd "$TMPDIR/" 
+trap popd ERR
+tar -czvf "$TMPDIR/input_test_4.tar.gz" ./input_test_4
+popd
+trap - ERR
+
+OUTPUT_DIR_4="$TMPDIR/output_test_4/"
+echo "Extracting '$TMPDIR/input_test_4.tar.gz' to '$OUTPUT_DIR_4'".
+./$meta_functionality_name \
+   --input "$TMPDIR/input_test_4.tar.gz" \
+   --output "$OUTPUT_DIR_4"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_4/test_file.txt" ]] && echo "Output file could not be found!" && exit 1
+
+echo ">>> Creating test tarball containing only 1 top-level directory, but it is nested."
+mkdir -p "$TMPDIR/input_test_5/nested/"
+cp "$INPUT_FILE" "$TMPDIR/input_test_5/nested/"
+tar -C "$TMPDIR" -czvf "$TMPDIR/input_test_5.tar.gz" $(basename "$TMPDIR/input_test_5")
+TARFILE_5="$TMPDIR/input_test_5.tar.gz"
+
+echo ">>> Creating temporary output directory for test 5."
+OUTPUT_DIR_5="$TMPDIR/output_test_5/"
+mkdir "$OUTPUT_DIR_5"
+
+echo "Extracting '$TARFILE_5' to '$OUTPUT_DIR_5'".
+./$meta_functionality_name \
+   --input "$TARFILE_5" \
+   --output "$OUTPUT_DIR_5"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_5/nested/test_file.txt" ]] && echo "Output file could not be found!" && exit 1
+
+echo ">>> Creating test tarball containing two top-level directories."
+mkdir -p "$TMPDIR/input_test_6/number_1/"
+mkdir "$TMPDIR/input_test_6/number_2/"
+cp "$INPUT_FILE" "$TMPDIR/input_test_6/number_1/"
+tar -C "$TMPDIR" -czvf "$TMPDIR/input_test_6.tar.gz" $(basename "$TMPDIR/input_test_6")
+TARFILE_6="$TMPDIR/input_test_6.tar.gz"
+
+echo ">>> Creating temporary output directory for test 6."
+OUTPUT_DIR_6="$TMPDIR/output_test_6/"
+mkdir "$OUTPUT_DIR_6"
+
+echo "Extracting '$TARFILE_6' to '$OUTPUT_DIR_6'".
+./$meta_functionality_name \
+   --input "$TARFILE_6" \
+   --output "$OUTPUT_DIR_6"
+
+echo ">>> Check whether extracted file exists"
+[[ ! -f "$OUTPUT_DIR_6/number_1/test_file.txt" ]] && echo "Output file could not be found!" && exit 1
+[[ ! -d "$OUTPUT_DIR_6/number_2" ]] && echo "Output directory could not be found!" && exit 1
+
+echo ">>> Test finished successfully"

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/.config.vsh.yaml

@@ -0,0 +1,412 @@
+name: "bcl_convert"
+version: "v0.1.0"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--bcl_input_directory"
+    alternatives:
+    - "-i"
+    description: "Input run directory"
+    info: null
+    example:
+    - "bcl_dir"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sample_sheet"
+    alternatives:
+    - "-s"
+    description: "Path to SampleSheet.csv file (default searched for in --bcl_input_directory)"
+    info: null
+    example:
+    - "bcl_dir/sample_sheet.csv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--run_info"
+    description: "Path to RunInfo.xml file (default root of BCL input directory)"
+    info: null
+    example:
+    - "bcl_dir/RunInfo.xml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Lane and tile settings"
+  arguments:
+  - type: "integer"
+    name: "--bcl_only_lane"
+    description: "Convert only specified lane number (default all lanes)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--first_tile_only"
+    description: "Only convert first tile of input (for testing & debugging)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--tiles"
+    description: "Process only a subset of tiles by a regular expression"
+    info: null
+    example:
+    - "s_[0-9]+_1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--exclude_tiles"
+    description: "Exclude set of tiles by a regular expression"
+    info: null
+    example:
+    - "s_[0-9]+_1"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Resource arguments"
+  arguments:
+  - type: "boolean"
+    name: "--shared_thread_odirect_output"
+    description: "Use linux native asynchronous io (io_submit) for file output (Default=false)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--bcl_num_parallel_tiles"
+    description: "\\# of tiles to process in parallel (default 1)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--bcl_num_conversion_threads"
+    description: "\\# of threads for conversion (per tile, default # cpu threads)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--bcl_num_compression_threads"
+    description: "\\# of threads for fastq.gz output compression (per tile, default\
+      \ # cpu threads, or HW+12)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--bcl_num_decompression_threads"
+    description: "\\# of threads for bcl/cbcl input decompression (per tile, default\
+      \ half # cpu threads, or HW+8). Only applies when preloading files"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Run arguments"
+  arguments:
+  - type: "boolean"
+    name: "--bcl_only_matched_reads"
+    description: "For pure BCL conversion, do not output files for 'Undetermined'\
+      \ [unmatched] reads (output by default)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--no_lane_splitting"
+    description: "Do not split FASTQ file by lane (false by default)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--num_unknown_barcodes_reported"
+    description: "\\# of Top Unknown Barcodes to output (1000 by default)"
+    info: null
+    example:
+    - 1000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--bcl_validate_sample_sheet_only"
+    description: "Only validate RunInfo.xml & SampleSheet files (produce no FASTQ\
+      \ files)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--strict_mode"
+    description: "Abort if any files are missing (false by default)"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--sample_name_column_enabled"
+    description: "Use sample sheet 'Sample_Name' column when naming fastq files &\
+      \ subdirectories"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output_directory"
+    alternatives:
+    - "-o"
+    description: "Output directory containig fastq files"
+    info: null
+    example:
+    - "fastq_dir"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean"
+    name: "--bcl_sampleproject_subdirectories"
+    description: "Output to subdirectories based upon sample sheet 'Sample_Project'\
+      \ column"
+    info: null
+    example:
+    - true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--fastq_gzip_compression_level"
+    description: "Set fastq output compression level 0-9 (default 1)"
+    info: null
+    example:
+    - 1
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--reports"
+    description: "Reports directory"
+    info: null
+    example:
+    - "reports_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--logs"
+    description: "Reports directory"
+    info: null
+    example:
+    - "logs_dir"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Convert bcl files to fastq files using bcl-convert.\nInformation about\
+  \ upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\n\
+  and [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/biobox"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "debian:trixie-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.1.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "wget"
+    - "gdb"
+    - "which"
+    - "hostname"
+    - "alien"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "wget https://s3.amazonaws.com/webdata.illumina.com/downloads/software/bcl-convert/bcl-convert-4.2.7-2.el8.x86_64.rpm\
+      \ -O /tmp/bcl-convert.rpm && \\\nalien -i /tmp/bcl-convert.rpm && \\\nrm -rf\
+      \ /var/lib/apt/lists/* && \\\nrm /tmp/bcl-convert.rpm\n"
+  - type: "docker"
+    run:
+    - "echo \"bcl-convert: \\\"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/\
+      \ s/^bcl-convert\\ Version //p')\\\"\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bcl_convert/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/bcl_convert"
+  executable: "target/nextflow/bcl_convert/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  git_remote: "https://github.com/viash-hub/biobox"
+package_config:
+  name: "biobox"
+  version: "v0.1.0"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'bcl_convert'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.1.0'
+  description = 'Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert/nextflow_schema.json

@@ -0,0 +1,349 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "bcl_convert",
+"description": "Convert bcl files to fastq files using bcl-convert.\nInformation about upgrading from bcl2fastq via\n[Upgrading from bcl2fastq to BCL Convert](https://emea.support.illumina.com/bulletins/2020/10/upgrading-from-bcl2fastq-to-bcl-convert.html)\nand [BCL Convert Compatible Products](https://support.illumina.com/sequencing/sequencing_software/bcl-convert/compatibility.html)\n",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input arguments" : {
+    "title": "Input arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "bcl_input_directory": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, example: `bcl_dir`. Input run directory",
+                "help_text": "Type: `file`, required, example: `bcl_dir`. Input run directory"
+            
+            }
+    
+
+        ,
+                "sample_sheet": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `bcl_dir/sample_sheet.csv`. Path to SampleSheet",
+                "help_text": "Type: `file`, example: `bcl_dir/sample_sheet.csv`. Path to SampleSheet.csv file (default searched for in --bcl_input_directory)"
+            
+            }
+    
+
+        ,
+                "run_info": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `bcl_dir/RunInfo.xml`. Path to RunInfo",
+                "help_text": "Type: `file`, example: `bcl_dir/RunInfo.xml`. Path to RunInfo.xml file (default root of BCL input directory)"
+            
+            }
+    
+
+}
+},
+    
+    
+    "lane and tile settings" : {
+    "title": "Lane and tile settings",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "bcl_only_lane": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `1`. Convert only specified lane number (default all lanes)",
+                "help_text": "Type: `integer`, example: `1`. Convert only specified lane number (default all lanes)"
+            
+            }
+    
+
+        ,
+                "first_tile_only": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. Only convert first tile of input (for testing \u0026 debugging)",
+                "help_text": "Type: `boolean`, example: `true`. Only convert first tile of input (for testing \u0026 debugging)"
+            
+            }
+    
+
+        ,
+                "tiles": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `s_[0-9]+_1`. Process only a subset of tiles by a regular expression",
+                "help_text": "Type: `string`, example: `s_[0-9]+_1`. Process only a subset of tiles by a regular expression"
+            
+            }
+    
+
+        ,
+                "exclude_tiles": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `s_[0-9]+_1`. Exclude set of tiles by a regular expression",
+                "help_text": "Type: `string`, example: `s_[0-9]+_1`. Exclude set of tiles by a regular expression"
+            
+            }
+    
+
+}
+},
+    
+    
+    "resource arguments" : {
+    "title": "Resource arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "shared_thread_odirect_output": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. Use linux native asynchronous io (io_submit) for file output (Default=false)",
+                "help_text": "Type: `boolean`, example: `true`. Use linux native asynchronous io (io_submit) for file output (Default=false)"
+            
+            }
+    
+
+        ,
+                "bcl_num_parallel_tiles": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `1`. \\# of tiles to process in parallel (default 1)",
+                "help_text": "Type: `integer`, example: `1`. \\# of tiles to process in parallel (default 1)"
+            
+            }
+    
+
+        ,
+                "bcl_num_conversion_threads": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `1`. \\# of threads for conversion (per tile, default # cpu threads)",
+                "help_text": "Type: `integer`, example: `1`. \\# of threads for conversion (per tile, default # cpu threads)"
+            
+            }
+    
+
+        ,
+                "bcl_num_compression_threads": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `1`. \\# of threads for fastq",
+                "help_text": "Type: `integer`, example: `1`. \\# of threads for fastq.gz output compression (per tile, default # cpu threads, or HW+12)"
+            
+            }
+    
+
+        ,
+                "bcl_num_decompression_threads": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `1`. \\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8)",
+                "help_text": "Type: `integer`, example: `1`. \\# of threads for bcl/cbcl input decompression (per tile, default half # cpu threads, or HW+8). Only applies when preloading files"
+            
+            }
+    
+
+}
+},
+    
+    
+    "run arguments" : {
+    "title": "Run arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "bcl_only_matched_reads": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. For pure BCL conversion, do not output files for \u0027Undetermined\u0027 [unmatched] reads (output by default)",
+                "help_text": "Type: `boolean`, example: `true`. For pure BCL conversion, do not output files for \u0027Undetermined\u0027 [unmatched] reads (output by default)"
+            
+            }
+    
+
+        ,
+                "no_lane_splitting": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. Do not split FASTQ file by lane (false by default)",
+                "help_text": "Type: `boolean`, example: `true`. Do not split FASTQ file by lane (false by default)"
+            
+            }
+    
+
+        ,
+                "num_unknown_barcodes_reported": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `1000`. \\# of Top Unknown Barcodes to output (1000 by default)",
+                "help_text": "Type: `integer`, example: `1000`. \\# of Top Unknown Barcodes to output (1000 by default)"
+            
+            }
+    
+
+        ,
+                "bcl_validate_sample_sheet_only": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. Only validate RunInfo",
+                "help_text": "Type: `boolean`, example: `true`. Only validate RunInfo.xml \u0026 SampleSheet files (produce no FASTQ files)"
+            
+            }
+    
+
+        ,
+                "strict_mode": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. Abort if any files are missing (false by default)",
+                "help_text": "Type: `boolean`, example: `true`. Abort if any files are missing (false by default)"
+            
+            }
+    
+
+        ,
+                "sample_name_column_enabled": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. Use sample sheet \u0027Sample_Name\u0027 column when naming fastq files \u0026 subdirectories",
+                "help_text": "Type: `boolean`, example: `true`. Use sample sheet \u0027Sample_Name\u0027 column when naming fastq files \u0026 subdirectories"
+            
+            }
+    
+
+}
+},
+    
+    
+    "output arguments" : {
+    "title": "Output arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output_directory": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Output directory containig fastq files",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_directory.output_directory`, example: `fastq_dir`. Output directory containig fastq files"
+            ,
+                "default": "$id.$key.output_directory.output_directory"
+            }
+    
+
+        ,
+                "bcl_sampleproject_subdirectories": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean`, example: `true`. Output to subdirectories based upon sample sheet \u0027Sample_Project\u0027 column",
+                "help_text": "Type: `boolean`, example: `true`. Output to subdirectories based upon sample sheet \u0027Sample_Project\u0027 column"
+            
+            }
+    
+
+        ,
+                "fastq_gzip_compression_level": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `1`. Set fastq output compression level 0-9 (default 1)",
+                "help_text": "Type: `integer`, example: `1`. Set fastq output compression level 0-9 (default 1)"
+            
+            }
+    
+
+        ,
+                "reports": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.reports.reports`, example: `reports_dir`. Reports directory",
+                "help_text": "Type: `file`, default: `$id.$key.reports.reports`, example: `reports_dir`. Reports directory"
+            ,
+                "default": "$id.$key.reports.reports"
+            }
+    
+
+        ,
+                "logs": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Reports directory",
+                "help_text": "Type: `file`, default: `$id.$key.logs.logs`, example: `logs_dir`. Reports directory"
+            ,
+                "default": "$id.$key.logs.logs"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input arguments"
+    },
+
+    {
+    "$ref": "#/definitions/lane and tile settings"
+    },
+
+    {
+    "$ref": "#/definitions/resource arguments"
+    },
+
+    {
+    "$ref": "#/definitions/run arguments"
+    },
+
+    {
+    "$ref": "#/definitions/output arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/.config.vsh.yaml

@@ -0,0 +1,330 @@
+name: "falco"
+version: "v0.1.0"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "input fastq files"
+    info: null
+    example:
+    - "input1.fastq;input2.fastq"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Run arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--nogroup"
+    description: "Disable grouping of bases for reads >50bp. \nAll reports will show\
+      \ data for every base in \nthe read. WARNING: When using this option, \nyour\
+      \ plots may end up a ridiculous size. You \nhave been warned!\n"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--contaminents"
+    description: "Specifies a non-default file which contains \nthe list of contaminants\
+      \ to screen \noverrepresented sequences against. The file \nmust contain sets\
+      \ of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith\
+      \ a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--adapters"
+    description: "Specifies a non-default file which contains \nthe list of adapter\
+      \ sequences which will be \nexplicity searched against the library. The \nfile\
+      \ must contain sets of named adapters in \nthe form name[tab]sequence. Lines\
+      \ prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--limits"
+    description: "Specifies a non-default file which contains \na set of criteria\
+      \ which will be used to \ndetermine the warn/error limits for the \nvarious\
+      \ modules. This file can also be used \nto selectively remove some modules from\
+      \ the \noutput all together. The format needs to \nmirror the default limits.txt\
+      \ file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--subsample"
+    alternatives:
+    - "-s"
+    description: "[Falco only] makes falco faster (but \npossibly less accurate) by\
+      \ only processing \nreads that are a multiple of this value (using \n0-based\
+      \ indexing to number reads).\n"
+    info: null
+    example:
+    - 10
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--bisulfite"
+    alternatives:
+    - "-b"
+    description: "[Falco only] reads are whole genome \nbisulfite sequencing, and\
+      \ more Ts and fewer \nCs are therefore expected and will be \naccounted for\
+      \ in base content.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--reverse_complliment"
+    alternatives:
+    - "-r"
+    description: "[Falco only] The input is a \nreverse-complement. All modules will\
+      \ be \ntested by swapping A/T and C/G\n"
+    info: null
+    direction: "input"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--outdir"
+    alternatives:
+    - "-o"
+    description: "Create all output files in the specified \noutput directory. FALCO-SPECIFIC:\
+      \ If the \ndirectory does not exists, the program will \ncreate it.\n"
+    info: null
+    example:
+    - "output"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--format"
+    alternatives:
+    - "-f"
+    description: "Bypasses the normal sequence file format \ndetection and forces\
+      \ the program to use the \nspecified format. Validformats are bam, sam, \nbam_mapped,\
+      \ sam_mapped, fastq, fq, fastq.gz \nor fq.gz.\n"
+    info: null
+    required: false
+    choices:
+    - "bam"
+    - "sam"
+    - "bam_mapped"
+    - "sam_mapped"
+    - "fastq"
+    - "fq"
+    - "fastq.gz"
+    - "fq.gz"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--data_filename"
+    alternatives:
+    - "-D"
+    description: "[Falco only] Specify filename for FastQC \ndata output (TXT). If\
+      \ not specified, it will \nbe called fastq_data.txt in either the input \nfile's\
+      \ directory or the one specified in the \n--output flag. Only available when\
+      \ running \nfalco with a single input.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--report_filename"
+    alternatives:
+    - "-R"
+    description: "[Falco only] Specify filename for FastQC \nreport output (HTML).\
+      \ If not specified, it \nwill be called fastq_report.html in either \nthe input\
+      \ file's directory or the one \nspecified in the --output flag. Only \navailable\
+      \ when running falco with a single \ninput.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--summary_filename"
+    alternatives:
+    - "-S"
+    description: "[Falco only] Specify filename for the short \nsummary output (TXT).\
+      \ If not specified, it \nwill be called fastq_report.html in either \nthe input\
+      \ file's directory or the one \nspecified in the --output flag. Only \navailable\
+      \ when running falco with a single \ninput.\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "A C++ drop-in replacement of FastQC to assess the quality of sequence\
+  \ read data"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "qc"
+- "fastqc"
+- "sequencing"
+license: "GPL-3.0"
+references:
+  doi:
+  - "10.12688/f1000research.21142.2"
+links:
+  repository: "https://github.com/smithlabcode/falco"
+  documentation: "https://falco.readthedocs.io/en/latest/"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "debian:trixie-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.1.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "wget"
+    - "build-essential"
+    - "g++"
+    - "zlib1g-dev"
+    - "procps"
+    interactive: false
+  - type: "docker"
+    run:
+    - "wget https://github.com/smithlabcode/falco/releases/download/v1.2.2/falco-1.2.2.tar.gz\
+      \ -O /tmp/falco.tar.gz && \\\ncd /tmp && \\\ntar xvf falco.tar.gz && \\\ncd\
+      \ falco-1.2.2 && \\\n./configure && \\\nmake all && \\\nmake install\n"
+  - type: "docker"
+    run:
+    - "echo \"falco: \\\"$(falco -v | sed -n 's/^falco //p')\\\"\" > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/falco/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/falco"
+  executable: "target/nextflow/falco/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  git_remote: "https://github.com/viash-hub/biobox"
+package_config:
+  name: "biobox"
+  version: "v0.1.0"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'falco'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.1.0'
+  description = 'A C++ drop-in replacement of FastQC to assess the quality of sequence read data'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco/nextflow_schema.json

@@ -0,0 +1,227 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "falco",
+"description": "A C++ drop-in replacement of FastQC to assess the quality of sequence read data",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input arguments" : {
+    "title": "Input arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\":\"`. input fastq files",
+                "help_text": "Type: List of `file`, required, example: `input1.fastq;input2.fastq`, multiple_sep: `\":\"`. input fastq files"
+            
+            }
+    
+
+}
+},
+    
+    
+    "run arguments" : {
+    "title": "Run arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "nogroup": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable grouping of bases for reads \u003e50bp",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable grouping of bases for reads \u003e50bp. \nAll reports will show data for every base in \nthe read. WARNING: When using this option, \nyour plots may end up a ridiculous size. You \nhave been warned!\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "contaminents": {
+                "type":
+                "string",
+                "description": "Type: `file`. Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against",
+                "help_text": "Type: `file`. Specifies a non-default file which contains \nthe list of contaminants to screen \noverrepresented sequences against. The file \nmust contain sets of named contaminants in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/contaminant_list.txt\n"
+            
+            }
+    
+
+        ,
+                "adapters": {
+                "type":
+                "string",
+                "description": "Type: `file`. Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library",
+                "help_text": "Type: `file`. Specifies a non-default file which contains \nthe list of adapter sequences which will be \nexplicity searched against the library. The \nfile must contain sets of named adapters in \nthe form name[tab]sequence. Lines prefixed \nwith a hash will be ignored. Default:\nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/adapter_list.txt\n"
+            
+            }
+    
+
+        ,
+                "limits": {
+                "type":
+                "string",
+                "description": "Type: `file`. Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules",
+                "help_text": "Type: `file`. Specifies a non-default file which contains \na set of criteria which will be used to \ndetermine the warn/error limits for the \nvarious modules. This file can also be used \nto selectively remove some modules from the \noutput all together. The format needs to \nmirror the default limits.txt file found in \nthe Configuration folder. Default: \nhttps://github.com/smithlabcode/falco/blob/v1.2.2/Configuration/limits.txt\n"
+            
+            }
+    
+
+        ,
+                "subsample": {
+                "type":
+                "integer",
+                "description": "Type: `integer`, example: `10`. [Falco only] makes falco faster (but \npossibly less accurate) by only processing \nreads that are a multiple of this value (using \n0-based indexing to number reads)",
+                "help_text": "Type: `integer`, example: `10`. [Falco only] makes falco faster (but \npossibly less accurate) by only processing \nreads that are a multiple of this value (using \n0-based indexing to number reads).\n"
+            
+            }
+    
+
+        ,
+                "bisulfite": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. [Falco only] reads are whole genome \nbisulfite sequencing, and more Ts and fewer \nCs are therefore expected and will be \naccounted for in base content",
+                "help_text": "Type: `boolean_true`, default: `false`. [Falco only] reads are whole genome \nbisulfite sequencing, and more Ts and fewer \nCs are therefore expected and will be \naccounted for in base content.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "reverse_complliment": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. [Falco only] The input is a \nreverse-complement",
+                "help_text": "Type: `boolean_true`, default: `false`. [Falco only] The input is a \nreverse-complement. All modules will be \ntested by swapping A/T and C/G\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "output arguments" : {
+    "title": "Output arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "outdir": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.outdir.outdir`, example: `output`. Create all output files in the specified \noutput directory",
+                "help_text": "Type: `file`, required, default: `$id.$key.outdir.outdir`, example: `output`. Create all output files in the specified \noutput directory. FALCO-SPECIFIC: If the \ndirectory does not exists, the program will \ncreate it.\n"
+            ,
+                "default": "$id.$key.outdir.outdir"
+            }
+    
+
+        ,
+                "format": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``bam`, `sam`, `bam_mapped`, `sam_mapped`, `fastq`, `fq`, `fastq.gz`, `fq.gz``. Bypasses the normal sequence file format \ndetection and forces the program to use the \nspecified format",
+                "help_text": "Type: `string`, choices: ``bam`, `sam`, `bam_mapped`, `sam_mapped`, `fastq`, `fq`, `fastq.gz`, `fq.gz``. Bypasses the normal sequence file format \ndetection and forces the program to use the \nspecified format. Validformats are bam, sam, \nbam_mapped, sam_mapped, fastq, fq, fastq.gz \nor fq.gz.\n",
+                "enum": ["bam", "sam", "bam_mapped", "sam_mapped", "fastq", "fq", "fastq.gz", "fq.gz"]
+            
+            
+            }
+    
+
+        ,
+                "data_filename": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.data_filename.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT)",
+                "help_text": "Type: `file`, default: `$id.$key.data_filename.data_filename`. [Falco only] Specify filename for FastQC \ndata output (TXT). If not specified, it will \nbe called fastq_data.txt in either the input \nfile\u0027s directory or the one specified in the \n--output flag. Only available when running \nfalco with a single input.\n"
+            ,
+                "default": "$id.$key.data_filename.data_filename"
+            }
+    
+
+        ,
+                "report_filename": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.report_filename.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML)",
+                "help_text": "Type: `file`, default: `$id.$key.report_filename.report_filename`. [Falco only] Specify filename for FastQC \nreport output (HTML). If not specified, it \nwill be called fastq_report.html in either \nthe input file\u0027s directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n"
+            ,
+                "default": "$id.$key.report_filename.report_filename"
+            }
+    
+
+        ,
+                "summary_filename": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.summary_filename.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT)",
+                "help_text": "Type: `file`, default: `$id.$key.summary_filename.summary_filename`. [Falco only] Specify filename for the short \nsummary output (TXT). If not specified, it \nwill be called fastq_report.html in either \nthe input file\u0027s directory or the one \nspecified in the --output flag. Only \navailable when running falco with a single \ninput.\n"
+            ,
+                "default": "$id.$key.summary_filename.summary_filename"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input arguments"
+    },
+
+    {
+    "$ref": "#/definitions/run arguments"
+    },
+
+    {
+    "$ref": "#/definitions/output arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/.config.vsh.yaml

@@ -0,0 +1,464 @@
+name: "multiqc"
+version: "v0.1.0"
+argument_groups:
+- name: "Input"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "File paths to be searched for analysis results to be included in\
+      \ the report.\n"
+    info: null
+    example:
+    - "data/results"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Ouput"
+  arguments:
+  - type: "file"
+    name: "--output_report"
+    description: "Filepath of the generated report.\n"
+    info: null
+    example:
+    - "multiqc_report.html"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_data"
+    description: "Output directory for parsed data files. If not provided, parsed\
+      \ data will not be published.\n"
+    info: null
+    example:
+    - "multiqc_data"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_plots"
+    description: "Output directory for generated plots. If not provided, plots will\
+      \ not be published.\n"
+    info: null
+    example:
+    - "multiqc_plots"
+    must_exist: false
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Modules and analyses to run"
+  arguments:
+  - type: "string"
+    name: "--include_modules"
+    description: "Use only these module"
+    info: null
+    example:
+    - "fastqc,cutadapt"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "string"
+    name: "--exclude_modules"
+    description: "Do not use only these modules"
+    info: null
+    example:
+    - "fastqc,cutadapt"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "string"
+    name: "--ignore_analysis"
+    info: null
+    example:
+    - "run_one/*,run_two/*"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "string"
+    name: "--ignore_samples"
+    info: null
+    example:
+    - "sample_1*,sample_3*"
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ","
+  - type: "boolean_true"
+    name: "--ignore_symlinks"
+    description: "Ignore symlinked directories and files"
+    info: null
+    direction: "input"
+- name: "Sample name handling"
+  arguments:
+  - type: "boolean_true"
+    name: "--dirs"
+    description: "Prepend directory to sample names to avoid clashing filenames"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--dirs_depth"
+    description: "Prepend n directories to sample names. Negative number to take from\
+      \ start of path."
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--full_names"
+    description: "Do not clean the sample names (leave as full file name)"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--fn_as_s_name"
+    description: "Use the log filename as the sample name"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--replace_names"
+    description: "TSV file to rename sample names during report generation"
+    info: null
+    example:
+    - "replace_names.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Report Customisation"
+  arguments:
+  - type: "string"
+    name: "--title"
+    description: "Report title. Printed as page header, used for filename if not otherwise\
+      \ specified.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--comment"
+    description: "Custom comment, will be printed at the top of the report.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--template"
+    description: "Report template to use.\n"
+    info: null
+    required: false
+    choices:
+    - "default"
+    - "gathered"
+    - "geo"
+    - "highcharts"
+    - "sections"
+    - "simple"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sample_names"
+    description: "TSV file containing alternative sample names for renaming buttons\
+      \ in the report.\n"
+    info: null
+    example:
+    - "sample_names.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sample_filters"
+    description: "TSV file containing show/hide patterns for the report\n"
+    info: null
+    example:
+    - "sample_filters.tsv"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--custom_css_file"
+    description: "Custom CSS file to add to the final report\n"
+    info: null
+    example:
+    - "custom_style_sheet.css"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--profile_runtime"
+    description: "Add analysis of how long MultiQC takes to run to the report\n"
+    info: null
+    direction: "input"
+- name: "MultiQC behaviour"
+  arguments:
+  - type: "boolean_true"
+    name: "--verbose"
+    description: "Increase output verbosity.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--quiet"
+    description: "Only show log warnings\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--strict"
+    description: "Don't catch exceptions, run additional code checks to help development.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--development"
+    description: "Development mode. Do not compress and minimise JS, export uncompressed\
+      \ plot data.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--require_logs"
+    description: "Require all explicitly requested modules to have log files. If not,\
+      \ MultiQC will exit with an error.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_megaqc_upload"
+    description: "Don't upload generated report to MegaQC, even if MegaQC options\
+      \ are found.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_ansi"
+    description: "Disable coloured log output.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--cl_config"
+    description: "YAML formatted string that allows to customize MultiQC behaviour\
+      \ like input file detection.\n"
+    info: null
+    example:
+    - "qualimap_config: { general_stats_coverage: [20,40,200] }"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output format"
+  arguments:
+  - type: "boolean_true"
+    name: "--flat"
+    description: "Use only flat plots (static images).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--interactive"
+    description: "Use only interactive plots (in-browser Javascript).\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--data_dir"
+    description: "Force the parsed data directory to be created.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--no_data_dir"
+    description: "Prevent the parsed data directory from being created.\n"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--zip_data_dir"
+    description: "Compress the data directory.\n"
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--data_format"
+    description: "Output parsed data in a different format than the default 'txt'.\n"
+    info: null
+    required: false
+    choices:
+    - "tsv"
+    - "csv"
+    - "json"
+    - "yaml"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--pdf"
+    description: "Creates PDF report with the 'simple' template. Requires Pandoc to\
+      \ be installed.\n"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "MultiQC aggregates results from bioinformatics analyses across many\
+  \ samples into a single report.\nIt searches a given directory for analysis logs\
+  \ and compiles a HTML report. It's a general use tool, perfect for summarising the\
+  \ output from numerous bioinformatics tools.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info:
+  keywords:
+  - "QC"
+  - "html report"
+  - "aggregate analysis"
+  links:
+    homepage: "https://multiqc.info/"
+    documentation: "https://multiqc.info/docs/"
+    repository: "https://github.com/MultiQC/MultiQC"
+  references:
+    doi: "10.1093/bioinformatics/btw354"
+  licence: "GPL v3 or later"
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/biobox"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/multiqc:1.21--pyhdfd78af_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.1.0"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "multiqc --version | sed 's/multiqc, version\\s\\(.*\\)/multiqc: \"\\1\"/' >\
+      \ /var/software_versions.txt\n"
+  test_setup:
+  - type: "apt"
+    packages:
+    - "jq"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/multiqc/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/multiqc"
+  executable: "target/nextflow/multiqc/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "b84b29747d0635f2ac83ea63b496be9a9edb6724"
+  git_remote: "https://github.com/viash-hub/biobox"
+package_config:
+  name: "biobox"
+  version: "v0.1.0"
+  description: "A collection of bioinformatics tools for working with sequence data.\n"
+  info: null
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'v0.1.0'"
+  keywords:
+  - "bioinformatics"
+  - "modules"
+  - "sequencing"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/biobox"
+    issue_tracker: "https://github.com/viash-hub/biobox/issues"

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'multiqc'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.1.0'
+  description = 'MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\'s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc/nextflow_schema.json

@@ -0,0 +1,529 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "multiqc",
+"description": "MultiQC aggregates results from bioinformatics analyses across many samples into a single report.\nIt searches a given directory for analysis logs and compiles a HTML report. It\u0027s a general use tool, perfect for summarising the output from numerous bioinformatics tools.\n",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input" : {
+    "title": "Input",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: List of `file`, required, example: `data/results/`, multiple_sep: `\":\"`. File paths to be searched for analysis results to be included in the report",
+                "help_text": "Type: List of `file`, required, example: `data/results/`, multiple_sep: `\":\"`. File paths to be searched for analysis results to be included in the report.\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "ouput" : {
+    "title": "Ouput",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output_report": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report",
+                "help_text": "Type: `file`, default: `$id.$key.output_report.html`, example: `multiqc_report.html`. Filepath of the generated report.\n"
+            ,
+                "default": "$id.$key.output_report.html"
+            }
+    
+
+        ,
+                "output_data": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files",
+                "help_text": "Type: `file`, default: `$id.$key.output_data.output_data`, example: `multiqc_data`. Output directory for parsed data files. If not provided, parsed data will not be published.\n"
+            ,
+                "default": "$id.$key.output_data.output_data"
+            }
+    
+
+        ,
+                "output_plots": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots",
+                "help_text": "Type: `file`, default: `$id.$key.output_plots.output_plots`, example: `multiqc_plots`. Output directory for generated plots. If not provided, plots will not be published.\n"
+            ,
+                "default": "$id.$key.output_plots.output_plots"
+            }
+    
+
+}
+},
+    
+    
+    "modules and analyses to run" : {
+    "title": "Modules and analyses to run",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "include_modules": {
+                "type":
+                "string",
+                "description": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Use only these module",
+                "help_text": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Use only these module"
+            
+            }
+    
+
+        ,
+                "exclude_modules": {
+                "type":
+                "string",
+                "description": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Do not use only these modules",
+                "help_text": "Type: List of `string`, example: `fastqc,cutadapt`, multiple_sep: `\",\"`. Do not use only these modules"
+            
+            }
+    
+
+        ,
+                "ignore_analysis": {
+                "type":
+                "string",
+                "description": "Type: List of `string`, example: `run_one/*,run_two/*`, multiple_sep: `\",\"`. ",
+                "help_text": "Type: List of `string`, example: `run_one/*,run_two/*`, multiple_sep: `\",\"`. "
+            
+            }
+    
+
+        ,
+                "ignore_samples": {
+                "type":
+                "string",
+                "description": "Type: List of `string`, example: `sample_1*,sample_3*`, multiple_sep: `\",\"`. ",
+                "help_text": "Type: List of `string`, example: `sample_1*,sample_3*`, multiple_sep: `\",\"`. "
+            
+            }
+    
+
+        ,
+                "ignore_symlinks": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files",
+                "help_text": "Type: `boolean_true`, default: `false`. Ignore symlinked directories and files"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "sample name handling" : {
+    "title": "Sample name handling",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "dirs": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames",
+                "help_text": "Type: `boolean_true`, default: `false`. Prepend directory to sample names to avoid clashing filenames"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "dirs_depth": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. Prepend n directories to sample names",
+                "help_text": "Type: `integer`. Prepend n directories to sample names. Negative number to take from start of path."
+            
+            }
+    
+
+        ,
+                "full_names": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)",
+                "help_text": "Type: `boolean_true`, default: `false`. Do not clean the sample names (leave as full file name)"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "fn_as_s_name": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name",
+                "help_text": "Type: `boolean_true`, default: `false`. Use the log filename as the sample name"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "replace_names": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `replace_names.tsv`. TSV file to rename sample names during report generation",
+                "help_text": "Type: `file`, example: `replace_names.tsv`. TSV file to rename sample names during report generation"
+            
+            }
+    
+
+}
+},
+    
+    
+    "report customisation" : {
+    "title": "Report Customisation",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "title": {
+                "type":
+                "string",
+                "description": "Type: `string`. Report title",
+                "help_text": "Type: `string`. Report title. Printed as page header, used for filename if not otherwise specified.\n"
+            
+            }
+    
+
+        ,
+                "comment": {
+                "type":
+                "string",
+                "description": "Type: `string`. Custom comment, will be printed at the top of the report",
+                "help_text": "Type: `string`. Custom comment, will be printed at the top of the report.\n"
+            
+            }
+    
+
+        ,
+                "template": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. Report template to use",
+                "help_text": "Type: `string`, choices: ``default`, `gathered`, `geo`, `highcharts`, `sections`, `simple``. Report template to use.\n",
+                "enum": ["default", "gathered", "geo", "highcharts", "sections", "simple"]
+            
+            
+            }
+    
+
+        ,
+                "sample_names": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `sample_names.tsv`. TSV file containing alternative sample names for renaming buttons in the report",
+                "help_text": "Type: `file`, example: `sample_names.tsv`. TSV file containing alternative sample names for renaming buttons in the report.\n"
+            
+            }
+    
+
+        ,
+                "sample_filters": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `sample_filters.tsv`. TSV file containing show/hide patterns for the report\n",
+                "help_text": "Type: `file`, example: `sample_filters.tsv`. TSV file containing show/hide patterns for the report\n"
+            
+            }
+    
+
+        ,
+                "custom_css_file": {
+                "type":
+                "string",
+                "description": "Type: `file`, example: `custom_style_sheet.css`. Custom CSS file to add to the final report\n",
+                "help_text": "Type: `file`, example: `custom_style_sheet.css`. Custom CSS file to add to the final report\n"
+            
+            }
+    
+
+        ,
+                "profile_runtime": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n",
+                "help_text": "Type: `boolean_true`, default: `false`. Add analysis of how long MultiQC takes to run to the report\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "multiqc behaviour" : {
+    "title": "MultiQC behaviour",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "verbose": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Increase output verbosity",
+                "help_text": "Type: `boolean_true`, default: `false`. Increase output verbosity.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "quiet": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Only show log warnings\n",
+                "help_text": "Type: `boolean_true`, default: `false`. Only show log warnings\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "strict": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development",
+                "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t catch exceptions, run additional code checks to help development.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "development": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Development mode",
+                "help_text": "Type: `boolean_true`, default: `false`. Development mode. Do not compress and minimise JS, export uncompressed plot data.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "require_logs": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files",
+                "help_text": "Type: `boolean_true`, default: `false`. Require all explicitly requested modules to have log files. If not, MultiQC will exit with an error.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_megaqc_upload": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found",
+                "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t upload generated report to MegaQC, even if MegaQC options are found.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_ansi": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Disable coloured log output",
+                "help_text": "Type: `boolean_true`, default: `false`. Disable coloured log output.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "cl_config": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `qualimap_config: { general_stats_coverage: [20,40,200] }`. YAML formatted string that allows to customize MultiQC behaviour like input file detection",
+                "help_text": "Type: `string`, example: `qualimap_config: { general_stats_coverage: [20,40,200] }`. YAML formatted string that allows to customize MultiQC behaviour like input file detection.\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "output format" : {
+    "title": "Output format",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "flat": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use only flat plots (static images)",
+                "help_text": "Type: `boolean_true`, default: `false`. Use only flat plots (static images).\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "interactive": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript)",
+                "help_text": "Type: `boolean_true`, default: `false`. Use only interactive plots (in-browser Javascript).\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "data_dir": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created",
+                "help_text": "Type: `boolean_true`, default: `false`. Force the parsed data directory to be created.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "no_data_dir": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created",
+                "help_text": "Type: `boolean_true`, default: `false`. Prevent the parsed data directory from being created.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "zip_data_dir": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Compress the data directory",
+                "help_text": "Type: `boolean_true`, default: `false`. Compress the data directory.\n"
+            ,
+                "default": "False"
+            }
+    
+
+        ,
+                "data_format": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``tsv`, `csv`, `json`, `yaml``. Output parsed data in a different format than the default \u0027txt\u0027",
+                "help_text": "Type: `string`, choices: ``tsv`, `csv`, `json`, `yaml``. Output parsed data in a different format than the default \u0027txt\u0027.\n",
+                "enum": ["tsv", "csv", "json", "yaml"]
+            
+            
+            }
+    
+
+        ,
+                "pdf": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template",
+                "help_text": "Type: `boolean_true`, default: `false`. Creates PDF report with the \u0027simple\u0027 template. Requires Pandoc to be installed.\n"
+            ,
+                "default": "False"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input"
+    },
+
+    {
+    "$ref": "#/definitions/ouput"
+    },
+
+    {
+    "$ref": "#/definitions/modules and analyses to run"
+    },
+
+    {
+    "$ref": "#/definitions/sample name handling"
+    },
+
+    {
+    "$ref": "#/definitions/report customisation"
+    },
+
+    {
+    "$ref": "#/definitions/multiqc behaviour"
+    },
+
+    {
+    "$ref": "#/definitions/output format"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}

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

@@ -0,0 +1,171 @@
+name: "interop_summary_to_csv"
+namespace: "io"
+version: "main"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Sequencing run folder (*not* InterOp folder)."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output_run_summary"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_index_summary"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/demultiplex"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "debian:stable-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "wget"
+    interactive: false
+  - type: "docker"
+    run:
+    - "wget https://github.com/Illumina/interop/releases/download/v1.3.1/interop-1.3.1-Linux-GNU.tar.gz\
+      \ -O /tmp/interop.tar.gz && \\\ntar -C /tmp/ --no-same-owner --no-same-permissions\
+      \ -xvf /tmp/interop.tar.gz && \\\nmv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary\
+      \ /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/io/interop_summary_to_csv/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/io/interop_summary_to_csv"
+  executable: "target/executable/io/interop_summary_to_csv/interop_summary_to_csv"
+  viash_version: "0.9.0-RC6"
+  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  git_remote: "https://github.com/viash-hub/demultiplex"
+package_config:
+  name: "demultiplex"
+  version: "main"
+  description: "Demultiplexing pipeline\n"
+  info:
+    test_resources:
+    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
+      dest: "test_resources"
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "sequence"
+  - "demultiplexing"
+  - "pipeline"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/demultiplex"
+    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"

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

@@ -0,0 +1,178 @@
+name: "untar"
+namespace: "io"
+version: "main"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Tarball file to be unpacked."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Directory to write the contents of the .tar file to."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Other arguments"
+  arguments:
+  - type: "string"
+    name: "--exclude"
+    alternatives:
+    - "-e"
+    description: "Prevents any file or member whose name matches the shell wildcard\
+      \ (pattern) from being extracted."
+    info: null
+    example:
+    - "docs/figures"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Unpack a .tar file. When the contents of the .tar file is just a single\
+  \ directory,\nput the contents of the directory into the output folder instead of\
+  \ that directory.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/demultiplex"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "debian:stable-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/io/untar/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/io/untar"
+  executable: "target/executable/io/untar/untar"
+  viash_version: "0.9.0-RC6"
+  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  git_remote: "https://github.com/viash-hub/demultiplex"
+package_config:
+  name: "demultiplex"
+  version: "main"
+  description: "Demultiplexing pipeline\n"
+  info:
+    test_resources:
+    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
+      dest: "test_resources"
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "sequence"
+  - "demultiplexing"
+  - "pipeline"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/demultiplex"
+    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"

target/nextflow/dataflow/combine_samples/.config.vsh.yaml

@@ -0,0 +1,169 @@
+name: "combine_samples"
+namespace: "dataflow"
+version: "main"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "string"
+    name: "--id"
+    description: "ID of the new event"
+    info: null
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--forward_input"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--reverse_input"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output_forward"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_reverse"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: true
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+description: "Combine fastq files from across samples into one event with a list of\
+  \ fastq files per orientation."
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/demultiplex"
+runners:
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "native"
+  id: "native"
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/dataflow/combine_samples/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "native|native"
+  output: "target/nextflow/dataflow/combine_samples"
+  executable: "target/nextflow/dataflow/combine_samples/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  git_remote: "https://github.com/viash-hub/demultiplex"
+package_config:
+  name: "demultiplex"
+  version: "main"
+  description: "Demultiplexing pipeline\n"
+  info:
+    test_resources:
+    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
+      dest: "test_resources"
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "sequence"
+  - "demultiplexing"
+  - "pipeline"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/demultiplex"
+    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"

target/nextflow/dataflow/combine_samples/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'dataflow/combine_samples'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'main'
+  description = 'Combine fastq files from across samples into one event with a list of fastq files per orientation.'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/nextflow/dataflow/combine_samples/nextflow_schema.json

@@ -0,0 +1,126 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "combine_samples",
+"description": "Combine fastq files from across samples into one event with a list of fastq files per orientation.",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input arguments" : {
+    "title": "Input arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "id": {
+                "type":
+                "string",
+                "description": "Type: `string`, required. ID of the new event",
+                "help_text": "Type: `string`, required. ID of the new event"
+            
+            }
+    
+
+        ,
+                "forward_input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. ",
+                "help_text": "Type: `file`, required. "
+            
+            }
+    
+
+        ,
+                "reverse_input": {
+                "type":
+                "string",
+                "description": "Type: `file`. ",
+                "help_text": "Type: `file`. "
+            
+            }
+    
+
+}
+},
+    
+    
+    "output arguments" : {
+    "title": "Output arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output_forward": {
+                "type":
+                "string",
+                "description": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. ",
+                "help_text": "Type: List of `file`, required, default: `$id.$key.output_forward_*.output_forward_*`, multiple_sep: `\":\"`. "
+            ,
+                "default": "$id.$key.output_forward_*.output_forward_*"
+            }
+    
+
+        ,
+                "output_reverse": {
+                "type":
+                "string",
+                "description": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. ",
+                "help_text": "Type: List of `file`, default: `$id.$key.output_reverse_*.output_reverse_*`, multiple_sep: `\":\"`. "
+            ,
+                "default": "$id.$key.output_reverse_*.output_reverse_*"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input arguments"
+    },
+
+    {
+    "$ref": "#/definitions/output arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}

target/nextflow/dataflow/gather_fastqs_and_validate/.config.vsh.yaml

@@ -0,0 +1,163 @@
+name: "gather_fastqs_and_validate"
+namespace: "dataflow"
+version: "main"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Directory containing .fastq files"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sample_sheet"
+    description: "Sample sheet"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--fastq_forward"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--fastq_reverse"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+description: "From a directory containing fastq files, gather the files per sample\
+  \ \nand validate according to the contents of the sample sheet.\n"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/demultiplex"
+runners:
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "native"
+  id: "native"
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/dataflow/gather_fastqs_and_validate/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "native|native"
+  output: "target/nextflow/dataflow/gather_fastqs_and_validate"
+  executable: "target/nextflow/dataflow/gather_fastqs_and_validate/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  git_remote: "https://github.com/viash-hub/demultiplex"
+package_config:
+  name: "demultiplex"
+  version: "main"
+  description: "Demultiplexing pipeline\n"
+  info:
+    test_resources:
+    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
+      dest: "test_resources"
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "sequence"
+  - "demultiplexing"
+  - "pipeline"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/demultiplex"
+    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"

target/nextflow/dataflow/gather_fastqs_and_validate/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'dataflow/gather_fastqs_and_validate'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'main'
+  description = 'From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/nextflow/dataflow/gather_fastqs_and_validate/nextflow_schema.json

@@ -0,0 +1,116 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "gather_fastqs_and_validate",
+"description": "From a directory containing fastq files, gather the files per sample \nand validate according to the contents of the sample sheet.\n",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input arguments" : {
+    "title": "Input arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. Directory containing ",
+                "help_text": "Type: `file`, required. Directory containing .fastq files"
+            
+            }
+    
+
+        ,
+                "sample_sheet": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. Sample sheet",
+                "help_text": "Type: `file`, required. Sample sheet"
+            
+            }
+    
+
+}
+},
+    
+    
+    "output arguments" : {
+    "title": "Output arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "fastq_forward": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.fastq_forward.fastq_forward`. ",
+                "help_text": "Type: `file`, required, default: `$id.$key.fastq_forward.fastq_forward`. "
+            ,
+                "default": "$id.$key.fastq_forward.fastq_forward"
+            }
+    
+
+        ,
+                "fastq_reverse": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.fastq_reverse.fastq_reverse`. ",
+                "help_text": "Type: `file`, default: `$id.$key.fastq_reverse.fastq_reverse`. "
+            ,
+                "default": "$id.$key.fastq_reverse.fastq_reverse"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input arguments"
+    },
+
+    {
+    "$ref": "#/definitions/output arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}

target/nextflow/demultiplex/.config.vsh.yaml

@@ -0,0 +1,224 @@
+name: "demultiplex"
+version: "main"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Directory containing raw sequencing data"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--sample_sheet"
+    description: "Sample sheet as input for BCL Convert. If not specified,\nwill try\
+      \ to autodetect the sample sheet in the input directory\n"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Directory to write fastq data to"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_falco"
+    description: "Directory to write falco output to"
+    info: null
+    default:
+    - "$id/falco"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_multiqc"
+    description: "Directory to write falco output to"
+    info: null
+    default:
+    - "$id/multiqc_report.html"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "nextflow_script"
+  path: "main.nf"
+  is_executable: true
+  entrypoint: "run_wf"
+description: "Demultiplexing of raw sequencing data"
+test_resources:
+- type: "nextflow_script"
+  path: "test.nf"
+  is_executable: true
+  entrypoint: "test_wf"
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+dependencies:
+- name: "io/untar"
+  repository:
+    type: "local"
+- name: "dataflow/gather_fastqs_and_validate"
+  repository:
+    type: "local"
+- name: "io/interop_summary_to_csv"
+  repository:
+    type: "local"
+- name: "dataflow/combine_samples"
+  repository:
+    type: "local"
+- name: "bcl_convert"
+  repository:
+    type: "vsh"
+    repo: "biobox"
+    tag: "v0.1.0"
+- name: "falco"
+  repository:
+    type: "vsh"
+    repo: "biobox"
+    tag: "v0.1.0"
+- name: "multiqc"
+  repository:
+    type: "vsh"
+    repo: "biobox"
+    tag: "v0.1.0"
+repositories:
+- type: "vsh"
+  name: "bb"
+  repo: "biobox"
+  tag: "v0.1.0"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/demultiplex"
+runners:
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "native"
+  id: "native"
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/demultiplex/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "native|native"
+  output: "target/nextflow/demultiplex"
+  executable: "target/nextflow/demultiplex/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  git_remote: "https://github.com/viash-hub/demultiplex"
+  dependencies:
+  - "target/nextflow/io/untar"
+  - "target/nextflow/dataflow/gather_fastqs_and_validate"
+  - "target/nextflow/io/interop_summary_to_csv"
+  - "target/nextflow/dataflow/combine_samples"
+  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/bcl_convert"
+  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/falco"
+  - "target/dependencies/vsh/vsh/biobox/v0.1.0/nextflow/multiqc"
+package_config:
+  name: "demultiplex"
+  version: "main"
+  description: "Demultiplexing pipeline\n"
+  info:
+    test_resources:
+    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
+      dest: "test_resources"
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "sequence"
+  - "demultiplexing"
+  - "pipeline"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/demultiplex"
+    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"

target/nextflow/demultiplex/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'demultiplex'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'main'
+  description = 'Demultiplexing of raw sequencing data'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/nextflow/demultiplex/nextflow_schema.json

@@ -0,0 +1,127 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "demultiplex",
+"description": "Demultiplexing of raw sequencing data",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input arguments" : {
+    "title": "Input arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. Directory containing raw sequencing data",
+                "help_text": "Type: `file`, required. Directory containing raw sequencing data"
+            
+            }
+    
+
+        ,
+                "sample_sheet": {
+                "type":
+                "string",
+                "description": "Type: `file`. Sample sheet as input for BCL Convert",
+                "help_text": "Type: `file`. Sample sheet as input for BCL Convert. If not specified,\nwill try to autodetect the sample sheet in the input directory\n"
+            
+            }
+    
+
+}
+},
+    
+    
+    "output arguments" : {
+    "title": "Output arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write fastq data to",
+                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write fastq data to"
+            ,
+                "default": "$id.$key.output.output"
+            }
+    
+
+        ,
+                "output_falco": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.output_falco.output_falco`. Directory to write falco output to",
+                "help_text": "Type: `file`, default: `$id.$key.output_falco.output_falco`. Directory to write falco output to"
+            ,
+                "default": "$id.$key.output_falco.output_falco"
+            }
+    
+
+        ,
+                "output_multiqc": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.output_multiqc.html`. Directory to write falco output to",
+                "help_text": "Type: `file`, default: `$id.$key.output_multiqc.html`. Directory to write falco output to"
+            ,
+                "default": "$id.$key.output_multiqc.html"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input arguments"
+    },
+
+    {
+    "$ref": "#/definitions/output arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}

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

@@ -0,0 +1,171 @@
+name: "interop_summary_to_csv"
+namespace: "io"
+version: "main"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Sequencing run folder (*not* InterOp folder)."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output_run_summary"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output_index_summary"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/demultiplex"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "debian:stable-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    - "wget"
+    interactive: false
+  - type: "docker"
+    run:
+    - "wget https://github.com/Illumina/interop/releases/download/v1.3.1/interop-1.3.1-Linux-GNU.tar.gz\
+      \ -O /tmp/interop.tar.gz && \\\ntar -C /tmp/ --no-same-owner --no-same-permissions\
+      \ -xvf /tmp/interop.tar.gz && \\\nmv /tmp/interop-1.3.1-Linux-GNU/bin/index-summary\
+      \ /tmp/interop-1.3.1-Linux-GNU/bin/summary /usr/local/bin/\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/io/interop_summary_to_csv/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/io/interop_summary_to_csv"
+  executable: "target/nextflow/io/interop_summary_to_csv/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  git_remote: "https://github.com/viash-hub/demultiplex"
+package_config:
+  name: "demultiplex"
+  version: "main"
+  description: "Demultiplexing pipeline\n"
+  info:
+    test_resources:
+    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
+      dest: "test_resources"
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "sequence"
+  - "demultiplexing"
+  - "pipeline"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/demultiplex"
+    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"

target/nextflow/io/interop_summary_to_csv/nextflow.config

@@ -0,0 +1,124 @@
+manifest {
+  name = 'io/interop_summary_to_csv'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'main'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/nextflow/io/interop_summary_to_csv/nextflow_schema.json

@@ -0,0 +1,106 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "interop_summary_to_csv",
+"description": "No description",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input arguments" : {
+    "title": "Input arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. Sequencing run folder (*not* InterOp folder)",
+                "help_text": "Type: `file`, required. Sequencing run folder (*not* InterOp folder)."
+            
+            }
+    
+
+}
+},
+    
+    
+    "output arguments" : {
+    "title": "Output arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output_run_summary": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output_run_summary.output_run_summary`. ",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_run_summary.output_run_summary`. "
+            ,
+                "default": "$id.$key.output_run_summary.output_run_summary"
+            }
+    
+
+        ,
+                "output_index_summary": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output_index_summary.output_index_summary`. ",
+                "help_text": "Type: `file`, required, default: `$id.$key.output_index_summary.output_index_summary`. "
+            ,
+                "default": "$id.$key.output_index_summary.output_index_summary"
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input arguments"
+    },
+
+    {
+    "$ref": "#/definitions/output arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}

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

@@ -0,0 +1,178 @@
+name: "untar"
+namespace: "io"
+version: "main"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Tarball file to be unpacked."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Directory to write the contents of the .tar file to."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Other arguments"
+  arguments:
+  - type: "string"
+    name: "--exclude"
+    alternatives:
+    - "-e"
+    description: "Prevents any file or member whose name matches the shell wildcard\
+      \ (pattern) from being extracted."
+    info: null
+    example:
+    - "docs/figures"
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Unpack a .tar file. When the contents of the .tar file is just a single\
+  \ directory,\nput the contents of the directory into the output folder instead of\
+  \ that directory.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/demultiplex"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "debian:stable-slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "main"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/io/untar/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/io/untar"
+  executable: "target/nextflow/io/untar/main.nf"
+  viash_version: "0.9.0-RC6"
+  git_commit: "ed860bed30c98b981270f104cffbdb9b7f1ce141"
+  git_remote: "https://github.com/viash-hub/demultiplex"
+package_config:
+  name: "demultiplex"
+  version: "main"
+  description: "Demultiplexing pipeline\n"
+  info:
+    test_resources:
+    - path: "https://raw.githubusercontent.com/nf-core/test-datasets/demultiplex/testdata/NovaSeq6000/200624_A00834_0183_BHMTFYDRXX.tar.gz"
+      dest: "test_resources"
+  viash_version: "0.9.0-RC6"
+  source: "src"
+  target: "target"
+  config_mods:
+  - ".requirements.commands := ['ps']\n"
+  - ".engines += { type: \"native\" }"
+  - ".engines[.type == 'docker'].target_registry := 'images.viash-hub.com'"
+  - ".engines[.type == 'docker'].target_tag := 'main'"
+  keywords:
+  - "bioinformatics"
+  - "sequence"
+  - "demultiplexing"
+  - "pipeline"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/demultiplex"
+    issue_tracker: "https://github.com/viash-hub/demultiplex/issues"

target/nextflow/io/untar/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'io/untar'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'main'
+  description = 'Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n'
+}
+
+process.container = 'nextflow/bash:latest'
+
+// detect tempdir
+tempDir = java.nio.file.Paths.get(
+  System.getenv('NXF_TEMP') ?:
+    System.getenv('VIASH_TEMP') ?: 
+    System.getenv('TEMPDIR') ?: 
+    System.getenv('TMPDIR') ?: 
+    '/tmp'
+).toAbsolutePath()
+
+profiles {
+  no_publish {
+    process {
+      withName: '.*' {
+        publishDir = [
+          enabled: false
+        ]
+      }
+    }
+  }
+  mount_temp {
+    docker.temp            = tempDir
+    podman.temp            = tempDir
+    charliecloud.temp      = tempDir
+  }
+  docker {
+    docker.enabled         = true
+    // docker.userEmulation   = true
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  singularity {
+    singularity.enabled    = true
+    singularity.autoMounts = true
+    docker.enabled         = false
+    podman.enabled         = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  podman {
+    podman.enabled         = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    shifter.enabled        = false
+    charliecloud.enabled   = false
+  }
+  shifter {
+    shifter.enabled        = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    charliecloud.enabled   = false
+  }
+  charliecloud {
+    charliecloud.enabled   = true
+    docker.enabled         = false
+    singularity.enabled    = false
+    podman.enabled         = false
+    shifter.enabled        = false
+  }
+}
+
+process{
+  withLabel: mem1gb { memory = 1000000000.B }
+  withLabel: mem2gb { memory = 2000000000.B }
+  withLabel: mem5gb { memory = 5000000000.B }
+  withLabel: mem10gb { memory = 10000000000.B }
+  withLabel: mem20gb { memory = 20000000000.B }
+  withLabel: mem50gb { memory = 50000000000.B }
+  withLabel: mem100gb { memory = 100000000000.B }
+  withLabel: mem200gb { memory = 200000000000.B }
+  withLabel: mem500gb { memory = 500000000000.B }
+  withLabel: mem1tb { memory = 1000000000000.B }
+  withLabel: mem2tb { memory = 2000000000000.B }
+  withLabel: mem5tb { memory = 5000000000000.B }
+  withLabel: mem10tb { memory = 10000000000000.B }
+  withLabel: mem20tb { memory = 20000000000000.B }
+  withLabel: mem50tb { memory = 50000000000000.B }
+  withLabel: mem100tb { memory = 100000000000000.B }
+  withLabel: mem200tb { memory = 200000000000000.B }
+  withLabel: mem500tb { memory = 500000000000000.B }
+  withLabel: mem1gib { memory = 1073741824.B }
+  withLabel: mem2gib { memory = 2147483648.B }
+  withLabel: mem4gib { memory = 4294967296.B }
+  withLabel: mem8gib { memory = 8589934592.B }
+  withLabel: mem16gib { memory = 17179869184.B }
+  withLabel: mem32gib { memory = 34359738368.B }
+  withLabel: mem64gib { memory = 68719476736.B }
+  withLabel: mem128gib { memory = 137438953472.B }
+  withLabel: mem256gib { memory = 274877906944.B }
+  withLabel: mem512gib { memory = 549755813888.B }
+  withLabel: mem1tib { memory = 1099511627776.B }
+  withLabel: mem2tib { memory = 2199023255552.B }
+  withLabel: mem4tib { memory = 4398046511104.B }
+  withLabel: mem8tib { memory = 8796093022208.B }
+  withLabel: mem16tib { memory = 17592186044416.B }
+  withLabel: mem32tib { memory = 35184372088832.B }
+  withLabel: mem64tib { memory = 70368744177664.B }
+  withLabel: mem128tib { memory = 140737488355328.B }
+  withLabel: mem256tib { memory = 281474976710656.B }
+  withLabel: mem512tib { memory = 562949953421312.B }
+  withLabel: cpu1 { cpus = 1 }
+  withLabel: cpu2 { cpus = 2 }
+  withLabel: cpu5 { cpus = 5 }
+  withLabel: cpu10 { cpus = 10 }
+  withLabel: cpu20 { cpus = 20 }
+  withLabel: cpu50 { cpus = 50 }
+  withLabel: cpu100 { cpus = 100 }
+  withLabel: cpu200 { cpus = 200 }
+  withLabel: cpu500 { cpus = 500 }
+  withLabel: cpu1000 { cpus = 1000 }
+}
+
+

target/nextflow/io/untar/nextflow_schema.json

@@ -0,0 +1,119 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "untar",
+"description": "Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n",
+"type": "object",
+"definitions": {
+
+    
+    
+    "input arguments" : {
+    "title": "Input arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. Tarball file to be unpacked",
+                "help_text": "Type: `file`, required. Tarball file to be unpacked."
+            
+            }
+    
+
+}
+},
+    
+    
+    "output arguments" : {
+    "title": "Output arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write the contents of the ",
+                "help_text": "Type: `file`, required, default: `$id.$key.output.output`. Directory to write the contents of the .tar file to."
+            ,
+                "default": "$id.$key.output.output"
+            }
+    
+
+}
+},
+    
+    
+    "other arguments" : {
+    "title": "Other arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "exclude": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `docs/figures`. Prevents any file or member whose name matches the shell wildcard (pattern) from being extracted",
+                "help_text": "Type: `string`, example: `docs/figures`. Prevents any file or member whose name matches the shell wildcard (pattern) from being extracted."
+            
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/input arguments"
+    },
+
+    {
+    "$ref": "#/definitions/output arguments"
+    },
+
+    {
+    "$ref": "#/definitions/other arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}