Build branch v0.3 with version v0.3.0 (4947872)

Build pipeline: viash-hub.craftbox.v0.3-s7x9q

Source commit: 4947872a1c

Source message: Bump version to v0.3.0

CHANGELOG.md

@@ -0,0 +1,43 @@
+# craftbox 0.3.0
+
+## NEW FEATURES
+
+* `move_files_to_directory`: add support for preserving symbolic links (PR #13).
+
+# craftbox 0.2.0
+
+## NEW FEATURES
+
+* `sync_resources`: Sync a Viash package's test resources to the local filesystem (PR #7).
+
+* `move_files_to_directory`: Publish one or multiple files to an output directory (PR #10).
+
+* `check_disk_space`: Add functionality to check available system resources (PR #14).
+
+
+## MINOR CHANGES
+
+* Add documentation to multiple components (PR #9).
+
+* Bump Viash to 0.9.4 (PR #9, PR #11).
+
+* Update documentation and package metadata (PR #11).
+
+## BUG FIXES
+
+* `untar`: Fix usage of a deprecated environment variable (PR #8).
+
+# craftbox 0.1.0
+
+## NEW FEATURES
+
+* `concat_text`: Concatenate a number of text files
+
+* `csv2fasta`: Convert two columns from a CSV file to FASTA entries (PR #1).
+
+* `untar`: 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 (PR #3).
+
+## MINOR CHANGES
+
+* Bump viash to 0.9.0

CONTRIBUTING.md

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+
+# Contributing guidelines
+
+We encourage contributions from the community. To contribute:
+
+1. **Fork the Repository**: Start by forking this repository to your account.
+2. **Develop Your Component**: Create your Viash component, ensuring it aligns with our best practices (detailed below).
+3. **Submit a Pull Request**: After testing your component, submit a pull request for review.
+
+## Procedure of adding a component
+
+### Step 1: Find a component to contribute
+
+* Find a tool to contribute to this repo.
+
+* Check whether it is already in the [Project board](https://github.com/orgs/viash-hub/projects/1).
+
+* Check whether there is a corresponding [Snakemake wrapper](https://github.com/snakemake/snakemake-wrappers/blob/master/bio) or [nf-core module](https://github.com/nf-core/modules/tree/master/modules/nf-core) which we can use as inspiration.
+
+* Create an issue to show that you are working on this component.
+
+
+### Step 2: Add config template
+
+Change all occurrences of `xxx` to the name of the component.
+
+Create a file at `src/xxx/config.vsh.yaml` with contents:
+
+```yaml
+name: xxx
+description: xxx
+keywords: [tag1, tag2]
+links:
+  homepage: yyy
+  documentation: yyy
+  issue_tracker: yyy
+  repository: yyy
+references: 
+  doi: 12345/12345678.yz
+license: MIT/Apache-2.0/GPL-3.0/...
+argument_groups:
+  - name: Inputs
+    arguments: <...>
+  - name: Outputs
+    arguments: <...>
+  - name: Arguments
+    arguments: <...>
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+engines:
+  - <...>
+runners:
+  - type: executable
+  - type: nextflow
+```
+
+### Step 3: Fill in the metadata
+
+Fill in the relevant metadata fields in the config. Here is an example of the metadata of an existing component.
+
+```yaml
+functionality:
+  name: arriba
+  description: Detect gene fusions from RNA-Seq data
+  keywords: [Gene fusion, RNA-Seq]
+  links:
+    homepage: https://arriba.readthedocs.io/en/latest/
+    documentation: https://arriba.readthedocs.io/en/latest/
+    repository: https://github.com/suhrig/arriba
+    issue_tracker: https://github.com/suhrig/arriba/issues
+  references:
+    doi: 10.1101/gr.257246.119
+    bibtex: |
+      @article{
+        ... a bibtex entry in case the doi is not available ...
+      }
+  license: MIT
+```
+
+### Step 4: Find a suitable container
+
+Google `biocontainer <name of component>` and find the container that is most suitable. Typically the link will be `https://quay.io/repository/biocontainers/xxx?tab=tags`.
+
+If no such container is found, you can create a custom container in the next step. 
+
+
+### Step 5: Create help file
+
+To help develop the component, we store the `--help` output of the tool in a file at `src/xxx/help.txt`.
+
+````bash
+cat <<EOF > src/xxx/help.txt
+```sh
+xxx --help
+```
+EOF
+
+docker run quay.io/biocontainers/xxx:tag xxx --help >> src/xxx/help.txt
+````
+
+Notes:
+
+* This help file has no functional purpose, but it is useful for the developer to see the help output of the tool.
+
+* Some tools might not have a `--help` argument but instead have a `-h` argument. For example, for `arriba`, the help message is obtained by running `arriba -h`:
+  
+  ```bash
+  docker run quay.io/biocontainers/arriba:2.4.0--h0033a41_2 arriba -h
+  ```
+
+
+### Step 6: Create or fetch test data
+
+To help develop the component, it's interesting to have some test data available. In most cases, we can use the test data from the Snakemake wrappers. 
+
+To make sure we can reproduce the test data in the future, we store the command to fetch the test data in a file at `src/xxx/test_data/script.sh`.
+
+```bash
+cat <<EOF > src/xxx/test_data/script.sh
+
+# clone repo
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+# copy test data
+cp -r /tmp/snakemake-wrappers/bio/xxx/test/* src/xxx/test_data
+EOF
+```
+
+The test data should be suitable for testing this component. Ensure that the test data is small enough: ideally <1KB, preferably <10KB, if need be <100KB.
+
+### Step 7: Add arguments for the input files
+
+By looking at the help file, we add the input arguments to the config file. Here is an example of the input arguments of an existing component.
+
+For instance, in the [arriba help file](src/arriba/help.txt), we see the following:
+
+    Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
+                  -g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
+                  [-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
+                  -o fusions.tsv [-O fusions.discarded.tsv] \
+                  [OPTIONS]
+
+    -x FILE  File in SAM/BAM/CRAM format with main alignments as generated by STAR 
+              (Aligned.out.sam). Arriba extracts candidate reads from this file. 
+
+Based on this information, we can add the following input arguments to the config file.
+
+```yaml
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: --bam
+      alternatives: -x
+      type: file
+      description: |
+        File in SAM/BAM/CRAM format with main alignments as generated by STAR
+        (Aligned.out.sam). Arriba extracts candidate reads from this file.
+      required: true
+      example: Aligned.out.bam
+```
+
+Check the [documentation](https://viash.io/reference/config/functionality/arguments) for more information on the format of input arguments.
+
+Several notes:
+
+* Argument names should be formatted in `--snake_case`. This means arguments like `--foo-bar` should be formatted as `--foo_bar`, and short arguments like `-f` should receive a longer name like `--foo`.
+
+* Input arguments can have `multiple: true` to allow the user to specify multiple files.
+
+
+
+### Step 8: Add arguments for the output files
+
+By looking at the help file, we now also add output arguments to the config file.
+
+For example, in the [arriba help file](src/arriba/help.txt), we see the following:
+
+
+    Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
+                  -g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
+                  [-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
+                  -o fusions.tsv [-O fusions.discarded.tsv] \
+                  [OPTIONS]
+
+     -o FILE  Output file with fusions that have passed all filters. 
+
+     -O FILE  Output file with fusions that were discarded due to filtering. 
+
+Based on this information, we can add the following output arguments to the config file.
+
+```yaml
+argument_groups:
+  - name: Outputs
+    arguments:
+      - name: --fusions
+        alternatives: -o
+        type: file
+        direction: output
+        description: |
+          Output file with fusions that have passed all filters.
+        required: true
+        example: fusions.tsv
+      - name: --fusions_discarded
+        alternatives: -O
+        type: file
+        direction: output
+        description: |
+          Output file with fusions that were discarded due to filtering. 
+        required: false
+        example: fusions.discarded.tsv
+```
+
+Note: 
+
+* Preferably, these outputs should not be directores but files. For example, if a tool outputs a directory `foo/` containing files `foo/bar.txt` and `foo/baz.txt`, there should be two output arguments `--bar` and `--baz` (as opposed to one output argument which outputs the whole `foo/` directory).
+
+### Step 9: Add arguments for the other arguments
+
+Finally, add all other arguments to the config file. There are a few exceptions:
+
+* Arguments related to specifying CPU and memory requirements are handled separately and should not be added to the config file.
+
+* Arguments related to printing the information such as printing the version (`-v`, `--version`) or printing the help (`-h`, `--help`) should not be added to the config file.
+
+
+### Step 10: Add a Docker engine
+
+To ensure reproducibility of components, we require that all components are run in a Docker container. 
+
+```yaml
+engines:
+  - type: docker
+    image: quay.io/biocontainers/xxx:0.1.0--py_0
+```
+
+The container should have your tool installed, as well as `ps`.
+
+If you didn't find a suitable container in the previous step, you can create a custom container. For example:
+
+```yaml
+engines:
+  - type: docker
+    image: python:3.10
+    setup:
+      - type: python
+        packages: numpy
+```
+
+For more information on how to do this, see the [documentation](https://viash.io/guide/component/add-dependencies.html#steps-for-creating-a-custom-docker-platform).
+
+Here is a list of base containers we can recommend:
+
+* Bash: [`bash`](https://hub.docker.com/_/bash), [`ubuntu`](https://hub.docker.com/_/ubuntu)
+* C#: [`ghcr.io/data-intuitive/dotnet-script`](https://github.com/data-intuitive/ghcr-dotnet-script/pkgs/container/dotnet-script)
+* JavaScript: [`node`](https://hub.docker.com/_/node)
+* Python: [`python`](https://hub.docker.com/_/python), [`nvcr.io/nvidia/pytorch`](https://catalog.ngc.nvidia.com/orgs/nvidia/containers/pytorch)
+* R: [`eddelbuettel/r2u`](https://hub.docker.com/r/eddelbuettel/r2u), [`rocker/tidyverse`](https://hub.docker.com/r/rocker/tidyverse)
+* Scala: [`sbtscala/scala-sbt`](https://hub.docker.com/r/sbtscala/scala-sbt)
+
+### Step 11: Write a runner script
+
+Next, we need to write a runner script that runs the tool with the input arguments. Create a Bash script named `src/xxx/script.sh` which runs the tool with the input arguments.
+
+```bash
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+xxx \
+  --input "$par_input" \
+  --output "$par_output" \
+  $([ "$par_option" = "true" ] && echo "--option")
+```
+
+When building a Viash component, Viash will automatically replace the `## VIASH START` and `## VIASH END` lines (and anything in between) with environment variables based on the arguments specified in the config.
+
+As an example, this is what the Bash script for the `arriba` component looks like:
+
+```bash
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+arriba \
+  -x "$par_bam" \
+  -a "$par_genome" \
+  -g "$par_gene_annotation" \
+  -o "$par_fusions" \
+  ${par_known_fusions:+-k "${par_known_fusions}"} \
+  ${par_blacklist:+-b "${par_blacklist}"} \
+  ${par_structural_variants:+-d "${par_structural_variants}"} \
+  $([ "$par_skip_duplicate_marking" = "true" ] && echo "-u") \
+  $([ "$par_extra_information" = "true" ] && echo "-X") \
+  $([ "$par_fill_gaps" = "true" ] && echo "-I")
+```
+
+
+### Step 12: Create test script
+
+
+If the unit test requires test resources, these should be provided in the `test_resources` section of the component. 
+
+```yaml
+functionality:
+  # ...
+  test_resources:
+    - type: bash_script
+      path: test.sh
+    - type: file
+      path: test_data
+```
+
+Create a test script at `src/xxx/test.sh` that runs the component with the test data. This script should run the component (available with `$meta_executable`) with the test data and check if the output is as expected. The script should exit with a non-zero exit code if the output is not as expected. For example:
+
+```bash
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+echo "> Run xxx with test data"
+"$meta_executable" \
+  --input "$meta_resources_dir/test_data/input.txt" \
+  --output "output.txt" \
+  --option
+
+echo ">> Checking output"
+[ ! -f "output.txt" ] && echo "Output file output.txt does not exist" && exit 1
+```
+
+
+For example, this is what the test script for the `arriba` component looks like:
+
+```bash
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+echo "> Run arriba with blacklist"
+"$meta_executable" \
+  --bam "$meta_resources_dir/test_data/A.bam" \
+  --genome "$meta_resources_dir/test_data/genome.fasta" \
+  --gene_annotation "$meta_resources_dir/test_data/annotation.gtf" \
+  --blacklist "$meta_resources_dir/test_data/blacklist.tsv" \
+  --fusions "fusions.tsv" \
+  --fusions_discarded "fusions_discarded.tsv" \
+  --interesting_contigs "1,2"
+
+echo ">> Checking output"
+[ ! -f "fusions.tsv" ] && echo "Output file fusions.tsv does not exist" && exit 1
+[ ! -f "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv does not exist" && exit 1
+
+echo ">> Check if output is empty"
+[ ! -s "fusions.tsv" ] && echo "Output file fusions.tsv is empty" && exit 1
+[ ! -s "fusions_discarded.tsv" ] && echo "Output file fusions_discarded.tsv is empty" && exit 1
+```
+
+### Step 12: Create a `/var/software_versions.txt` file
+
+For the sake of transparency and reproducibility, we require that the versions of the software used in the component are documented.
+
+For now, this is managed by creating a file `/var/software_versions.txt` in the `setup` section of the Docker engine.
+
+```yaml
+engines:
+  - type: docker
+    image: quay.io/biocontainers/xxx:0.1.0--py_0
+    setup:
+      - type: docker
+        run: |
+          echo "xxx: \"0.1.0\"" > /var/software_versions.txt
+```

LICENSE

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+MIT License
+
+Copyright (c) 2024 Data Intuitive
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

README.md

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+
+
+# 🪡📦 craftbox
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-craftbox-7a4baa.svg)](https://www.viash-hub.com/packages/craftbox)
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fcraftbox-blue.svg)](https://github.com/viash-hub/craftbox)
+[![GitHub
+License](https://img.shields.io/github/license/viash-hub/craftbox.svg)](https://github.com/viash-hub/craftbox/blob/main/LICENSE)
+[![GitHub
+Issues](https://img.shields.io/github/issues/viash-hub/craftbox.svg)](https://github.com/viash-hub/craftbox/issues)
+[![Viash
+version](https://img.shields.io/badge/Viash-v0.9.4-blue.svg)](https://viash.io)
+
+A collection of custom-tailored scripts and applied utilities built with
+Viash.
+
+## Introduction
+
+`craftbox` is a curated collection of custom scripts and utilities
+designed to tackle context-specific tasks.
+
+Emphasizing the Viash principles, `craftbox` components aim for
+**reusability**, **reproducibility**, and adherence to **best
+practices**. Key features generally include:
+
+- **Standalone & Nextflow Ready:** Components are built to run directly
+  via the command line or be smoothly integrated into Nextflow
+  workflows.
+- **Custom Implementations:** Contains scripts and tools developed for
+  particular tasks that may not be found in broader collections.
+- **High Quality Standards (promoted by Viash):**
+  - Clear documentation for components and their parameters.
+  - Full exposure of underlying script/tool arguments for fine-grained
+    control.
+  - Containerized (Docker) to ensure dependency management and a
+    consistent, reproducible runtime environment.
+  - Unit tested where applicable to ensure components function as
+    expected.
+
+## Example Usage
+
+Viash components in craftbox can be run in various ways:
+
+``` mermaid lang="mermaid
+flowchart TD
+    A[craftbox v0.2.0] --> B(Viash Hub Launch)
+    A --> C(Viash CLI)
+    A --> D(Nextflow CLI)
+    A --> E(Seqera Cloud)
+    A --> F(As a dependency)
+```
+
+### 1. Via the Viash Hub Launch interface
+
+You can run this component directly from the Viash Hub [Launch
+interface](https://www.viash-hub.com/launch?package=craftbox&version=v0.2.0&component=concat_rtext&runner=Executable).
+
+![](docs/viash-hub.png)
+
+### 2. Via the Viash CLI
+
+You can run this component directly from the command line using the
+Viash CLI.
+
+``` bash
+viash run vsh://craftbox@v0.2.0/concat_rtext -- --help
+
+viash run vsh://craftbox@v0.2.0/concat_rtext -- \
+  --input path/to/input.txt \
+  --input path/to/compressed.txt.gz \
+  --output path/to/output.txt
+```
+
+This will run the component with the specified input files and output
+the results to the specified output file.
+
+### 3. Via the Nextflow CLI or Seqera Cloud
+
+You can run this component as a Nextflow pipeline.
+
+``` bash
+nextflow run https://packages.viash-hub.com/vsh/craftbox \
+  -revision v0.2.0 \
+  -main-script target/nextflow/concat_rtext/main.nf \
+  -latest -resume \
+  -profile docker \
+  --input "path/to/input.txt;path/to/compressed.txt.gz" \
+  --output path/to/output.txt
+```
+
+**Note:** Make sure that the [Nextflow
+SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) is
+set up properly. You can do this by adding the following lines to your
+`~/.nextflow/scm` file:
+
+``` groovy
+providers.vsh.platform = 'gitlab'
+providers.vsh.server = 'https://packages.viash-hub.com'
+```
+
+**Tip:** This will also work with Seqera Cloud or other
+Nextflow-compatible platforms.
+
+### 4. As a dependency
+
+In your Viash config file (`config.vsh.yaml`), you can add this
+component as a dependency:
+
+``` yaml
+dependencies:
+  - name: concat_rtext
+    repository: vsh://craftbox@v0.2.0
+```
+
+**Tip:** See the [Viash
+documentation](https://viash.io/guide/nextflow_vdsl3/create-a-pipeline.html#pipeline-as-a-component)
+for more details on how to use Viash components as a dependency in your
+own Nextflow workflows.
+
+## Contributing
+
+Contributions are welcome! We aim to build a comprehensive collection of
+high-quality bioinformatics components. If you’d like to contribute,
+please follow these general steps:
+
+1.  Find a component to contribute
+2.  Add config template
+3.  Fill in the metadata
+4.  Find a suitable container
+5.  Create help file
+6.  Create or fetch test data
+7.  Add arguments for the input files
+8.  Add arguments for the output files
+9.  Add arguments for the other arguments
+10. Add a Docker engine
+11. Write a runner script
+12. Create test script
+13. Create a `/var/software_versions.txt` file
+
+See the
+[CONTRIBUTING](https://github.com/viash-hub/craftbox/blob/main/CONTRIBUTING.md)
+file for more details.

README.qmd

@@ -0,0 +1,120 @@
+---
+format: gfm
+---
+```{r setup, include=FALSE}
+package <- yaml::read_yaml("_viash.yaml")
+license <- paste0(package$links$repository, "/blob/main/LICENSE")
+contributing <- paste0(package$links$repository, "/blob/main/CONTRIBUTING.md")
+
+pkg <- package$name
+ver <- if (!is.null(package$version)) package$version else "v0.2.0"
+comp <- "concat_rtext"
+```
+# 🪡📦 `r pkg`
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-`r pkg`-7a4baa.svg)](https://www.viash-hub.com/packages/`r pkg`) 
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r pkg`-blue.svg)](`r package$links$repository`) 
+[![GitHub License](https://img.shields.io/github/license/viash-hub/`r pkg`.svg)](`r license`) 
+[![GitHub Issues](https://img.shields.io/github/issues/viash-hub/`r pkg`.svg)](`r package$links$issue_tracker`) 
+[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", package$viash_version)`-blue.svg)](https://viash.io)
+
+`r package$summary`
+
+## Introduction
+
+`r package$description`
+
+## Example Usage
+
+Viash components in `r pkg` can be run in various ways:
+
+```{r mmd, echo=FALSE, results='asis'}
+cat(
+  "```mermaid\n",
+  "flowchart TD\n",
+  "    A[", pkg, " ", ver, "] --> B(Viash Hub Launch)\n",
+  "    A --> C(Viash CLI)\n",
+  "    A --> D(Nextflow CLI)\n",
+  "    A --> E(Seqera Cloud)\n",
+  "    A --> F(As a dependency)\n",
+  "```\n",
+  sep = ""
+)
+```
+
+### 1. Via the Viash Hub Launch interface
+
+You can run this component directly from the Viash Hub [Launch interface](https://www.viash-hub.com/launch?package=`r pkg`&version=`r ver`&component=`r comp`&runner=Executable).
+
+![](docs/viash-hub.png)
+
+### 2. Via the Viash CLI
+
+You can run this component directly from the command line using the Viash CLI.
+
+```bash
+viash run vsh://`r pkg`@`r ver`/`r comp` -- --help
+
+viash run vsh://`r pkg`@`r ver`/`r comp` -- \
+  --input path/to/input.txt \
+  --input path/to/compressed.txt.gz \
+  --output path/to/output.txt
+```
+
+This will run the component with the specified input files and output the results to the specified output file.
+
+### 3. Via the Nextflow CLI or Seqera Cloud
+
+You can run this component as a Nextflow pipeline.
+
+```bash
+nextflow run https://packages.viash-hub.com/vsh/`r pkg` \
+  -revision `r ver` \
+  -main-script target/nextflow/`r comp`/main.nf \
+  -latest -resume \
+  -profile docker \
+  --input "path/to/input.txt;path/to/compressed.txt.gz" \
+  --output path/to/output.txt
+```
+
+**Note:** Make sure that the [Nextflow SCM](https://www.nextflow.io/docs/latest/git.html#git-configuration) is set up properly. You can do this by adding the following lines to your `~/.nextflow/scm` file:
+
+```groovy
+providers.vsh.platform = 'gitlab'
+providers.vsh.server = 'https://packages.viash-hub.com'
+```
+
+**Tip:** This will also work with Seqera Cloud or other Nextflow-compatible platforms.
+
+### 4. As a dependency
+
+In your Viash config file (`config.vsh.yaml`), you can add this component as a dependency:
+
+```yaml
+dependencies:
+  - name: `r comp`
+    repository: vsh://`r pkg`@`r ver`
+```
+
+**Tip:** See the [Viash documentation](https://viash.io/guide/nextflow_vdsl3/create-a-pipeline.html#pipeline-as-a-component) for more details on how to use Viash components as a dependency in your own Nextflow workflows.
+
+## Contributing
+
+Contributions are welcome! We aim to build a comprehensive collection of high-quality bioinformatics components. If you'd like to contribute, please follow these general steps:
+
+
+```{r echo=FALSE}
+lines <- readr::read_lines("CONTRIBUTING.md")
+
+index_start <- grep("^### Step [0-9]*:", lines)
+
+index_end <- c(index_start[-1] - 1, length(lines))
+
+name <- gsub("^### Step [0-9]*: *", "", lines[index_start])
+
+knitr::asis_output(
+  paste(paste0(" 1. ", name, "\n"), collapse = "")
+)
+```
+
+See the [CONTRIBUTING](`r contributing`) file for more details.

_viash.yaml

@@ -0,0 +1,26 @@
+name: craftbox
+version: v0.3.0
+summary: |
+  A collection of custom-tailored scripts and applied utilities built with Viash.
+description: |
+  `craftbox` is a curated collection of custom scripts and utilities designed to tackle context-specific tasks.
+
+  Emphasizing the Viash principles, `craftbox` components aim for **reusability**, **reproducibility**, and adherence to **best practices**. Key features generally include:
+
+  * **Standalone & Nextflow Ready:** Components are built to run directly via the command line or be smoothly integrated into Nextflow workflows.
+  * **Custom Implementations:** Contains scripts and tools developed for particular tasks that may not be found in broader collections.
+  * **High Quality Standards (promoted by Viash):**
+      * Clear documentation for components and their parameters.
+      * Full exposure of underlying script/tool arguments for fine-grained control.
+      * Containerized (Docker) to ensure dependency management and a consistent, reproducible runtime environment.
+      * Unit tested where applicable to ensure components function as expected.
+keywords: [scripts, custom, implementations, utilities]
+license: MIT
+links:
+  issue_tracker: https://github.com/viash-hub/craftbox/issues
+  repository: https://github.com/viash-hub/craftbox
+
+viash_version: 0.9.4
+
+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 = "craftbox"
+  version = "v0.3.0"
+  defaultBranch = "main"
+  nextflowVersion = "!>=20.12.1-edge"
+}

src/_authors/dorien_roosen.yaml

@@ -0,0 +1,10 @@
+name: Dorien Roosen
+info:
+  links:
+    email: dorien@data-intuitive.com
+    github: dorien-er
+    linkedin: dorien-roosen
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Data Scientist

src/_authors/dries_schaumont.yaml

@@ -0,0 +1,11 @@
+name: Dries Schaumont
+info:
+  links:
+    email: dries@data-intuitive.com
+    github: DriesSchaumont
+    orcid: "0000-0002-4389-0440"
+    linkedin: dries-schaumont
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Data Scientist

src/_authors/robrecht_cannoodt.yaml

@@ -0,0 +1,14 @@
+name: Robrecht Cannoodt
+info:
+  links:
+    email: robrecht@data-intuitive.com
+    github: rcannood
+    orcid: "0000-0003-3641-729X"
+    linkedin: robrechtcannoodt
+  organizations:
+    - name: Data Intuitive
+      href: https://www.data-intuitive.com
+      role: Data Science Engineer
+    - name: Open Problems
+      href: https://openproblems.bio
+      role: Core Member

src/_authors/toni_verbeiren.yaml

@@ -0,0 +1,9 @@
+name: Toni Verbeiren
+info:
+  links:
+    github: tverbeiren
+    linkedin: verbeiren
+  organizations:
+  - name: Data Intuitive
+    href: https://www.data-intuitive.com
+    role: Data Scientist and CEO

src/check_disk_space/config.vsh.yaml

@@ -0,0 +1,56 @@
+name: check_disk_space
+description: |
+  Check for available disk space on the system.
+
+  This component is only useful when working with persistent storage environments
+  where all workflow steps execute on the same instance or share the same
+  storage volume. That is, running thus component on e.g. AWS Batch or
+  other cloud-based systems will not work as expected, since each step
+  can run on a different instance and resources will not be shared.
+  
+  For distributed environments, consider integrating resource checks directly
+  into the components that will actually consume the storage, rather than
+  using this standalone check.
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --tmp_space_required
+        type: integer
+        description: Temporary space required in MB.
+        required: false
+        default: 1000
+      - name: --publish_space_required
+        type: integer
+        description: Publish space required in MB.
+        required: false
+        default: 500
+      - name: --publish_dir
+        type: file
+        description: Directory where workflow outputs will be published.
+        required: false
+
+  - name: Outputs
+    arguments:
+      - name: --output
+        type: file
+        direction: output
+        description: Output file containing system resources details.
+        required: false
+        default: output.txt
+
+resources:
+  - type: bash_script
+    path: script.sh
+
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: bash:latest
+
+runners:
+  - type: executable
+  - type: nextflow

src/check_disk_space/script.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+
+# Check temporary directory space
+tmp_avail_kb=$(df -k "$meta_temp_dir" | awk 'NR==2 {print $4}')
+tmp_avail_mb=$((tmp_avail_kb / 1024))
+echo -e "\nTemporary directory ($meta_temp_dir) available space: ${tmp_avail_mb}MB" >> "$par_output"
+
+if [ "$tmp_avail_mb" -lt "$par_tmp_space_required" ]; then
+    echo "WARNING: Available temporary space (${tmp_avail_mb}MB) is less than required (${par_tmp_space_required}MB)" | tee -a "$par_output"
+fi
+
+# Check publish directory space if specified
+publish_avail_kb=$(df -k "$par_publish_dir" | awk 'NR==2 {print $4}')
+publish_avail_mb=$((publish_avail_kb / 1024))
+echo -e "\nPublish directory ($par_publish_dir) available space: ${publish_avail_mb}MB" >> "$par_output"
+
+if [ "$publish_avail_mb" -lt "$par_publish_space_required" ]; then
+    echo "WARNING: Available publish space (${publish_avail_mb}MB) is less than required (${par_publish_space_required}MB)" | tee -a "$par_output"
+fi

src/check_disk_space/test.sh

@@ -0,0 +1,92 @@
+#!/bin/bash
+
+set -eo pipefail
+
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
+function clean_up {
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
+
+# Create test directories
+mkdir -p "$TMPDIR/publish"
+
+echo "Test 1: Both directories have enough space"
+# Define normal space df function
+df() {
+  echo "Filesystem     1K-blocks    Used Available Use% Mounted on"
+  echo "ext4             20485760 5000000  15485760  25% $2"
+}
+# Export the function
+export -f df
+# Run the component
+"$meta_executable" \
+  --publish_dir "$TMPDIR/publish" \
+  --tmp_space_required "500" \
+  --publish_space_required "300" \
+  --output "$TMPDIR/output1.txt"
+
+# Verify Test 1 - should have no warnings
+if grep -q "WARNING:" "$TMPDIR/output1.txt"; then
+    echo "FAIL: Unexpected warning in normal space test"
+else
+    echo "PASS: No warnings with sufficient space"
+fi
+
+echo "Test 2: Temporary directory doesn't have enough space"
+# Define low temp space df function
+df() {
+  if [[ "$2" == "$meta_temp_dir" ]]; then
+    echo "Filesystem     1K-blocks    Used Available Use% Mounted on"
+    echo "tmpfs            10485760 5000000   921600  50% $2"
+  else
+    echo "Filesystem     1K-blocks    Used Available Use% Mounted on"
+    echo "ext4             20485760 5000000  15485760  25% $2"
+  fi
+}
+# Export the function
+export -f df
+# Run the component
+"$meta_executable" \
+  --publish_dir "$TMPDIR/publish" \
+  --tmp_space_required "1000" \
+  --publish_space_required "300" \
+  --output "$TMPDIR/output2.txt"
+
+# Verify Test 2
+if grep -q "WARNING: Available temporary space" "$TMPDIR/output2.txt"; then
+    echo "PASS: Low temp space warning detected"
+else
+    echo "FAIL: No warning detected for low temp space"
+fi
+
+echo "Test 3: Publish directory doesn't have enough space"
+# Define low publish space df function
+df() {
+  if [[ "$2" =~ /publish ]]; then
+    echo "Filesystem     1K-blocks    Used Available Use% Mounted on"
+    echo "ext4             20485760 16384000   409600  80% $2"
+  else
+    echo "Filesystem     1K-blocks    Used Available Use% Mounted on"
+    echo "ext4             20485760 5000000  15485760  25% $2"
+  fi
+}
+# Export the function
+export -f df
+# Run the component
+"$meta_executable" \
+  --publish_dir "$TMPDIR/publish" \
+  --tmp_space_required "500" \
+  --publish_space_required "500" \
+  --output "$TMPDIR/output3.txt"
+
+# Verify Test 3
+if grep -q "WARNING: Available publish space" "$TMPDIR/output3.txt"; then
+    echo "PASS: Low publish space warning detected"
+else
+    echo "FAIL: No warning detected for low publish space"
+fi
+
+echo "All tests completed"
+
+exit 0

src/concat_text/config.vsh.yaml

@@ -0,0 +1,60 @@
+name: concat_text
+summary: Concatenate a number of text files
+description: |
+  Concatenate a number of text files, handle gzipped text files gracefully and
+  optionally gzip the output text file.
+
+  This component is useful for concatening fastq files from different lanes, for instance.
+
+authors:
+  - __merge__: /src/_authors/toni_verbeiren.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/dries_schaumont.yaml
+    roles: [ reviewer ]
+
+info:
+  improvements: |
+    This component could be improved in 2 ways:
+      1. Allow for a mix of zipped and plain input files
+      2. Allow to specify a compression algorithm for the output
+
+argument_groups:
+  - name: Input arguments
+    arguments:
+      - name: --input
+        description: A list of (gzipped) text files.
+        type: file
+        multiple: true
+        required: true
+        example: input?.txt.gz
+  - name: Output arguments
+    arguments:
+      - name: "--gzip_output"
+        type: boolean_true
+        description: Should the output be zipped?
+      - name: --output
+        description: File to write the output to, optionally gzipped.
+        type: file
+        direction: output
+        example: output.txt
+
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+  - type: docker
+    image: alpine:latest
+    setup:
+      - type: apk
+        packages:
+          - bash
+          - procps
+          - file
+
+runners:
+  - type: executable
+  - type: nextflow

src/concat_text/script.sh

@@ -0,0 +1,34 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+TMPDIR=$(mktemp -d "$meta_temp_dir/concat_text-XXXXXX")
+function clean_up {
+  [[ -d "$TMPDIR" ]] && rm -r "$TMPDIR"
+}
+trap clean_up EXIT
+
+par_input="$(echo "$par_input" | tr ';' ' ')"
+
+echo -n ">> Check if input is gzipped... "
+set +eo pipefail
+file $par_input | grep -q 'gzip'
+is_zipped="$?"
+set -euo pipefail
+[[ "$is_zipped" == "0" ]] && echo "yes" || echo "no"
+
+if [[ "$is_zipped" == "0" ]]; then
+  echo ">> zcat gzipped files"
+  zcat $par_input > $TMPDIR/contents
+else
+  echo ">> cat plain files"
+  cat $par_input > $TMPDIR/contents
+fi
+
+if [ "$par_gzip_output" == true ]; then
+  echo ">> Zip output file"
+  gzip $TMPDIR/contents
+  mv $TMPDIR/contents.gz $par_output
+else
+  mv $TMPDIR/contents $par_output
+fi

src/concat_text/test.sh

@@ -0,0 +1,70 @@
+#!/usr/bin/env bash
+
+set -euo pipefail
+
+echo ">> Creating test input files file[1-3].txt"
+INPUT_FILE_1="file1.txt"
+INPUT_FILE_2="file2.txt"
+INPUT_FILE_3="file3.txt"
+echo "one" > "$INPUT_FILE_1"
+echo "two" > "$INPUT_FILE_2"
+echo "three" > "$INPUT_FILE_3"
+echo ">> Created input files"
+
+echo ">> Creating zipped versions at file[1-3].txt.gz"
+gzip -k $INPUT_FILE_1
+gzip -k $INPUT_FILE_2
+gzip -k $INPUT_FILE_3
+
+echo ">> Creating expected output file expected_output.txt and zipped version"
+cat > "expected_output.txt" <<EOF
+one
+two
+three
+EOF
+
+gzip -k "expected_output.txt"
+
+echo ">> Run component on 3 plain input files, plain output"
+$meta_executable \
+  --input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
+  --output "output1.txt"
+
+[[ ! -f "output1.txt" ]] \
+  && echo "Output file output1.txt not found!" && exit 1
+[[ $(cmp "output1.txt" "expected_output.txt") ]] \
+  && echo "Output file output1.txt is not as expected!" && exit 1
+
+echo ">> Run component on 3 zipped input files, plain output"
+$meta_executable \
+  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
+  --output "output2.txt"
+
+[[ ! -f "output2.txt" ]] \
+  && echo "Output file output2.txt not found!" && exit 1
+[[ $(cmp "output2.txt" "expected_output.txt") ]] \
+  && echo "Output file output2.txt is not as expected!" && exit 1
+
+echo ">> Run component on 3 plain input files, zipped output"
+$meta_executable \
+  --input "$INPUT_FILE_1;$INPUT_FILE_2;$INPUT_FILE_3" \
+  --output "output3.txt.gz" \
+  --gzip_output
+
+[[ ! -f "output3.txt.gz" ]] \
+  && echo "Output file output3.txt.gz not found!" && exit 1
+[[ $(cmp "output3.txt.gz" "expected_output.txt.gz") ]] \
+  && echo "Output file output3.txt.gz is not as expected!" && exit 1
+
+echo ">> Run component on 3 zipped input files, zipped output"
+$meta_executable \
+  --input "$INPUT_FILE_1.gz;$INPUT_FILE_2.gz;$INPUT_FILE_3.gz" \
+  --output "output4.txt.gz" \
+  --gzip_output
+
+[[ ! -f "output4.txt.gz" ]] \
+  && echo "Output file output4.txt.gz not found!" && exit 1
+[[ $(cmp "output4.txt.gz" "expected_output.txt.gz") ]] \
+  && echo "Output file output4.txt.gz is not as expected!" && exit 1
+
+echo ">> Tests done"

src/csv2fasta/config.vsh.yaml

@@ -0,0 +1,110 @@
+name: csv2fasta
+summary: Convert a CSV file to FASTA entries
+description: |
+  Convert two columns from a CSV file to FASTA entries. The CSV file can
+  contain an optional header and each row (other than the header) becomes
+  a single FASTA record. One of the two columns will be used as the names
+  for the FASTA entries, while the other become the sequences. The sequences
+  column must only contain characters that are valid IUPAC notation for 
+  nucleotides or a group thereof (wildcard characters).
+
+authors:
+  - __merge__: /src/_authors/dries_schaumont.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ reviewer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: --input
+      type: file
+      direction: input
+      example: barcodes.csv
+      description: CSV file to be processed.
+      required: true
+    - name: --header
+      type: boolean_true
+      description: |
+        Parse the first line of the CSV file as a header.
+  - name: "CSV dialect options"
+    description: |
+      Options that can be used to override the automatically detected
+      dialect of the CSV file.
+    arguments:
+      - name: --delimiter
+        type: string
+        description: |
+          Overwrite the column delimiter character.
+      - name: --quote_character
+        type: string
+        description: |
+          Overwrite the character used to denote the start and end of a quoted item.
+  - name: "CSV column arguments"
+    description: |
+      Parameters for the selection of columns from the CSV file.
+      Only required when your CSV file contains more than 2 columns,
+      otherwise the first column will be used for the FASTA header
+      and the second for the FASTA nucleotide sequences. This default
+      can still be overwritten by using the options below.
+    arguments:
+      - name: --sequence_column
+        type: string
+        description: |
+          Name of the column containing the sequences. Implies 'header'.
+          Cannot be used together with 'sequence_column_index'.
+        required: false
+      - name: "--name_column"
+        type: string
+        description: |
+          Name of the column describing the FASTA headers. Implies 'header'.
+          Cannot be used together with 'name_column_index'.
+        required: false
+      - name: "--sequence_column_index"
+        type: integer
+        min: 0
+        description: | 
+          Index of the column to use as the FASTA sequences, counter from the left and
+          starting from 0. Cannot be used in combination with the 'sequence_column' argument.
+        required: false
+      - name: "--name_column_index"
+        type: integer
+        min: 0
+        description: | 
+          Index of the column to use as the FASTA headers, counter from the left and
+          starting from 0. Cannot be used in combination with 'name_column'.
+        required: false 
+  - name: Outputs
+    arguments:
+      - name: "--output"
+        type: file
+        example: barcodes.fasta
+        direction: output
+        description: Output fasta file.
+
+resources:
+  - type: python_script
+    path: script.py
+test_resources:
+  - type: python_script
+    path: test_csv2fasta.py
+
+engines:
+  - type: docker
+    image: python:slim
+    setup:
+      - type: apt
+        packages:
+          - procps
+      - type: python
+        packages: 
+          - dnaio
+    test_setup:
+      - type: python
+        packages:
+          - pytest
+          - viashpy
+
+runners:
+  - type: executable
+  - type: nextflow

src/csv2fasta/script.py

@@ -0,0 +1,102 @@
+from pathlib import Path
+import dnaio
+import csv
+
+## VIASH START
+par = {
+
+}
+## VIASH END
+
+iupac = frozenset("ABCDGHKMNRSTUVWXY")
+
+def resolve_header_name_to_index(header_entries, column_name):
+    try:
+        return header_entries.index(column_name)
+    except ValueError as e:
+        raise ValueError(f"Column name '{column_name}' could not "
+                         "be found in the header of the CSV file.") from e
+
+
+def csv_records(csv_file, delimiter, quote_character, 
+                header, sequence_column, name_column,
+                sequence_column_index, name_column_index):
+    with open(csv_file, newline='') as csvfile:
+        # Deduce CSV dialect based on first 5 lines.
+        hint = "\n".join([csvfile.readline() for _ in range(5)])
+        csvfile.seek(0)
+        dialect = csv.Sniffer().sniff(hint)
+        reader_args = {"dialect": dialect}
+        delimiter_arg = {"delimiter": delimiter} if delimiter else {}
+        quotechar_arg = {"quotechar": quote_character} if delimiter else {}
+        all_args = reader_args | delimiter_arg | quotechar_arg
+        csv_reader = csv.reader(csvfile, **all_args)
+        for linenum, line in enumerate(csv_reader):
+            if not linenum: # First row
+                num_columns = len(line)
+                if header:
+                    if sequence_column:
+                        sequence_column_index = resolve_header_name_to_index(line, sequence_column)
+                    if name_column:
+                        name_column_index = resolve_header_name_to_index(line, name_column)
+                    continue
+            if not (linenum - header): # First 'data' line
+                if (not sequence_column_index and not name_column_index and len(line) == 2):
+                    name_column_index, sequence_column_index = 0, 1
+                if sequence_column_index == name_column_index:
+                    raise ValueError("The same columns were selected for both the FASTQ sequences and "
+                                     "headers.")
+                if sequence_column_index is None:
+                    raise ValueError("Either 'sequence_column_index' or 'sequence_column' needs "
+                                     "to be specified.")
+                if name_column_index is None:
+                    raise ValueError("Either 'name_column' or 'name_column_index' needs to "
+                                     "be specified.")
+                if name_column_index >= num_columns:
+                    raise ValueError(f"Requested to use column number {name_column_index} "
+                                     f"(0 based) for the FASTA headers, but only {num_columns} "
+                                     "were found on the first line.")
+                if sequence_column_index >= num_columns:
+                    raise ValueError(f"Requested to use column number {sequence_column_index} "
+                                     f"(0 based) for the FASTA sequences, but only {num_columns} "
+                                     "were found on the first line.") 
+            if len(line) != num_columns:
+                raise ValueError(f"Number of columns ({len(line)}) found on line {linenum+1} "
+                                 "is different compared to number of columns found "
+                                 f"previously ({num_columns}).")
+            sequence_name, sequence = line[name_column_index], line[sequence_column_index]
+            invalid_characters = set(sequence.upper()) - iupac 
+            if set(sequence.upper()) - iupac:
+                raise ValueError(f"The sequence ('{sequence}') found on line {linenum+1} "
+                                 f"contains characters ({','.join(invalid_characters)}) "
+                                 "which are not valid IUPAC identifiers for nucleotides.")
+            yield sequence_name, sequence
+                
+
+def main(par):
+    par['input'], par['output'] = Path(par['input']), Path(par['output'])
+    sequence_column, name_column = par['sequence_column'], par['name_column'] 
+    sequence_column_index, name_column_index = par['sequence_column_index'], par['name_column_index']
+    if (sequence_column or name_column) and not par['header']:
+        par["header"] = True
+    if sequence_column_index and sequence_column:
+        raise ValueError("Cannot specify both 'sequence_column_index' and 'sequence_column'")
+    if name_column and name_column_index:
+        raise ValueError("Cannot specify both 'name_column_index' and 'name_column'")
+    if (sequence_column_index or name_column_index) and \
+        (sequence_column_index == name_column_index):
+        raise ValueError("The value specified for 'sequence_column_index' cannot be the same as "
+                         "the value for 'name_column_index'.")
+    with dnaio.open(par['output'], mode='w', fileformat="fasta") as writer:
+        for header, sequence in csv_records(par['input'],
+                                            par['delimiter'],
+                                            par['quote_character'],
+                                            par['header'],
+                                            sequence_column,
+                                            name_column,
+                                            sequence_column_index,
+                                            name_column_index):
+            writer.write(dnaio.SequenceRecord(header, sequence))
+    
+if __name__ == "__main__":
+    main(par)

src/csv2fasta/test_csv2fasta.py

@@ -0,0 +1,366 @@
+import pytest
+import re
+import sys
+from uuid import uuid4
+from textwrap import dedent
+from subprocess import CalledProcessError
+
+## VIASH START
+meta = {
+    'config': 'src/sequenceformats/csv2fasta/config.vsh.yaml',
+    'executable': 'target/executable/sequenceformats/csv2fasta'
+}
+## VIASH END
+
+@pytest.fixture
+def random_path(tmp_path):
+    def wrapper(extension=None):
+        extension = "" if not extension else f".{extension}"
+        return tmp_path / f"{uuid4()}{extension}"
+    return wrapper 
+
+@pytest.mark.parametrize("arg,val,expected_err", [("name_column", "barcode_name",
+                                                   ("sequence_column_index", "sequence_column")),
+                                                  ("sequence_column", "sequence",
+                                                   ("name_column", "name_column_index"))])
+def test_csvtofasta_no_columns_selected_raises(run_component, random_path, arg, val, expected_err):
+    csv_contents = dedent("""\
+    barcode_name,some_other_column,sequence
+    barcode1,foo,ACGT
+    barcode2,bar,TTTA
+    """)
+
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    args = [
+        "--input", input_path,
+        "--output", output_path,
+        "--header"
+    ]
+    args.extend([f"--{arg}", val])
+    with pytest.raises(CalledProcessError) as err:
+        run_component(args)
+    assert f"ValueError: Either '{expected_err[0]}' or '{expected_err[1]}' needs to be specified." in \
+        err.value.stdout.decode('utf-8')
+
+def test_csvtofasta_column_does_not_exist_raises(run_component, random_path):
+    csv_contents = dedent("""\
+    barcode_name,some_other_column,sequence
+    barcode1,foo,ACGT
+    barcode2,bar,TTTA
+    """)
+
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    args = [
+        "--input", input_path,
+        "--output", output_path,
+        "--sequence_column", "foo",
+    ]
+    with pytest.raises(CalledProcessError) as err:
+        run_component(args)
+    assert "ValueError: Column name 'foo' could not be found in the " + \
+           "header of the CSV file." in err.value.stdout.decode('utf-8')
+
+def test_csvtofasta_same_column_selected_raises(run_component, random_path):
+    csv_contents = dedent("""\
+    barcode_name,some_other_column,sequence
+    barcode1,foo,ACGT
+    barcode2,bar,TTTA
+    """)
+
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    args = [
+        "--input", input_path,
+        "--output", output_path,
+        "--sequence_column_index", "1",
+        "--name_column_index", "1",
+    ]
+    with pytest.raises(CalledProcessError) as err:
+        run_component(args)
+    assert "ValueError: The value specified for 'sequence_column_index' cannot " + \
+           "be the same as the value for 'name_column_index'" in \
+            err.value.stdout.decode('utf-8')
+
+@pytest.mark.parametrize("arg,val,expected_err", [("sequence_column_index", "3", "sequences"),
+                                                  ("name_column_index", "4", "headers")])
+def test_csvtofasta_header_select_index_out_of_bounds_raises(run_component, random_path, arg, val, expected_err):
+    csv_contents = dedent("""\
+    barcode_name,some_other_column,sequence
+    barcode1,foo,ACGT
+    barcode2,bar,TTTA
+    """)
+
+    other_column_map = {
+        "sequence_column_index": ["--name_column_index", "1"],
+        "name_column_index": ["--sequence_column_index", "2"],
+    }
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    args = [
+        "--input", input_path,
+        "--output", output_path,
+        "--header",
+    ]
+    args += [f"--{arg}", val]
+    args += other_column_map[arg] 
+    with pytest.raises(CalledProcessError) as err:
+        run_component(args)
+    assert f"ValueError: Requested to use column number {val} (0 based) for the FASTA " + \
+           f"{expected_err}, but only 3 were found on the first line." in \
+        err.value.stdout.decode('utf-8')
+
+def test_csvtofasta_header_select_column_by_both_name_and_index(run_component, random_path):
+    csv_contents = dedent("""\
+    barcode_name,some_other_column,sequence
+    barcode1,foo,ACGT
+    barcode2,bar,TTTA
+    """)
+
+    expected= dedent("""\
+    >barcode1
+    ACGT
+    >barcode2
+    TTTA
+    """)
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    run_component([
+        "--input", input_path,
+        "--output", output_path,
+        "--header", 
+        "--name_column", "barcode_name",
+        "--sequence_column_index", "2",
+        ]
+    )
+    assert output_path.is_file()
+    with output_path.open('r') as open_output:
+        output_contents = open_output.read()
+    assert output_contents == expected
+
+def test_csvtofasta_autodetect_dialect(run_component, random_path):
+    csv_contents = dedent("""\
+    barcode_name\tsome_other_column\tsequence
+    barcode1\tfoo\tACGT
+    barcode2\tbar\tTTTA
+    """)
+
+    expected= dedent("""\
+    >barcode1
+    ACGT
+    >barcode2
+    TTTA
+    """)
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    run_component([
+        "--input", input_path,
+        "--output", output_path,
+        "--header", 
+        "--name_column", "barcode_name",
+        "--sequence_column_index", "2",
+        ]
+    )
+    assert output_path.is_file()
+    with output_path.open('r') as open_output:
+        output_contents = open_output.read()
+    assert output_contents == expected
+
+    csv_contents = dedent("""\
+    "barcode_name"\t"some_other_column"\t"sequence"
+    "barcode1"\t"foo"\t"ACGT"
+    "barcode2"\t"bar"\t"TTTA"
+    """)
+
+    expected= dedent("""\
+    >barcode1
+    ACGT
+    >barcode2
+    TTTA
+    """)
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    run_component([
+        "--input", input_path,
+        "--output", output_path,
+        "--header", 
+        "--name_column", "barcode_name",
+        "--sequence_column_index", "2",
+        ]
+    )
+    assert output_path.is_file()
+    with output_path.open('r') as open_output:
+        output_contents = open_output.read()
+    assert output_contents == expected
+
+def test_csvtofasta_header_select_column_by_name(run_component, random_path):
+    csv_contents = dedent("""\
+    barcode_name,some_other_column,sequence
+    barcode1,foo,ACGT
+    barcode2,bar,TTTA
+    """)
+
+    expected= dedent("""\
+    >barcode1
+    ACGT
+    >barcode2
+    TTTA
+    """)
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    run_component([
+        "--input", input_path,
+        "--output", output_path,
+        "--header", 
+        "--name_column", "barcode_name",
+        "--sequence_column", "sequence"
+        ]
+    )
+    assert output_path.is_file()
+    with output_path.open('r') as open_output:
+        output_contents = open_output.read()
+    assert output_contents == expected
+
+def test_csvtofasta_header_2_columns(run_component, random_path):
+    csv_contents = dedent("""\
+    barcode_name,sequence
+    barcode1,ACGT
+    barcode2,TTTA
+    """)
+
+    expected= dedent("""\
+    >barcode1
+    ACGT
+    >barcode2
+    TTTA
+    """)
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    run_component([
+        "--input", input_path,
+        "--output", output_path,
+        "--header"
+        ]
+    )
+    assert output_path.is_file()
+    with output_path.open('r') as open_output:
+        output_contents = open_output.read()
+    assert output_contents == expected
+
+def test_csvtofasta_2_columns(run_component, random_path):
+    csv_contents = dedent("""\
+    barcode1,ACGT
+    barcode2,TTTA
+    """)
+
+    expected= dedent("""\
+    >barcode1
+    ACGT
+    >barcode2
+    TTTA
+    """)
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    run_component([
+        "--input", input_path,
+        "--output", output_path]
+    )
+    assert output_path.is_file()
+    with output_path.open('r') as open_output:
+        output_contents = open_output.read()
+    assert output_contents == expected
+
+def test_csvtofasta_2_columns_but_still_swap(run_component, random_path):
+    csv_contents = dedent("""\
+    ACGT,barcode1
+    TTTA,barcode2
+    """)
+
+    expected= dedent("""\
+    >barcode1
+    ACGT
+    >barcode2
+    TTTA
+    """)
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    run_component([
+        "--input", input_path,
+        "--output", output_path,
+        "--sequence_column_index", "0",
+        "--name_column_index", "1"]
+    )
+    assert output_path.is_file()
+    with output_path.open('r') as open_output:
+        output_contents = open_output.read()
+    assert output_contents == expected
+
+def test_csvtofasta_2_columns_but_not_valid_sequence(run_component, random_path):
+    csv_contents = dedent("""\
+    barcodes,sequences
+    barcode1,ACGT
+    barcode2,TTTA
+    """)
+
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    with pytest.raises(CalledProcessError) as err:
+        run_component([
+            "--input", input_path,
+            "--output", output_path]
+        )
+    assert re.search(r"ValueError: The sequence \('sequences'\) found on line "
+                     r"1 contains characters \(.+\) which are not valid "
+                     r"IUPAC identifiers for nucleotides\.", 
+                     err.value.stdout.decode('utf-8'))
+
+    csv_contents = dedent("""\
+    barcodes,sequences
+    barcode1,ACGT
+    barcode2,TTEA
+    """)
+
+    input_path = random_path("csv")
+    with input_path.open('w') as open_input:
+        open_input.write(csv_contents)
+    output_path = random_path("csv")
+    with pytest.raises(CalledProcessError) as err:
+        run_component([
+            "--input", input_path,
+            "--output", output_path,
+            "--header"]
+        )
+    assert re.search(r"ValueError: The sequence \('TTEA'\) found on line "
+                     r"3 contains characters \(E\) which are not valid "
+                     r"IUPAC identifiers for nucleotides\.", 
+                     err.value.stdout.decode('utf-8'))
+
+
+
+if __name__ == "__main__":
+    sys.exit(pytest.main([__file__]))

src/move_files_to_directory/config.vsh.yaml

@@ -0,0 +1,39 @@
+name: move_files_to_directory
+summary: Publish one or multiple files to the same directory
+description: This component copies one or multiple files to the same destination directory, creating the output directory if it doesn't exist.
+authors:
+  - __merge__: /src/_authors/dorien_roosen.yaml
+    roles: [ maintainer ]
+arguments:
+  - name: "--input"
+    type: file
+    direction: input
+    required: true
+    multiple: true
+    description: Paths of the files that will be copied into the output directory.
+  - name: "--output"
+    type: file
+    direction: output
+    required: true
+    description: Path to output directory
+  - name: "--keep_symbolic_links"
+    alternatives: [-d]
+    type: boolean_true
+    description: Preserve symbolic links.
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+
+engines:
+- type: docker
+  image: debian:latest
+  setup:
+      - type: apt
+        packages: [procps]
+
+runners:
+- type: executable
+- type: nextflow

src/move_files_to_directory/script.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+set -eo pipefail
+
+## VIASH START
+par_input="input.txt;input_2.txt"
+par_output="output"
+## VIASH END
+
+
+if [[ ! -d "$par_output" ]]; then
+  mkdir -p "$par_output"
+fi
+
+extra_params=( )
+
+if [ "$par_keep_symbolic_links" == "true" ]; then
+  extra_params+=( "-d" )
+fi
+
+# Process multiple input files
+IFS=";" read -ra input_files <<< "$par_input"
+for file in "${input_files[@]}"; do
+  # Check if the file exists before copying
+  if [[ -f "$file" ]]; then
+
+    cp ${extra_params[@]} "$file" "$par_output/"
+    echo "Copied $file to $par_output/"
+  else
+    echo "Warning: Input file $file does not exist, skipping"
+  fi
+done

src/move_files_to_directory/test.sh

@@ -0,0 +1,31 @@
+#!/usr/bin/env bash
+set -ex
+
+# create temporary directory and clean up on exit
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
+function clean_up {
+ [[ -d "$TMPDIR" ]] && rm -rf "$TMPDIR"
+}
+trap clean_up EXIT
+
+touch "$TMPDIR/test_file.txt"
+touch "$TMPDIR/another_file.txt"
+
+./move_files_to_directory \
+  --input "$TMPDIR/test_file.txt" \
+  --input "$TMPDIR/another_file.txt" \
+  --output "$TMPDIR/test_output"
+
+[[ ! -d "$TMPDIR/test_output" ]] && echo "It seems no output directory is generated" && exit 1
+[[ ! -f "$TMPDIR/test_output/test_file.txt" ]] && [[ ! -f test_output/another_file.txt ]] && echo "Output files were not copied to the output directory" && exit 1
+
+ln -s "$TMPDIR/test_file.txt" "$TMPDIR/symlink.txt"
+
+./move_files_to_directory \
+  --input "$TMPDIR/symlink.txt" \
+  --output "$TMPDIR/test_output_symlink" \
+  --keep_symbolic_links
+[[ ! -d "$TMPDIR/test_output_symlink" ]] && echo "It seems no output directory (test_output_symlink) is generated" && exit 1
+[[ ! -h "$TMPDIR/test_output_symlink/symlink.txt" ]] && echo "Symbolic links were not properly copied." && exit 1
+
+echo ">> Test succeeded!"

src/sync_resources/config.vsh.yaml

@@ -0,0 +1,63 @@
+name: sync_resources
+summary: Sync a Viash package's test resources to the local filesystem
+description: |
+  Sync a Viash package's test resources to the local filesystem based on the
+  the `.info.test_resources` field in the `_viash.yaml` file. This is useful for
+  testing and debugging purposes.
+usage: |
+  sync_resources
+  sync_resources --input _viash.yaml --output .
+
+authors:
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/dries_schaumont.yaml
+    roles: [ reviewer ]
+
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: "--input"
+        alternatives: ["-i"]
+        type: file
+        description: "Path to the _viash.yaml project configuration file."
+        default: _viash.yaml
+  - name: Outputs
+    arguments:
+      - name: "--output"
+        alternatives: ["-o"]
+        type: file
+        default: .
+        direction: output
+        description: "Path to the directory where the resources will be synced to."
+  - name: Arguments
+    arguments:
+      - name: "--dryrun"
+        type: boolean_true
+        description: "Does not display the operations performed from the specified command."
+      - name: "--exclude"
+        type: "string"
+        multiple: true
+        description: Exclude all files or objects from the command that matches the specified pattern.
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+engines:
+  - type: docker
+    image: alpine:3
+    setup:
+      - type: apk
+        packages:
+          - bash
+          - rclone
+          - yq
+      - type: docker
+        run:
+          - rclone config create s3 s3 anonymous=true
+          - rclone config create gs gcs anonymous=true
+runners:
+  - type: executable
+  - type: nextflow

src/sync_resources/script.sh

@@ -0,0 +1,32 @@
+#!/bin/bash
+
+## VIASH START
+par_input='_viash.yaml'
+par_output='.'
+## VIASH END
+
+extra_params=( )
+
+if [ "$par_dryrun" == "true" ]; then
+  extra_params+=( "--dry-run" )
+fi
+
+if [ ! -z ${par_exclude+x} ]; then
+  IFS=";"
+  for var in $par_exclude; do
+    unset IFS
+    extra_params+=( "--exclude" "$var" )
+  done
+fi
+
+yq e \
+  '.info.test_resources[] | "{type: " + (.type // "s3") + ", path: " + .path + ", dest: " + .dest + "}"' \
+  "${par_input}" | \
+  while read -r line; do
+    path=$(echo "$line" | yq e '.path')
+    dest=$(echo "$line" | yq e '.dest')
+
+    echo "Syncing '$path' to '$dest'..."
+
+    rclone sync "$path" "$par_output/$dest"
+  done

src/sync_resources/test.sh

@@ -0,0 +1,23 @@
+#!/bin/bash
+
+## VIASH START
+## VIASH END
+
+cat > _viash.yaml << EOM
+info:
+  test_resources:
+    - type: s3
+      path: s3://openproblems-data/resources_test/common/pancreas
+      dest: foo
+EOM
+
+echo ">> Run aws s3 sync"
+"$meta_executable" \
+  --input _viash.yaml \
+  --output . \
+  --quiet
+
+echo ">> Check whether the right files were copied"
+[ ! -f foo/dataset.h5ad ] && echo test file should have been copied && exit 1
+
+echo ">> Test succeeded!"

src/untar/config.vsh.yaml

@@ -0,0 +1,51 @@
+name: untar
+summary: Unpack a .tar file
+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.
+
+authors:
+  - __merge__: /src/_authors/dries_schaumont.yaml
+    roles: [ author, maintainer ]
+  - __merge__: /src/_authors/robrecht_cannoodt.yaml
+    roles: [ reviewer ]
+
+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/untar/script.sh

@@ -0,0 +1,41 @@
+#!/usr/bin/env bash
+
+set -eo pipefail
+
+extra_args=()
+
+TMPDIR=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXX")
+function clean_up {
+  [[ -d "$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/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/$meta_name-XXXXXX")
+function clean_up {
+  [[ -d "$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'".
+$meta_executable \
+   --input "$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'".
+$meta_executable \
+   --input "$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_executable \
+   --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_executable \
+   --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_executable \
+   --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_executable \
+   --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/executable/check_disk_space/.config.vsh.yaml

@@ -0,0 +1,198 @@
+name: "check_disk_space"
+version: "v0.3.0"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "integer"
+    name: "--tmp_space_required"
+    description: "Temporary space required in MB."
+    info: null
+    default:
+    - 1000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--publish_space_required"
+    description: "Publish space required in MB."
+    info: null
+    default:
+    - 500
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--publish_dir"
+    description: "Directory where workflow outputs will be published."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output file containing system resources details."
+    info: null
+    default:
+    - "output.txt"
+    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: "Check for available disk space on the system.\n\nThis component is only\
+  \ useful when working with persistent storage environments\nwhere all workflow steps\
+  \ execute on the same instance or share the same\nstorage volume. That is, running\
+  \ thus component on e.g. AWS Batch or\nother cloud-based systems will not work as\
+  \ expected, since each step\ncan run on a different instance and resources will\
+  \ not be shared.\n\nFor distributed environments, consider integrating resource\
+  \ checks directly\ninto the components that will actually consume the storage, rather\
+  \ than\nusing this standalone check.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "bash:latest"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/check_disk_space/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/check_disk_space"
+  executable: "target/executable/check_disk_space/check_disk_space"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/executable/concat_text/.config.vsh.yaml

@@ -0,0 +1,216 @@
+name: "concat_text"
+version: "v0.3.0"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
+- name: "Dries Schaumont"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "A list of (gzipped) text files."
+    info: null
+    example:
+    - "input?.txt.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--gzip_output"
+    description: "Should the output be zipped?"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--output"
+    description: "File to write the output to, optionally gzipped."
+    info: null
+    example:
+    - "output.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+summary: "Concatenate a number of text files"
+description: "Concatenate a number of text files, handle gzipped text files gracefully\
+  \ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
+  \ fastq files from different lanes, for instance.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info:
+  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
+    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
+    \ for the output\n"
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "alpine:latest"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apk"
+    packages:
+    - "bash"
+    - "procps"
+    - "file"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/concat_text/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/concat_text"
+  executable: "target/executable/concat_text/concat_text"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/executable/csv2fasta/.config.vsh.yaml

@@ -0,0 +1,298 @@
+name: "csv2fasta"
+version: "v0.3.0"
+authors:
+- name: "Dries Schaumont"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "CSV file to be processed."
+    info: null
+    example:
+    - "barcodes.csv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--header"
+    description: "Parse the first line of the CSV file as a header.\n"
+    info: null
+    direction: "input"
+- name: "CSV dialect options"
+  description: "Options that can be used to override the automatically detected\n\
+    dialect of the CSV file.\n"
+  arguments:
+  - type: "string"
+    name: "--delimiter"
+    description: "Overwrite the column delimiter character.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quote_character"
+    description: "Overwrite the character used to denote the start and end of a quoted\
+      \ item.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "CSV column arguments"
+  description: "Parameters for the selection of columns from the CSV file.\nOnly required\
+    \ when your CSV file contains more than 2 columns,\notherwise the first column\
+    \ will be used for the FASTA header\nand the second for the FASTA nucleotide sequences.\
+    \ This default\ncan still be overwritten by using the options below.\n"
+  arguments:
+  - type: "string"
+    name: "--sequence_column"
+    description: "Name of the column containing the sequences. Implies 'header'.\n\
+      Cannot be used together with 'sequence_column_index'.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--name_column"
+    description: "Name of the column describing the FASTA headers. Implies 'header'.\n\
+      Cannot be used together with 'name_column_index'.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sequence_column_index"
+    description: "Index of the column to use as the FASTA sequences, counter from\
+      \ the left and\nstarting from 0. Cannot be used in combination with the 'sequence_column'\
+      \ argument.\n"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--name_column_index"
+    description: "Index of the column to use as the FASTA headers, counter from the\
+      \ left and\nstarting from 0. Cannot be used in combination with 'name_column'.\n"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output fasta file."
+    info: null
+    example:
+    - "barcodes.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+summary: "Convert a CSV file to FASTA entries"
+description: "Convert two columns from a CSV file to FASTA entries. The CSV file can\n\
+  contain an optional header and each row (other than the header) becomes\na single\
+  \ FASTA record. One of the two columns will be used as the names\nfor the FASTA\
+  \ entries, while the other become the sequences. The sequences\ncolumn must only\
+  \ contain characters that are valid IUPAC notation for \nnucleotides or a group\
+  \ thereof (wildcard characters).\n"
+test_resources:
+- type: "python_script"
+  path: "test_csv2fasta.py"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "python:slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "dnaio"
+    upgrade: true
+  test_setup:
+  - type: "python"
+    user: false
+    packages:
+    - "pytest"
+    - "viashpy"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/csv2fasta/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/csv2fasta"
+  executable: "target/executable/csv2fasta/csv2fasta"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/executable/move_files_to_directory/.config.vsh.yaml

@@ -0,0 +1,194 @@
+name: "move_files_to_directory"
+version: "v0.3.0"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Paths of the files that will be copied into the output directory."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output"
+    description: "Path to output directory"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--keep_symbolic_links"
+    alternatives:
+    - "-d"
+    description: "Preserve symbolic links."
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+summary: "Publish one or multiple files to the same directory"
+description: "This component copies one or multiple files to the same destination\
+  \ directory, creating the output directory if it doesn't exist."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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:latest"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/move_files_to_directory/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/move_files_to_directory"
+  executable: "target/executable/move_files_to_directory/move_files_to_directory"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/executable/sync_resources/.config.vsh.yaml

@@ -0,0 +1,238 @@
+name: "sync_resources"
+version: "v0.3.0"
+authors:
+- name: "Robrecht Cannoodt"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+- name: "Dries Schaumont"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Path to the _viash.yaml project configuration file."
+    info: null
+    default:
+    - "_viash.yaml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Path to the directory where the resources will be synced to."
+    info: null
+    default:
+    - "."
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--dryrun"
+    description: "Does not display the operations performed from the specified command."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--exclude"
+    description: "Exclude all files or objects from the command that matches the specified\
+      \ pattern."
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+summary: "Sync a Viash package's test resources to the local filesystem"
+description: "Sync a Viash package's test resources to the local filesystem based\
+  \ on the\nthe `.info.test_resources` field in the `_viash.yaml` file. This is useful\
+  \ for\ntesting and debugging purposes.\n"
+usage: "sync_resources\nsync_resources --input _viash.yaml --output .\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "alpine:3"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apk"
+    packages:
+    - "bash"
+    - "rclone"
+    - "yq"
+  - type: "docker"
+    run:
+    - "rclone config create s3 s3 anonymous=true"
+    - "rclone config create gs gcs anonymous=true"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/sync_resources/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/sync_resources"
+  executable: "target/executable/sync_resources/sync_resources"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

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

@@ -0,0 +1,223 @@
+name: "untar"
+version: "v0.3.0"
+authors:
+- name: "Dries Schaumont"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+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
+summary: "Unpack a .tar file"
+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"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/untar/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/untar"
+  executable: "target/executable/untar/untar"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/nextflow/check_disk_space/.config.vsh.yaml

@@ -0,0 +1,198 @@
+name: "check_disk_space"
+version: "v0.3.0"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "integer"
+    name: "--tmp_space_required"
+    description: "Temporary space required in MB."
+    info: null
+    default:
+    - 1000
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--publish_space_required"
+    description: "Publish space required in MB."
+    info: null
+    default:
+    - 500
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--publish_dir"
+    description: "Directory where workflow outputs will be published."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output file containing system resources details."
+    info: null
+    default:
+    - "output.txt"
+    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: "Check for available disk space on the system.\n\nThis component is only\
+  \ useful when working with persistent storage environments\nwhere all workflow steps\
+  \ execute on the same instance or share the same\nstorage volume. That is, running\
+  \ thus component on e.g. AWS Batch or\nother cloud-based systems will not work as\
+  \ expected, since each step\ncan run on a different instance and resources will\
+  \ not be shared.\n\nFor distributed environments, consider integrating resource\
+  \ checks directly\ninto the components that will actually consume the storage, rather\
+  \ than\nusing this standalone check.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "bash:latest"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/check_disk_space/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/check_disk_space"
+  executable: "target/nextflow/check_disk_space/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/nextflow/check_disk_space/nextflow.config

@@ -0,0 +1,125 @@
+manifest {
+  name = 'check_disk_space'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.3.0'
+  description = 'Check for available disk space on the system.\n\nThis component is only useful when working with persistent storage environments\nwhere all workflow steps execute on the same instance or share the same\nstorage volume. That is, running thus component on e.g. AWS Batch or\nother cloud-based systems will not work as expected, since each step\ncan run on a different instance and resources will not be shared.\n\nFor distributed environments, consider integrating resource checks directly\ninto the components that will actually consume the storage, rather than\nusing this standalone check.\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/check_disk_space/nextflow_schema.json

@@ -0,0 +1,70 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "check_disk_space",
+  "description": "Check for available disk space on the system.\n\nThis component is only useful when working with persistent storage environments\nwhere all workflow steps execute on the same instance or share the same\nstorage volume. That is, running thus component on e.g. AWS Batch or\nother cloud-based systems will not work as expected, since each step\ncan run on a different instance and resources will not be shared.\n\nFor distributed environments, consider integrating resource checks directly\ninto the components that will actually consume the storage, rather than\nusing this standalone check.\n",
+  "type": "object",
+  "$defs": {
+    "inputs": {
+      "title": "Inputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "tmp_space_required": {
+          "type": "integer",
+          "description": "Temporary space required in MB.",
+          "help_text": "Type: `integer`, multiple: `False`, default: `1000`. ",
+          "default": 1000
+        },
+        "publish_space_required": {
+          "type": "integer",
+          "description": "Publish space required in MB.",
+          "help_text": "Type: `integer`, multiple: `False`, default: `500`. ",
+          "default": 500
+        },
+        "publish_dir": {
+          "type": "string",
+          "format": "path",
+          "description": "Directory where workflow outputs will be published.",
+          "help_text": "Type: `file`, multiple: `False`, direction: `input`. "
+        }
+      }
+    },
+    "outputs": {
+      "title": "Outputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "Output file containing system resources details.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"output.txt\"`, direction: `output`. ",
+          "default": "output.txt"
+        }
+      }
+    },
+    "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": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/inputs"
+    },
+    {
+      "$ref": "#/$defs/outputs"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}

target/nextflow/concat_text/.config.vsh.yaml

@@ -0,0 +1,216 @@
+name: "concat_text"
+version: "v0.3.0"
+authors:
+- name: "Toni Verbeiren"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      github: "tverbeiren"
+      linkedin: "verbeiren"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist and CEO"
+- name: "Dries Schaumont"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Input arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "A list of (gzipped) text files."
+    info: null
+    example:
+    - "input?.txt.gz"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+- name: "Output arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--gzip_output"
+    description: "Should the output be zipped?"
+    info: null
+    direction: "input"
+  - type: "file"
+    name: "--output"
+    description: "File to write the output to, optionally gzipped."
+    info: null
+    example:
+    - "output.txt"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+summary: "Concatenate a number of text files"
+description: "Concatenate a number of text files, handle gzipped text files gracefully\
+  \ and\noptionally gzip the output text file.\n\nThis component is useful for concatening\
+  \ fastq files from different lanes, for instance.\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info:
+  improvements: "This component could be improved in 2 ways:\n  1. Allow for a mix\
+    \ of zipped and plain input files\n  2. Allow to specify a compression algorithm\
+    \ for the output\n"
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "alpine:latest"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apk"
+    packages:
+    - "bash"
+    - "procps"
+    - "file"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/concat_text/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/concat_text"
+  executable: "target/nextflow/concat_text/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/nextflow/concat_text/nextflow.config

@@ -0,0 +1,126 @@
+manifest {
+  name = 'concat_text'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.3.0'
+  description = 'Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n'
+  author = 'Toni Verbeiren, Dries Schaumont'
+}
+
+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/concat_text/nextflow_schema.json

@@ -0,0 +1,68 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "concat_text",
+  "description": "Concatenate a number of text files, handle gzipped text files gracefully and\noptionally gzip the output text file.\n\nThis component is useful for concatening fastq files from different lanes, for instance.\n",
+  "type": "object",
+  "$defs": {
+    "input arguments": {
+      "title": "Input arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "input": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "format": "path",
+          "exists": true,
+          "description": "A list of (gzipped) text files.",
+          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`, example: `[\"input?.txt.gz\"]`. "
+        }
+      }
+    },
+    "output arguments": {
+      "title": "Output arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "gzip_output": {
+          "type": "boolean",
+          "description": "Should the output be zipped?",
+          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
+          "default": false
+        },
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "File to write the output to, optionally gzipped.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.txt\"`, direction: `output`, example: `\"output.txt\"`. ",
+          "default": "$id.$key.output.txt"
+        }
+      }
+    },
+    "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": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/input arguments"
+    },
+    {
+      "$ref": "#/$defs/output arguments"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}

target/nextflow/csv2fasta/.config.vsh.yaml

@@ -0,0 +1,298 @@
+name: "csv2fasta"
+version: "v0.3.0"
+authors:
+- name: "Dries Schaumont"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "CSV file to be processed."
+    info: null
+    example:
+    - "barcodes.csv"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--header"
+    description: "Parse the first line of the CSV file as a header.\n"
+    info: null
+    direction: "input"
+- name: "CSV dialect options"
+  description: "Options that can be used to override the automatically detected\n\
+    dialect of the CSV file.\n"
+  arguments:
+  - type: "string"
+    name: "--delimiter"
+    description: "Overwrite the column delimiter character.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--quote_character"
+    description: "Overwrite the character used to denote the start and end of a quoted\
+      \ item.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "CSV column arguments"
+  description: "Parameters for the selection of columns from the CSV file.\nOnly required\
+    \ when your CSV file contains more than 2 columns,\notherwise the first column\
+    \ will be used for the FASTA header\nand the second for the FASTA nucleotide sequences.\
+    \ This default\ncan still be overwritten by using the options below.\n"
+  arguments:
+  - type: "string"
+    name: "--sequence_column"
+    description: "Name of the column containing the sequences. Implies 'header'.\n\
+      Cannot be used together with 'sequence_column_index'.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--name_column"
+    description: "Name of the column describing the FASTA headers. Implies 'header'.\n\
+      Cannot be used together with 'name_column_index'.\n"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--sequence_column_index"
+    description: "Index of the column to use as the FASTA sequences, counter from\
+      \ the left and\nstarting from 0. Cannot be used in combination with the 'sequence_column'\
+      \ argument.\n"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--name_column_index"
+    description: "Index of the column to use as the FASTA headers, counter from the\
+      \ left and\nstarting from 0. Cannot be used in combination with 'name_column'.\n"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "Output fasta file."
+    info: null
+    example:
+    - "barcodes.fasta"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+resources:
+- type: "python_script"
+  path: "script.py"
+  is_executable: true
+summary: "Convert a CSV file to FASTA entries"
+description: "Convert two columns from a CSV file to FASTA entries. The CSV file can\n\
+  contain an optional header and each row (other than the header) becomes\na single\
+  \ FASTA record. One of the two columns will be used as the names\nfor the FASTA\
+  \ entries, while the other become the sequences. The sequences\ncolumn must only\
+  \ contain characters that are valid IUPAC notation for \nnucleotides or a group\
+  \ thereof (wildcard characters).\n"
+test_resources:
+- type: "python_script"
+  path: "test_csv2fasta.py"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "python:slim"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  - type: "python"
+    user: false
+    packages:
+    - "dnaio"
+    upgrade: true
+  test_setup:
+  - type: "python"
+    user: false
+    packages:
+    - "pytest"
+    - "viashpy"
+    upgrade: true
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/csv2fasta/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/csv2fasta"
+  executable: "target/nextflow/csv2fasta/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/nextflow/csv2fasta/nextflow.config

@@ -0,0 +1,126 @@
+manifest {
+  name = 'csv2fasta'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.3.0'
+  description = 'Convert two columns from a CSV file to FASTA entries. The CSV file can\ncontain an optional header and each row (other than the header) becomes\na single FASTA record. One of the two columns will be used as the names\nfor the FASTA entries, while the other become the sequences. The sequences\ncolumn must only contain characters that are valid IUPAC notation for \nnucleotides or a group thereof (wildcard characters).\n'
+  author = 'Dries Schaumont, Robrecht Cannoodt'
+}
+
+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/csv2fasta/nextflow_schema.json

@@ -0,0 +1,115 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "csv2fasta",
+  "description": "Convert two columns from a CSV file to FASTA entries. The CSV file can\ncontain an optional header and each row (other than the header) becomes\na single FASTA record. One of the two columns will be used as the names\nfor the FASTA entries, while the other become the sequences. The sequences\ncolumn must only contain characters that are valid IUPAC notation for \nnucleotides or a group thereof (wildcard characters).\n",
+  "type": "object",
+  "$defs": {
+    "inputs": {
+      "title": "Inputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "input": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "CSV file to be processed.",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`, example: `\"barcodes.csv\"`. "
+        },
+        "header": {
+          "type": "boolean",
+          "description": "Parse the first line of the CSV file as a header.\n",
+          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
+          "default": false
+        }
+      }
+    },
+    "outputs": {
+      "title": "Outputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "Output fasta file.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"$id.$key.output.fasta\"`, direction: `output`, example: `\"barcodes.fasta\"`. ",
+          "default": "$id.$key.output.fasta"
+        }
+      }
+    },
+    "csv dialect options": {
+      "title": "CSV dialect options",
+      "type": "object",
+      "description": "Options that can be used to override the automatically detected\ndialect of the CSV file.\n",
+      "properties": {
+        "delimiter": {
+          "type": "string",
+          "description": "Overwrite the column delimiter character.\n",
+          "help_text": "Type: `string`, multiple: `False`. "
+        },
+        "quote_character": {
+          "type": "string",
+          "description": "Overwrite the character used to denote the start and end of a quoted item.\n",
+          "help_text": "Type: `string`, multiple: `False`. "
+        }
+      }
+    },
+    "csv column arguments": {
+      "title": "CSV column arguments",
+      "type": "object",
+      "description": "Parameters for the selection of columns from the CSV file.\nOnly required when your CSV file contains more than 2 columns,\notherwise the first column will be used for the FASTA header\nand the second for the FASTA nucleotide sequences. This default\ncan still be overwritten by using the options below.\n",
+      "properties": {
+        "sequence_column": {
+          "type": "string",
+          "description": "Name of the column containing the sequences",
+          "help_text": "Type: `string`, multiple: `False`. "
+        },
+        "name_column": {
+          "type": "string",
+          "description": "Name of the column describing the FASTA headers",
+          "help_text": "Type: `string`, multiple: `False`. "
+        },
+        "sequence_column_index": {
+          "type": "integer",
+          "description": "Index of the column to use as the FASTA sequences, counter from the left and\nstarting from 0",
+          "help_text": "Type: `integer`, multiple: `False`. "
+        },
+        "name_column_index": {
+          "type": "integer",
+          "description": "Index of the column to use as the FASTA headers, counter from the left and\nstarting from 0",
+          "help_text": "Type: `integer`, multiple: `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": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/inputs"
+    },
+    {
+      "$ref": "#/$defs/outputs"
+    },
+    {
+      "$ref": "#/$defs/csv dialect options"
+    },
+    {
+      "$ref": "#/$defs/csv column arguments"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}

target/nextflow/move_files_to_directory/.config.vsh.yaml

@@ -0,0 +1,194 @@
+name: "move_files_to_directory"
+version: "v0.3.0"
+authors:
+- name: "Dorien Roosen"
+  roles:
+  - "maintainer"
+  info:
+    links:
+      email: "dorien@data-intuitive.com"
+      github: "dorien-er"
+      linkedin: "dorien-roosen"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Arguments"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "Paths of the files that will be copied into the output directory."
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+  - type: "file"
+    name: "--output"
+    description: "Path to output directory"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--keep_symbolic_links"
+    alternatives:
+    - "-d"
+    description: "Preserve symbolic links."
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+summary: "Publish one or multiple files to the same directory"
+description: "This component copies one or multiple files to the same destination\
+  \ directory, creating the output directory if it doesn't exist."
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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:latest"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/move_files_to_directory/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/move_files_to_directory"
+  executable: "target/nextflow/move_files_to_directory/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/nextflow/move_files_to_directory/nextflow.config

@@ -0,0 +1,126 @@
+manifest {
+  name = 'move_files_to_directory'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.3.0'
+  description = 'This component copies one or multiple files to the same destination directory, creating the output directory if it doesn\'t exist.'
+  author = 'Dorien Roosen'
+}
+
+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/move_files_to_directory/nextflow_schema.json

@@ -0,0 +1,58 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "move_files_to_directory",
+  "description": "This component copies one or multiple files to the same destination directory, creating the output directory if it doesn't exist.",
+  "type": "object",
+  "$defs": {
+    "arguments": {
+      "title": "Arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "input": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "format": "path",
+          "exists": true,
+          "description": "Paths of the files that will be copied into the output directory.",
+          "help_text": "Type: `file`, multiple: `True`, required, direction: `input`. "
+        },
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to output directory",
+          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
+          "default": "$id.$key.output"
+        },
+        "keep_symbolic_links": {
+          "type": "boolean",
+          "description": "Preserve symbolic links.",
+          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
+          "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": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/arguments"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}

target/nextflow/sync_resources/.config.vsh.yaml

@@ -0,0 +1,238 @@
+name: "sync_resources"
+version: "v0.3.0"
+authors:
+- name: "Robrecht Cannoodt"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+- name: "Dries Schaumont"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    alternatives:
+    - "-i"
+    description: "Path to the _viash.yaml project configuration file."
+    info: null
+    default:
+    - "_viash.yaml"
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    alternatives:
+    - "-o"
+    description: "Path to the directory where the resources will be synced to."
+    info: null
+    default:
+    - "."
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "boolean_true"
+    name: "--dryrun"
+    description: "Does not display the operations performed from the specified command."
+    info: null
+    direction: "input"
+  - type: "string"
+    name: "--exclude"
+    description: "Exclude all files or objects from the command that matches the specified\
+      \ pattern."
+    info: null
+    required: false
+    direction: "input"
+    multiple: true
+    multiple_sep: ";"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+summary: "Sync a Viash package's test resources to the local filesystem"
+description: "Sync a Viash package's test resources to the local filesystem based\
+  \ on the\nthe `.info.test_resources` field in the `_viash.yaml` file. This is useful\
+  \ for\ntesting and debugging purposes.\n"
+usage: "sync_resources\nsync_resources --input _viash.yaml --output .\n"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "alpine:3"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apk"
+    packages:
+    - "bash"
+    - "rclone"
+    - "yq"
+  - type: "docker"
+    run:
+    - "rclone config create s3 s3 anonymous=true"
+    - "rclone config create gs gcs anonymous=true"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/sync_resources/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/sync_resources"
+  executable: "target/nextflow/sync_resources/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/nextflow/sync_resources/nextflow.config

@@ -0,0 +1,126 @@
+manifest {
+  name = 'sync_resources'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.3.0'
+  description = 'Sync a Viash package\'s test resources to the local filesystem based on the\nthe `.info.test_resources` field in the `_viash.yaml` file. This is useful for\ntesting and debugging purposes.\n'
+  author = 'Robrecht Cannoodt, Dries Schaumont'
+}
+
+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/sync_resources/nextflow_schema.json

@@ -0,0 +1,83 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "sync_resources",
+  "description": "Sync a Viash package's test resources to the local filesystem based on the\nthe `.info.test_resources` field in the `_viash.yaml` file. This is useful for\ntesting and debugging purposes.\n",
+  "type": "object",
+  "$defs": {
+    "inputs": {
+      "title": "Inputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "input": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the _viash.yaml project configuration file.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\"_viash.yaml\"`, direction: `input`. ",
+          "default": "_viash.yaml"
+        }
+      }
+    },
+    "outputs": {
+      "title": "Outputs",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "Path to the directory where the resources will be synced to.",
+          "help_text": "Type: `file`, multiple: `False`, default: `\".\"`, direction: `output`. ",
+          "default": "."
+        }
+      }
+    },
+    "arguments": {
+      "title": "Arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "dryrun": {
+          "type": "boolean",
+          "description": "Does not display the operations performed from the specified command.",
+          "help_text": "Type: `boolean_true`, multiple: `False`, default: `false`. ",
+          "default": false
+        },
+        "exclude": {
+          "type": "array",
+          "items": {
+            "type": "string"
+          },
+          "description": "Exclude all files or objects from the command that matches the specified pattern.",
+          "help_text": "Type: `string`, multiple: `True`. "
+        }
+      }
+    },
+    "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": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/inputs"
+    },
+    {
+      "$ref": "#/$defs/outputs"
+    },
+    {
+      "$ref": "#/$defs/arguments"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}

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

@@ -0,0 +1,223 @@
+name: "untar"
+version: "v0.3.0"
+authors:
+- name: "Dries Schaumont"
+  roles:
+  - "author"
+  - "maintainer"
+  info:
+    links:
+      email: "dries@data-intuitive.com"
+      github: "DriesSchaumont"
+      orcid: "0000-0002-4389-0440"
+      linkedin: "dries-schaumont"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Scientist"
+- name: "Robrecht Cannoodt"
+  roles:
+  - "reviewer"
+  info:
+    links:
+      email: "robrecht@data-intuitive.com"
+      github: "rcannood"
+      orcid: "0000-0003-3641-729X"
+      linkedin: "robrechtcannoodt"
+    organizations:
+    - name: "Data Intuitive"
+      href: "https://www.data-intuitive.com"
+      role: "Data Science Engineer"
+    - name: "Open Problems"
+      href: "https://openproblems.bio"
+      role: "Core Member"
+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
+summary: "Unpack a .tar file"
+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"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+links:
+  repository: "https://github.com/viash-hub/craftbox"
+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: "v0.3.0"
+  namespace_separator: "/"
+  setup:
+  - type: "apt"
+    packages:
+    - "procps"
+    interactive: false
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/untar/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/untar"
+  executable: "target/nextflow/untar/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "4947872a1c4b9b2b8c6bfe12b843b6b8d4ea8b61"
+  git_remote: "https://github.com/viash-hub/craftbox"
+  git_tag: "v0.1.0-9-g4947872"
+package_config:
+  name: "craftbox"
+  version: "v0.3.0"
+  summary: "A collection of custom-tailored scripts and applied utilities built with\
+    \ Viash.\n"
+  description: "`craftbox` is a curated collection of custom scripts and utilities\
+    \ designed to tackle context-specific tasks.\n\nEmphasizing the Viash principles,\
+    \ `craftbox` components aim for **reusability**, **reproducibility**, and adherence\
+    \ to **best practices**. Key features generally include:\n\n* **Standalone & Nextflow\
+    \ Ready:** Components are built to run directly via the command line or be smoothly\
+    \ integrated into Nextflow workflows.\n* **Custom Implementations:** Contains\
+    \ scripts and tools developed for particular tasks that may not be found in broader\
+    \ collections.\n* **High Quality Standards (promoted by Viash):**\n    * Clear\
+    \ documentation for components and their parameters.\n    * Full exposure of underlying\
+    \ script/tool arguments for fine-grained control.\n    * Containerized (Docker)\
+    \ to ensure dependency management and a consistent, reproducible runtime environment.\n\
+    \    * Unit tested where applicable to ensure components function as expected.\n"
+  info: null
+  viash_version: "0.9.4"
+  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 := 'v0.3.0'"
+  keywords:
+  - "scripts"
+  - "custom"
+  - "implementations"
+  - "utilities"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/craftbox"
+    issue_tracker: "https://github.com/viash-hub/craftbox/issues"

target/nextflow/untar/nextflow.config

@@ -0,0 +1,126 @@
+manifest {
+  name = 'untar'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.3.0'
+  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'
+  author = 'Dries Schaumont, Robrecht Cannoodt'
+}
+
+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/untar/nextflow_schema.json

@@ -0,0 +1,74 @@
+{
+  "$schema": "https://json-schema.org/draft/2020-12/schema",
+  "title": "untar",
+  "description": "Unpack a .tar file. When the contents of the .tar file is just a single directory,\nput the contents of the directory into the output folder instead of that directory.\n",
+  "type": "object",
+  "$defs": {
+    "input arguments": {
+      "title": "Input arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "input": {
+          "type": "string",
+          "format": "path",
+          "exists": true,
+          "description": "Tarball file to be unpacked.",
+          "help_text": "Type: `file`, multiple: `False`, required, direction: `input`. "
+        }
+      }
+    },
+    "output arguments": {
+      "title": "Output arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "output": {
+          "type": "string",
+          "format": "path",
+          "description": "Directory to write the contents of the .tar file to.",
+          "help_text": "Type: `file`, multiple: `False`, required, default: `\"$id.$key.output\"`, direction: `output`. ",
+          "default": "$id.$key.output"
+        }
+      }
+    },
+    "other arguments": {
+      "title": "Other arguments",
+      "type": "object",
+      "description": "No description",
+      "properties": {
+        "exclude": {
+          "type": "string",
+          "description": "Prevents any file or member whose name matches the shell wildcard (pattern) from being extracted.",
+          "help_text": "Type: `string`, multiple: `False`, example: `\"docs/figures\"`. "
+        }
+      }
+    },
+    "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": "Path to an output directory.",
+          "help_text": "Type: `string`, multiple: `False`, required, example: `\"output/\"`. "
+        }
+      }
+    }
+  },
+  "allOf": [
+    {
+      "$ref": "#/$defs/input arguments"
+    },
+    {
+      "$ref": "#/$defs/output arguments"
+    },
+    {
+      "$ref": "#/$defs/other arguments"
+    },
+    {
+      "$ref": "#/$defs/nextflow input-output arguments"
+    }
+  ]
+}