Build branch v0.1.x with version v0.1.1 (2c07979)

Build pipeline: viash-hub.toolbox.v0.1.x-fphr8 Source commit: 2c07979559 Source message: Merge remote-tracking branch 'origin/main' into v0.1.x
2025-05-06 20:43:01 +00:00
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--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -0,0 +1,23 @@
+# toolbox v0.1.1
+
+## MINOR CHANGES
+
+* Updated the test CI (PR #6).
+
+* Bump viash to 0.9.0 (PR #10).
+
+* Bump viash to 0.9.4 (PR #13).
+
+* Update README (PR #13).
+
+# toolbox v0.1.0
+
+## NEW FEATURES
+
+* `bgzip`: Add bgzip functionality to compress and decompress files (initial commit).
+
+* `yq`: A portable YAML, JSON, XML, CSV, TOML and properties processor (PR #1).
+
+## MINOR CHANGES
+
+* Use newer viash-actions updated for Viash 0.9 (PR #2).
--- a/CONTRIBUTING.md
+++ b/CONTRIBUTING.md
@@ -0,0 +1,383 @@
+
+# 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
+```
--- a/21
+++ b/21
@@ -0,0 +1,21 @@
+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.
--- a/README.md
+++ b/README.md
@@ -0,0 +1,139 @@
+
+
+# 🛠📦 toolbox
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-toolbox-7a4baa.svg)](https://www.viash-hub.com/packages/toolbox)
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Ftoolbox-blue.svg)](https://github.com/viash-hub/toolbox)
+[![GitHub
+License](https://img.shields.io/github/license/viash-hub/toolbox.svg)](https://github.com/viash-hub/toolbox/blob/main/LICENSE)
+[![GitHub
+Issues](https://img.shields.io/github/issues/viash-hub/toolbox.svg)](https://github.com/viash-hub/toolbox/issues)
+[![Viash
+version](https://img.shields.io/badge/Viash-v0.9.4-blue.svg)](https://viash.io)
+
+A collection of curated command-line tools for general IT tasks, built
+with Viash.
+
+## Introduction
+
+`toolbox` provides a versatile suite of IT components, following the
+robust Viash (https://viash.io) framework. This package focuses on
+delivering reliable, standalone tools that can be easily integrated into
+larger computational workflows.
+
+The core philosophy emphasizes **reusability**, **reproducibility**, and
+adherence to **best practices** in component creation. Key features of
+`toolbox` components include:
+
+- **Standalone & Nextflow Ready:** Execute components directly from the
+  command line or seamlessly incorporate them into Nextflow workflows.
+- **High Quality Standards:**
+  - Comprehensive documentation for each component and its parameters.
+  - Full exposure of the underlying tool’s arguments for maximum
+    flexibility.
+  - Containerized (Docker) to ensure consistent environments and manage
+    dependencies, leading to enhanced reproducibility.
+  - Unit tested to verify functionality and ensure reliability.
+
+## Example Usage
+
+Viash components in toolbox can be run in various ways:
+
+``` mermaid lang="mermaid"
+flowchart TD
+    A[toolbox v0.1.0] --> 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=toolbox&version=v0.1.0&component=yq&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://toolbox@v0.1.0/yq -- --help
+
+viash run vsh://toolbox@v0.1.0/yq -- \
+  --input path/to/input.yaml \
+  --output output.yaml
+```
+
+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/toolbox \
+  -revision v0.1.0 \
+  -main-script target/nextflow/yq/main.nf \
+  -latest -resume \
+  -profile docker \
+  --input path/to/input.yaml \
+  --publish_dir path/to/output
+```
+
+**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: yq
+    repository: vsh://toolbox@v0.1.0
+```
+
+**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/toolbox/blob/main/CONTRIBUTING.md)
+file for more details.
--- a/README.qmd
+++ b/README.qmd
@@ -0,0 +1,119 @@
+---
+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$version else "v0.1.0"
+comp <- "yq"
+```
+# 🛠📦 `r pkg`
+
+[![ViashHub](https://img.shields.io/badge/ViashHub-`r pkg`-7a4baa.svg)](https://www.viash-hub.com/packages/`r pkg`) 
+[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r pkg`-blue.svg)](`r package$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.yaml \
+  --output output.yaml
+```
+
+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.yaml \
+  --publish_dir path/to/output
+```
+
+**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.
--- a/_viash.yaml
+++ b/_viash.yaml
@@ -0,0 +1,26 @@
+name: toolbox
+version: v0.1.1
+summary: |
+  A collection of curated command-line tools for general IT tasks, built with Viash.
+description: |
+  `toolbox` provides a versatile suite of IT components, following the robust Viash (https://viash.io) framework.
+  This package focuses on delivering reliable, standalone tools that can be easily integrated into larger computational workflows.
+
+  The core philosophy emphasizes **reusability**, **reproducibility**, and adherence to **best practices** in component creation. Key features of `toolbox` components include:
+
+  * **Standalone & Nextflow Ready:** Execute components directly from the command line or seamlessly incorporate them into Nextflow workflows.
+  * **High Quality Standards:**
+      * Comprehensive documentation for each component and its parameters.
+      * Full exposure of the underlying tool's arguments for maximum flexibility.
+      * Containerized (Docker) to ensure consistent environments and manage dependencies, leading to enhanced reproducibility.
+      * Unit tested to verify functionality and ensure reliability.
+license: MIT
+keywords: [toolbox, command-line, tools]
+links:
+  issue_tracker: https://github.com/viash-hub/toolbox/issues
+  repository: https://github.com/viash-hub/toolbox
+
+viash_version: 0.9.4
+
+config_mods: |
+  .requirements.commands := ['ps']
--- a/docs/viash-hub.png
+++ b/docs/viash-hub.png
--- a/main.nf
+++ b/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.")
+}
--- a/nextflow.config
+++ b/nextflow.config
@@ -0,0 +1,6 @@
+manifest {
+  name = "toolbox"
+  version = "v0.1.1"
+  defaultBranch = "main"
+  nextflowVersion = "!>=20.12.1-edge"
+}
--- a/src/bgzip/config.vsh.yaml
+++ b/src/bgzip/config.vsh.yaml
@@ -0,0 +1,90 @@
+name: bgzip
+description: Block compression/decompression utility
+links:
+  homepage: https://www.htslib.org/
+  documentation: https://www.htslib.org/doc/bgzip.html
+  repository: https://github.com/samtools/htslib
+references:
+  doi: 10.1093/gigascience/giab007
+license: MIT
+requirements:
+  commands: [ bgzip ]
+argument_groups:
+  - name: Inputs
+    arguments:
+    - name: --input
+      type: file
+      direction: input
+      description: file to be compressed or decompressed
+      required: true
+  - name: Outputs
+    arguments:
+    - name: --output
+      type: file
+      direction: output
+      description: compressed or decompressed output
+      required: true
+    - name: --index_name
+      alternatives: -I
+      type: file
+      direction: output
+      description: name of BGZF index file [file.gz.gzi]
+  - name: Arguments
+    arguments:
+    - name: --offset
+      alternatives: -b
+      type: integer
+      description: decompress at virtual file pointer (0-based uncompressed offset)
+    - name: --decompress
+      alternatives: -d
+      type: boolean_true
+      description: decompress the input file
+    - name: --rebgzip
+      alternatives: -g
+      type: boolean_true
+      description: use an index file to bgzip a file
+    - name: --index
+      alternatives: -i
+      type: boolean_true
+      description: compress and create BGZF index
+    - name: --compress_level
+      alternatives: -l
+      type: integer
+      description: compression level to use when compressing; 0 to 9, or -1 for default [-1]
+      min: -1
+      max: 9
+    - name: --reindex
+      alternatives: -r
+      type: boolean_true
+      description: (re)index the output file
+    - name: --size
+      alternatives: -s
+      type: integer
+      description: decompress INT bytes (uncompressed size)
+      min: 0
+    - name: --test
+      alternatives: -t
+      type: boolean_true
+      description: test integrity of compressed file
+    - name: --binary
+      type: boolean_true
+      description: Don't align blocks with text lines
+resources:
+  - type: bash_script
+    path: script.sh
+test_resources:
+  - type: bash_script
+    path: test.sh
+  - type: file
+    path: test_data
+
+engines:
+  - type: docker
+    image: quay.io/biocontainers/htslib:1.19--h81da01d_0
+    setup:
+      - type: docker
+        run: |
+          bgzip -h | grep 'Version:' 2>&1 |  sed 's/Version:\s\(.*\)/bgzip: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/bgzip/help.txt
+++ b/src/bgzip/help.txt
@@ -0,0 +1,22 @@
+```bash
+bgzip -h
+```
+
+Version: 1.19
+Usage:   bgzip [OPTIONS] [FILE] ...
+Options:
+   -b, --offset INT           decompress at virtual file pointer (0-based uncompressed offset)
+   -c, --stdout               write on standard output, keep original files unchanged
+   -d, --decompress           decompress
+   -f, --force                overwrite files without asking
+   -g, --rebgzip              use an index file to bgzip a file
+   -h, --help                 give this help
+   -i, --index                compress and create BGZF index
+   -I, --index-name FILE      name of BGZF index file [file.gz.gzi]
+   -k, --keep                 don't delete input files during operation
+   -l, --compress-level INT   Compression level to use when compressing; 0 to 9, or -1 for default [-1]
+   -r, --reindex              (re)index compressed file
+   -s, --size INT             decompress INT bytes (uncompressed size)
+   -t, --test                 test integrity of compressed file
+       --binary               Don't align blocks with text lines
+   -@, --threads INT          number of compression threads to use [1]
--- a/src/bgzip/script.sh
+++ b/src/bgzip/script.sh
@@ -0,0 +1,21 @@
+#!/bin/bash
+
+[[ "$par_decompress" == "false" ]] && unset par_decompress
+[[ "$par_rebgzip" == "false" ]] && unset par_rebgzip
+[[ "$par_index" == "false" ]] && unset par_index
+[[ "$par_reindex" == "false" ]] && unset par_reindex
+[[ "$par_test" == "false" ]] && unset par_test
+[[ "$par_binary" == "false" ]] && unset par_binary
+bgzip -c \
+  ${meta_cpus:+--threads "${meta_cpus}"} \
+  ${par_offset:+-b "${par_offset}"} \
+  ${par_decompress:+-d} \
+  ${par_rebgzip:+-g} \
+  ${par_index:+-i} \
+  ${par_index_name:+-I "${par_index_name}"} \
+  ${par_compress_level:+-l "${par_compress_level}"} \
+  ${par_reindex:+-r} \
+  ${par_size:+-s "${par_size}"} \
+  ${par_test:+-t} \
+  ${par_binary:+--binary} \
+  "$par_input" > "$par_output"
--- a/src/bgzip/test.sh
+++ b/src/bgzip/test.sh
@@ -0,0 +1,19 @@
+set -e
+
+"$meta_executable" --input "$meta_resources_dir/test_data/test.vcf" --output "test.vcf.gz"
+
+echo ">> Checking output of compressing"
+[ ! -f "test.vcf.gz" ] && echo "Output file test.vcf.gz does not exist" && exit 1
+
+"$meta_executable" --input "test.vcf.gz" --output "test.vcf" --decompress
+
+echo ">> Checking output of decompressing"
+[ ! -f "test.vcf" ] && echo "Output file test.vcf does not exist" && exit 1
+
+echo ">> Checking original and decompressed files are the same"
+set +e
+cmp --silent -- "$meta_resources_dir/test_data/test.vcf" "test.vcf"
+[ $? -ne 0 ] && echo "files are different" && exit 1
+set -e
+
+echo "> Test successful"
--- a/src/bgzip/test_data/script.sh
+++ b/src/bgzip/test_data/script.sh
@@ -0,0 +1,10 @@
+# bgzip test data
+
+# Test data was obtained from https://github.com/snakemake/snakemake-wrappers/tree/master/bio/bgzip/test.
+
+if [ ! -d /tmp/snakemake-wrappers ]; then
+  git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
+fi
+
+cp -r /tmp/snakemake-wrappers/bio/bgzip/test/* src/bgzip/test_data
+
--- a/src/bgzip/test_data/test.vcf
+++ b/src/bgzip/test_data/test.vcf
@@ -0,0 +1,23 @@
+##fileformat=VCFv4.0
+##fileDate=20090805
+##source=https://www.internationalgenome.org/wiki/Analysis/vcf4.0/
+##reference=1000GenomesPilot-NCBI36
+##phasing=partial
+##INFO=<ID=NS,Number=1,Type=Integer,Description="Number of Samples With Data">
+##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
+##INFO=<ID=AF,Number=.,Type=Float,Description="Allele Frequency">
+##INFO=<ID=AA,Number=1,Type=String,Description="Ancestral Allele">
+##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP membership, build 129">
+##INFO=<ID=H2,Number=0,Type=Flag,Description="HapMap2 membership">
+##FILTER=<ID=q10,Description="Quality below 10">
+##FILTER=<ID=s50,Description="Less than 50% of samples have data">
+##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
+##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
+##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Read Depth">
+##FORMAT=<ID=HQ,Number=2,Type=Integer,Description="Haplotype Quality">
+#CHROM POS     ID        REF ALT    QUAL FILTER INFO                              FORMAT      NA00001        NA00002        NA00003
+20     14370   rs6054257 G      A       29   PASS   NS=3;DP=14;AF=0.5;DB;H2           GT:GQ:DP:HQ 0|0:48:1:51,51 1|0:48:8:51,51 1/1:43:5:.,.
+20     17330   .         T      A       3    q10    NS=3;DP=11;AF=0.017               GT:GQ:DP:HQ 0|0:49:3:58,50 0|1:3:5:65,3   0/0:41:3
+20     1110696 rs6040355 A      G,T     67   PASS   NS=2;DP=10;AF=0.333,0.667;AA=T;DB GT:GQ:DP:HQ 1|2:21:6:23,27 2|1:2:0:18,2   2/2:35:4
+20     1230237 .         T      .       47   PASS   NS=3;DP=13;AA=T                   GT:GQ:DP:HQ 0|0:54:7:56,60 0|0:48:4:51,51 0/0:61:2
+20     1234567 microsat1 GTCT   G,GTACT 50   PASS   NS=3;DP=9;AA=G                    GT:GQ:DP    0/1:35:4       0/2:17:2       1/1:40:3
--- a/src/yq/config.vsh.yaml
+++ b/src/yq/config.vsh.yaml
@@ -0,0 +1,87 @@
+name: yq
+description: A portable YAML, JSON, XML, CSV, TOML and properties processor
+keywords: [ yaml, json, xml, csv, toml, properties ]
+links:
+  homepage: https://mikefarah.gitbook.io/yq
+  documentation: https://mikefarah.gitbook.io/yq/
+  repository: https://github.com/mikefarah/yq
+license: MIT
+requirements:
+  commands: [ yq ]
+argument_groups:
+  - name: Inputs
+    arguments:
+      - name: --input
+        type: file
+        direction: input
+        description: files to be processed
+        required: true
+        example: input.yaml
+  - name: Outputs
+    arguments:
+      - name: --output
+        type: file
+        direction: output
+        description: output file
+        required: true
+        example: output.yaml
+  - name: Arguments
+    arguments:
+      - name: --eval
+        type: string
+        description: expression to evaluate
+        required: true
+        example: '.name = "foo"'
+      - name: --indent
+        type: integer
+        description: sets indent level for output (default 2)
+        alternatives: -I
+      - name: --input_format
+        type: string
+        description: 'parse format for input. (default "auto")'
+        alternatives: -p
+        choices: [ auto, a, yaml, "y", json, j, props, p, csv, c, tsv, t, xml, x, base64, uri, toml, shell, s, lua, l ]
+      - name: --output_format
+        type: string
+        description: 'output format type. (default "auto")'
+        alternatives: -o
+        choices: [ auto, a, yaml, "y", json, j, props, p, csv, c, tsv, t, xml, x, base64, uri, toml, shell, s, lua, l ]
+      - name: --pretty_print
+        type: boolean_true
+        description: pretty print, shorthand for '... style = ""'
+        alternatives: -P
+
+resources:
+  - type: bash_script
+    text: |
+      #!/bin/sh
+      [[ "$par_pretty_print" == "false" ]] && unset par_pretty_print
+      yq eval \
+        ${par_indent:+-I "${par_indent}"} \
+        ${par_input_format:+-p "${par_input_format}"} \
+        ${par_output_format:+-o "${par_output_format}"} \
+        ${par_pretty_print:+-P} \
+        --expression "$par_eval" \
+        --no-colors \
+        "$par_input" > "$par_output"
+test_resources:
+  - type: bash_script
+    text: |
+      set -e
+      echo "name: 'bar'" > test.yaml
+      "$meta_executable" --input test.yaml --output output.yaml --eval '.name = "foo"'
+      "$meta_executable" --input output.yaml --output output2.yaml --eval '.name'
+      grep "^foo$" output2.yaml
+
+engines:
+  - type: docker
+    image: alpine:latest
+    setup:
+      - type: apk
+        packages: [bash, yq-go]
+      - type: docker
+        run: |
+          /usr/bin/yq --version | sed 's/.*version\sv\(.*\)/yq: "\1"/' > /var/software_versions.txt
+runners:
+  - type: executable
+  - type: nextflow
--- a/src/yq/help.txt
+++ b/src/yq/help.txt
@@ -0,0 +1,72 @@
+yq is a portable command-line data file processor (https://github.com/mikefarah/yq/) 
+See https://mikefarah.gitbook.io/yq/ for detailed documentation and examples.
+
+Usage:
+  yq [flags]
+  yq [command]
+
+Examples:
+
+# yq tries to auto-detect the file format based off the extension, and defaults to YAML if it's unknown (or piping through STDIN)
+# Use the '-p/--input-format' flag to specify a format type.
+cat file.xml | yq -p xml
+
+# read the "stuff" node from "myfile.yml"
+yq '.stuff' < myfile.yml
+
+# update myfile.yml in place
+yq -i '.stuff = "foo"' myfile.yml
+
+# print contents of sample.json as idiomatic YAML
+yq -P -oy sample.json
+
+
+Available Commands:
+  completion  Generate the autocompletion script for the specified shell
+  eval        (default) Apply the expression to each document in each yaml file in sequence
+  eval-all    Loads _all_ yaml documents of _all_ yaml files and runs expression once
+  help        Help about any command
+
+Flags:
+  -C, --colors                        force print with colors
+      --csv-auto-parse                parse CSV YAML/JSON values (default true)
+      --csv-separator char            CSV Separator character (default ,)
+  -e, --exit-status                   set exit status if there are no matches or null or false is returned
+      --expression string             forcibly set the expression argument. Useful when yq argument detection thinks your expression is a file.
+      --from-file string              Load expression from specified file.
+  -f, --front-matter string           (extract|process) first input as yaml front-matter. Extract will pull out the yaml content, process will run the expression against the yaml content, leaving the remaining data intact
+      --header-preprocess             Slurp any header comments and separators before processing expression. (default true)
+  -h, --help                          help for yq
+  -I, --indent int                    sets indent level for output (default 2)
+  -i, --inplace                       update the file in place of first file given.
+  -p, --input-format string           [auto|a|yaml|y|json|j|props|p|csv|c|tsv|t|xml|x|base64|uri|toml|lua|l] parse format for input. (default "auto")
+      --lua-globals                   output keys as top-level global variables
+      --lua-prefix string             prefix (default "return ")
+      --lua-suffix string             suffix (default ";\n")
+      --lua-unquoted                  output unquoted string keys (e.g. {foo="bar"})
+  -M, --no-colors                     force print with no colors
+  -N, --no-doc                        Don't print document separators (---)
+  -0, --nul-output                    Use NUL char to separate values. If unwrap scalar is also set, fail if unwrapped scalar contains NUL char.
+  -n, --null-input                    Don't read input, simply evaluate the expression given. Useful for creating docs from scratch.
+  -o, --output-format string          [auto|a|yaml|y|json|j|props|p|csv|c|tsv|t|xml|x|base64|uri|toml|shell|s|lua|l] output format type. (default "auto")
+  -P, --prettyPrint                   pretty print, shorthand for '... style = ""'
+      --properties-array-brackets     use [x] in array paths (e.g. for SpringBoot)
+      --properties-separator string   separator to use between keys and values (default " = ")
+  -s, --split-exp string              print each result (or doc) into a file named (exp). [exp] argument must return a string. You can use $index in the expression as the result counter.
+      --split-exp-file string         Use a file to specify the split-exp expression.
+      --string-interpolation          Toggles strings interpolation of \(exp) (default true)
+      --tsv-auto-parse                parse TSV YAML/JSON values (default true)
+  -r, --unwrapScalar                  unwrap scalar, print the value with no quotes, colors or comments. Defaults to true for yaml (default true)
+  -v, --verbose                       verbose mode
+  -V, --version                       Print version information and quit
+      --xml-attribute-prefix string   prefix for xml attributes (default "+@")
+      --xml-content-name string       name for xml content (if no attribute name is present). (default "+content")
+      --xml-directive-name string     name for xml directives (e.g. <!DOCTYPE thing cat>) (default "+directive")
+      --xml-keep-namespace            enables keeping namespace after parsing attributes (default true)
+      --xml-proc-inst-prefix string   prefix for xml processing instructions (e.g. <?xml version="1"?>) (default "+p_")
+      --xml-raw-token                 enables using RawToken method instead Token. Commonly disables namespace translations. See https://pkg.go.dev/encoding/xml#Decoder.RawToken for details. (default true)
+      --xml-skip-directives           skip over directives (e.g. <!DOCTYPE thing cat>)
+      --xml-skip-proc-inst            skip over process instructions (e.g. <?xml version="1"?>)
+      --xml-strict-mode               enables strict parsing of XML. See https://pkg.go.dev/encoding/xml for more details.
+
+Use "yq [command] --help" for more information about a command.
--- a/target/.build.yaml
+++ b/target/.build.yaml
--- a/target/executable/bgzip/.config.vsh.yaml
+++ b/target/executable/bgzip/.config.vsh.yaml
@@ -0,0 +1,268 @@
+name: "bgzip"
+version: "v0.1.1"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "file to be compressed or decompressed"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "compressed or decompressed output"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--index_name"
+    alternatives:
+    - "-I"
+    description: "name of BGZF index file [file.gz.gzi]"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "integer"
+    name: "--offset"
+    alternatives:
+    - "-b"
+    description: "decompress at virtual file pointer (0-based uncompressed offset)"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--decompress"
+    alternatives:
+    - "-d"
+    description: "decompress the input file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--rebgzip"
+    alternatives:
+    - "-g"
+    description: "use an index file to bgzip a file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--index"
+    alternatives:
+    - "-i"
+    description: "compress and create BGZF index"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--compress_level"
+    alternatives:
+    - "-l"
+    description: "compression level to use when compressing; 0 to 9, or -1 for default\
+      \ [-1]"
+    info: null
+    required: false
+    min: -1
+    max: 9
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--reindex"
+    alternatives:
+    - "-r"
+    description: "(re)index the output file"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--size"
+    alternatives:
+    - "-s"
+    description: "decompress INT bytes (uncompressed size)"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--test"
+    alternatives:
+    - "-t"
+    description: "test integrity of compressed file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--binary"
+    description: "Don't align blocks with text lines"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Block compression/decompression utility"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+references:
+  doi:
+  - "10.1093/gigascience/giab007"
+links:
+  repository: "https://github.com/samtools/htslib"
+  homepage: "https://www.htslib.org/"
+  documentation: "https://www.htslib.org/doc/bgzip.html"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/htslib:1.19--h81da01d_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.1.1"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "bgzip -h | grep 'Version:' 2>&1 |  sed 's/Version:\\s\\(.*\\)/bgzip: \"\\1\"\
+      /' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bgzip/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/bgzip"
+  executable: "target/executable/bgzip/bgzip"
+  viash_version: "0.9.4"
+  git_commit: "2c079795592b75ecd0db2bacaf0b748fa84e1293"
+  git_remote: "https://github.com/viash-hub/toolbox"
+  git_tag: "v0.1.0-13-g2c07979"
+package_config:
+  name: "toolbox"
+  version: "v0.1.1"
+  summary: "A collection of curated command-line tools for general IT tasks, built\
+    \ with Viash.\n"
+  description: "`toolbox` provides a versatile suite of IT components, following the\
+    \ robust Viash (https://viash.io) framework.\nThis package focuses on delivering\
+    \ reliable, standalone tools that can be easily integrated into larger computational\
+    \ workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**,\
+    \ and adherence to **best practices** in component creation. Key features of `toolbox`\
+    \ components include:\n\n* **Standalone & Nextflow Ready:** Execute components\
+    \ directly from the command line or seamlessly incorporate them into Nextflow\
+    \ workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation\
+    \ for each component and its parameters.\n    * Full exposure of the underlying\
+    \ tool's arguments for maximum flexibility.\n    * Containerized (Docker) to ensure\
+    \ consistent environments and manage dependencies, leading to enhanced reproducibility.\n\
+    \    * Unit tested to verify functionality and ensure reliability.\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 := 'v0.1.1'"
+  keywords:
+  - "toolbox"
+  - "command-line"
+  - "tools"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/toolbox"
+    issue_tracker: "https://github.com/viash-hub/toolbox/issues"
--- a/target/executable/bgzip/bgzip
+++ b/target/executable/bgzip/bgzip
--- a/target/executable/yq/.config.vsh.yaml
+++ b/target/executable/yq/.config.vsh.yaml
@@ -0,0 +1,298 @@
+name: "yq"
+version: "v0.1.1"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "files to be processed"
+    info: null
+    example:
+    - "input.yaml"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "output file"
+    info: null
+    example:
+    - "output.yaml"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--eval"
+    description: "expression to evaluate"
+    info: null
+    example:
+    - ".name = \"foo\""
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--indent"
+    alternatives:
+    - "-I"
+    description: "sets indent level for output (default 2)"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_format"
+    alternatives:
+    - "-p"
+    description: "parse format for input. (default \"auto\")"
+    info: null
+    required: false
+    choices:
+    - "auto"
+    - "a"
+    - "yaml"
+    - "y"
+    - "json"
+    - "j"
+    - "props"
+    - "p"
+    - "csv"
+    - "c"
+    - "tsv"
+    - "t"
+    - "xml"
+    - "x"
+    - "base64"
+    - "uri"
+    - "toml"
+    - "shell"
+    - "s"
+    - "lua"
+    - "l"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_format"
+    alternatives:
+    - "-o"
+    description: "output format type. (default \"auto\")"
+    info: null
+    required: false
+    choices:
+    - "auto"
+    - "a"
+    - "yaml"
+    - "y"
+    - "json"
+    - "j"
+    - "props"
+    - "p"
+    - "csv"
+    - "c"
+    - "tsv"
+    - "t"
+    - "xml"
+    - "x"
+    - "base64"
+    - "uri"
+    - "toml"
+    - "shell"
+    - "s"
+    - "lua"
+    - "l"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--pretty_print"
+    alternatives:
+    - "-P"
+    description: "pretty print, shorthand for '... style = \"\"'"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  text: |
+    #!/bin/sh
+    [[ "$par_pretty_print" == "false" ]] && unset par_pretty_print
+    yq eval \
+      ${par_indent:+-I "${par_indent}"} \
+      ${par_input_format:+-p "${par_input_format}"} \
+      ${par_output_format:+-o "${par_output_format}"} \
+      ${par_pretty_print:+-P} \
+      --expression "$par_eval" \
+      --no-colors \
+      "$par_input" > "$par_output"
+    
+
+  dest: "./script.sh"
+  is_executable: true
+description: "A portable YAML, JSON, XML, CSV, TOML and properties processor"
+test_resources:
+- type: "bash_script"
+  text: "set -e\necho \"name: 'bar'\" > test.yaml\n\"$meta_executable\" --input test.yaml\
+    \ --output output.yaml --eval '.name = \"foo\"'\n\"$meta_executable\" --input\
+    \ output.yaml --output output2.yaml --eval '.name'\ngrep \"^foo$\" output2.yaml\n"
+  dest: "./script.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "yaml"
+- "json"
+- "xml"
+- "csv"
+- "toml"
+- "properties"
+license: "MIT"
+links:
+  repository: "https://github.com/mikefarah/yq"
+  homepage: "https://mikefarah.gitbook.io/yq"
+  documentation: "https://mikefarah.gitbook.io/yq/"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "v0.1.1"
+  namespace_separator: "/"
+  setup:
+  - type: "apk"
+    packages:
+    - "bash"
+    - "yq-go"
+  - type: "docker"
+    run:
+    - "/usr/bin/yq --version | sed 's/.*version\\sv\\(.*\\)/yq: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/yq/config.vsh.yaml"
+  runner: "executable"
+  engine: "docker|native"
+  output: "target/executable/yq"
+  executable: "target/executable/yq/yq"
+  viash_version: "0.9.4"
+  git_commit: "2c079795592b75ecd0db2bacaf0b748fa84e1293"
+  git_remote: "https://github.com/viash-hub/toolbox"
+  git_tag: "v0.1.0-13-g2c07979"
+package_config:
+  name: "toolbox"
+  version: "v0.1.1"
+  summary: "A collection of curated command-line tools for general IT tasks, built\
+    \ with Viash.\n"
+  description: "`toolbox` provides a versatile suite of IT components, following the\
+    \ robust Viash (https://viash.io) framework.\nThis package focuses on delivering\
+    \ reliable, standalone tools that can be easily integrated into larger computational\
+    \ workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**,\
+    \ and adherence to **best practices** in component creation. Key features of `toolbox`\
+    \ components include:\n\n* **Standalone & Nextflow Ready:** Execute components\
+    \ directly from the command line or seamlessly incorporate them into Nextflow\
+    \ workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation\
+    \ for each component and its parameters.\n    * Full exposure of the underlying\
+    \ tool's arguments for maximum flexibility.\n    * Containerized (Docker) to ensure\
+    \ consistent environments and manage dependencies, leading to enhanced reproducibility.\n\
+    \    * Unit tested to verify functionality and ensure reliability.\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 := 'v0.1.1'"
+  keywords:
+  - "toolbox"
+  - "command-line"
+  - "tools"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/toolbox"
+    issue_tracker: "https://github.com/viash-hub/toolbox/issues"
--- a/target/executable/yq/yq
+++ b/target/executable/yq/yq
--- a/target/nextflow/bgzip/.config.vsh.yaml
+++ b/target/nextflow/bgzip/.config.vsh.yaml
@@ -0,0 +1,268 @@
+name: "bgzip"
+version: "v0.1.1"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "file to be compressed or decompressed"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "compressed or decompressed output"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+  - type: "file"
+    name: "--index_name"
+    alternatives:
+    - "-I"
+    description: "name of BGZF index file [file.gz.gzi]"
+    info: null
+    must_exist: true
+    create_parent: true
+    required: false
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "integer"
+    name: "--offset"
+    alternatives:
+    - "-b"
+    description: "decompress at virtual file pointer (0-based uncompressed offset)"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--decompress"
+    alternatives:
+    - "-d"
+    description: "decompress the input file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--rebgzip"
+    alternatives:
+    - "-g"
+    description: "use an index file to bgzip a file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--index"
+    alternatives:
+    - "-i"
+    description: "compress and create BGZF index"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--compress_level"
+    alternatives:
+    - "-l"
+    description: "compression level to use when compressing; 0 to 9, or -1 for default\
+      \ [-1]"
+    info: null
+    required: false
+    min: -1
+    max: 9
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--reindex"
+    alternatives:
+    - "-r"
+    description: "(re)index the output file"
+    info: null
+    direction: "input"
+  - type: "integer"
+    name: "--size"
+    alternatives:
+    - "-s"
+    description: "decompress INT bytes (uncompressed size)"
+    info: null
+    required: false
+    min: 0
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--test"
+    alternatives:
+    - "-t"
+    description: "test integrity of compressed file"
+    info: null
+    direction: "input"
+  - type: "boolean_true"
+    name: "--binary"
+    description: "Don't align blocks with text lines"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  path: "script.sh"
+  is_executable: true
+description: "Block compression/decompression utility"
+test_resources:
+- type: "bash_script"
+  path: "test.sh"
+  is_executable: true
+- type: "file"
+  path: "test_data"
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+license: "MIT"
+references:
+  doi:
+  - "10.1093/gigascience/giab007"
+links:
+  repository: "https://github.com/samtools/htslib"
+  homepage: "https://www.htslib.org/"
+  documentation: "https://www.htslib.org/doc/bgzip.html"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$id"
+  auto:
+    simplifyInput: true
+    simplifyOutput: false
+    transcript: false
+    publish: false
+  config:
+    labels:
+      mem1gb: "memory = 1000000000.B"
+      mem2gb: "memory = 2000000000.B"
+      mem5gb: "memory = 5000000000.B"
+      mem10gb: "memory = 10000000000.B"
+      mem20gb: "memory = 20000000000.B"
+      mem50gb: "memory = 50000000000.B"
+      mem100gb: "memory = 100000000000.B"
+      mem200gb: "memory = 200000000000.B"
+      mem500gb: "memory = 500000000000.B"
+      mem1tb: "memory = 1000000000000.B"
+      mem2tb: "memory = 2000000000000.B"
+      mem5tb: "memory = 5000000000000.B"
+      mem10tb: "memory = 10000000000000.B"
+      mem20tb: "memory = 20000000000000.B"
+      mem50tb: "memory = 50000000000000.B"
+      mem100tb: "memory = 100000000000000.B"
+      mem200tb: "memory = 200000000000000.B"
+      mem500tb: "memory = 500000000000000.B"
+      mem1gib: "memory = 1073741824.B"
+      mem2gib: "memory = 2147483648.B"
+      mem4gib: "memory = 4294967296.B"
+      mem8gib: "memory = 8589934592.B"
+      mem16gib: "memory = 17179869184.B"
+      mem32gib: "memory = 34359738368.B"
+      mem64gib: "memory = 68719476736.B"
+      mem128gib: "memory = 137438953472.B"
+      mem256gib: "memory = 274877906944.B"
+      mem512gib: "memory = 549755813888.B"
+      mem1tib: "memory = 1099511627776.B"
+      mem2tib: "memory = 2199023255552.B"
+      mem4tib: "memory = 4398046511104.B"
+      mem8tib: "memory = 8796093022208.B"
+      mem16tib: "memory = 17592186044416.B"
+      mem32tib: "memory = 35184372088832.B"
+      mem64tib: "memory = 70368744177664.B"
+      mem128tib: "memory = 140737488355328.B"
+      mem256tib: "memory = 281474976710656.B"
+      mem512tib: "memory = 562949953421312.B"
+      cpu1: "cpus = 1"
+      cpu2: "cpus = 2"
+      cpu5: "cpus = 5"
+      cpu10: "cpus = 10"
+      cpu20: "cpus = 20"
+      cpu50: "cpus = 50"
+      cpu100: "cpus = 100"
+      cpu200: "cpus = 200"
+      cpu500: "cpus = 500"
+      cpu1000: "cpus = 1000"
+  debug: false
+  container: "docker"
+engines:
+- type: "docker"
+  id: "docker"
+  image: "quay.io/biocontainers/htslib:1.19--h81da01d_0"
+  target_registry: "images.viash-hub.com"
+  target_tag: "v0.1.1"
+  namespace_separator: "/"
+  setup:
+  - type: "docker"
+    run:
+    - "bgzip -h | grep 'Version:' 2>&1 |  sed 's/Version:\\s\\(.*\\)/bgzip: \"\\1\"\
+      /' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/bgzip/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/bgzip"
+  executable: "target/nextflow/bgzip/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "2c079795592b75ecd0db2bacaf0b748fa84e1293"
+  git_remote: "https://github.com/viash-hub/toolbox"
+  git_tag: "v0.1.0-13-g2c07979"
+package_config:
+  name: "toolbox"
+  version: "v0.1.1"
+  summary: "A collection of curated command-line tools for general IT tasks, built\
+    \ with Viash.\n"
+  description: "`toolbox` provides a versatile suite of IT components, following the\
+    \ robust Viash (https://viash.io) framework.\nThis package focuses on delivering\
+    \ reliable, standalone tools that can be easily integrated into larger computational\
+    \ workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**,\
+    \ and adherence to **best practices** in component creation. Key features of `toolbox`\
+    \ components include:\n\n* **Standalone & Nextflow Ready:** Execute components\
+    \ directly from the command line or seamlessly incorporate them into Nextflow\
+    \ workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation\
+    \ for each component and its parameters.\n    * Full exposure of the underlying\
+    \ tool's arguments for maximum flexibility.\n    * Containerized (Docker) to ensure\
+    \ consistent environments and manage dependencies, leading to enhanced reproducibility.\n\
+    \    * Unit tested to verify functionality and ensure reliability.\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 := 'v0.1.1'"
+  keywords:
+  - "toolbox"
+  - "command-line"
+  - "tools"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/toolbox"
+    issue_tracker: "https://github.com/viash-hub/toolbox/issues"
--- a/target/nextflow/bgzip/main.nf
+++ b/target/nextflow/bgzip/main.nf
--- a/target/nextflow/bgzip/nextflow.config
+++ b/target/nextflow/bgzip/nextflow.config
@@ -0,0 +1,125 @@
+manifest {
+  name = 'bgzip'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.1.1'
+  description = 'Block compression/decompression utility'
+}
+
+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 }
+}
+
+
--- a/target/nextflow/bgzip/nextflow_schema.json
+++ b/target/nextflow/bgzip/nextflow_schema.json
@@ -0,0 +1,216 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "bgzip",
+"description": "Block compression/decompression utility",
+"type": "object",
+"definitions": {
+
+    
+    
+    "inputs" : {
+    "title": "Inputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required. file to be compressed or decompressed",
+                "help_text": "Type: `file`, required. file to be compressed or decompressed"
+            
+            }
+    
+
+}
+},
+    
+    
+    "outputs" : {
+    "title": "Outputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output`. compressed or decompressed output",
+                "help_text": "Type: `file`, required, default: `$id.$key.output`. compressed or decompressed output"
+            ,
+                "default":"$id.$key.output"
+            }
+    
+
+        ,
+                "index_name": {
+                "type":
+                "string",
+                "description": "Type: `file`, default: `$id.$key.index_name`. name of BGZF index file [file",
+                "help_text": "Type: `file`, default: `$id.$key.index_name`. name of BGZF index file [file.gz.gzi]"
+            ,
+                "default":"$id.$key.index_name"
+            }
+    
+
+}
+},
+    
+    
+    "arguments" : {
+    "title": "Arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "offset": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. decompress at virtual file pointer (0-based uncompressed offset)",
+                "help_text": "Type: `integer`. decompress at virtual file pointer (0-based uncompressed offset)"
+            
+            }
+    
+
+        ,
+                "decompress": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. decompress the input file",
+                "help_text": "Type: `boolean_true`, default: `false`. decompress the input file"
+            ,
+                "default":false
+            }
+    
+
+        ,
+                "rebgzip": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. use an index file to bgzip a file",
+                "help_text": "Type: `boolean_true`, default: `false`. use an index file to bgzip a file"
+            ,
+                "default":false
+            }
+    
+
+        ,
+                "index": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. compress and create BGZF index",
+                "help_text": "Type: `boolean_true`, default: `false`. compress and create BGZF index"
+            ,
+                "default":false
+            }
+    
+
+        ,
+                "compress_level": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. compression level to use when compressing; 0 to 9, or -1 for default [-1]",
+                "help_text": "Type: `integer`. compression level to use when compressing; 0 to 9, or -1 for default [-1]"
+            
+            }
+    
+
+        ,
+                "reindex": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. (re)index the output file",
+                "help_text": "Type: `boolean_true`, default: `false`. (re)index the output file"
+            ,
+                "default":false
+            }
+    
+
+        ,
+                "size": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. decompress INT bytes (uncompressed size)",
+                "help_text": "Type: `integer`. decompress INT bytes (uncompressed size)"
+            
+            }
+    
+
+        ,
+                "test": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. test integrity of compressed file",
+                "help_text": "Type: `boolean_true`, default: `false`. test integrity of compressed file"
+            ,
+                "default":false
+            }
+    
+
+        ,
+                "binary": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. Don\u0027t align blocks with text lines",
+                "help_text": "Type: `boolean_true`, default: `false`. Don\u0027t align blocks with text lines"
+            ,
+                "default":false
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/inputs"
+    },
+
+    {
+    "$ref": "#/definitions/outputs"
+    },
+
+    {
+    "$ref": "#/definitions/arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}
--- a/target/nextflow/yq/.config.vsh.yaml
+++ b/target/nextflow/yq/.config.vsh.yaml
@@ -0,0 +1,298 @@
+name: "yq"
+version: "v0.1.1"
+argument_groups:
+- name: "Inputs"
+  arguments:
+  - type: "file"
+    name: "--input"
+    description: "files to be processed"
+    info: null
+    example:
+    - "input.yaml"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+- name: "Outputs"
+  arguments:
+  - type: "file"
+    name: "--output"
+    description: "output file"
+    info: null
+    example:
+    - "output.yaml"
+    must_exist: true
+    create_parent: true
+    required: true
+    direction: "output"
+    multiple: false
+    multiple_sep: ";"
+- name: "Arguments"
+  arguments:
+  - type: "string"
+    name: "--eval"
+    description: "expression to evaluate"
+    info: null
+    example:
+    - ".name = \"foo\""
+    required: true
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "integer"
+    name: "--indent"
+    alternatives:
+    - "-I"
+    description: "sets indent level for output (default 2)"
+    info: null
+    required: false
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--input_format"
+    alternatives:
+    - "-p"
+    description: "parse format for input. (default \"auto\")"
+    info: null
+    required: false
+    choices:
+    - "auto"
+    - "a"
+    - "yaml"
+    - "y"
+    - "json"
+    - "j"
+    - "props"
+    - "p"
+    - "csv"
+    - "c"
+    - "tsv"
+    - "t"
+    - "xml"
+    - "x"
+    - "base64"
+    - "uri"
+    - "toml"
+    - "shell"
+    - "s"
+    - "lua"
+    - "l"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "string"
+    name: "--output_format"
+    alternatives:
+    - "-o"
+    description: "output format type. (default \"auto\")"
+    info: null
+    required: false
+    choices:
+    - "auto"
+    - "a"
+    - "yaml"
+    - "y"
+    - "json"
+    - "j"
+    - "props"
+    - "p"
+    - "csv"
+    - "c"
+    - "tsv"
+    - "t"
+    - "xml"
+    - "x"
+    - "base64"
+    - "uri"
+    - "toml"
+    - "shell"
+    - "s"
+    - "lua"
+    - "l"
+    direction: "input"
+    multiple: false
+    multiple_sep: ";"
+  - type: "boolean_true"
+    name: "--pretty_print"
+    alternatives:
+    - "-P"
+    description: "pretty print, shorthand for '... style = \"\"'"
+    info: null
+    direction: "input"
+resources:
+- type: "bash_script"
+  text: |
+    #!/bin/sh
+    [[ "$par_pretty_print" == "false" ]] && unset par_pretty_print
+    yq eval \
+      ${par_indent:+-I "${par_indent}"} \
+      ${par_input_format:+-p "${par_input_format}"} \
+      ${par_output_format:+-o "${par_output_format}"} \
+      ${par_pretty_print:+-P} \
+      --expression "$par_eval" \
+      --no-colors \
+      "$par_input" > "$par_output"
+    
+
+  dest: "./script.sh"
+  is_executable: true
+description: "A portable YAML, JSON, XML, CSV, TOML and properties processor"
+test_resources:
+- type: "bash_script"
+  text: "set -e\necho \"name: 'bar'\" > test.yaml\n\"$meta_executable\" --input test.yaml\
+    \ --output output.yaml --eval '.name = \"foo\"'\n\"$meta_executable\" --input\
+    \ output.yaml --output output2.yaml --eval '.name'\ngrep \"^foo$\" output2.yaml\n"
+  dest: "./script.sh"
+  is_executable: true
+info: null
+status: "enabled"
+scope:
+  image: "public"
+  target: "public"
+requirements:
+  commands:
+  - "ps"
+keywords:
+- "yaml"
+- "json"
+- "xml"
+- "csv"
+- "toml"
+- "properties"
+license: "MIT"
+links:
+  repository: "https://github.com/mikefarah/yq"
+  homepage: "https://mikefarah.gitbook.io/yq"
+  documentation: "https://mikefarah.gitbook.io/yq/"
+runners:
+- type: "executable"
+  id: "executable"
+  docker_setup_strategy: "ifneedbepullelsecachedbuild"
+- type: "nextflow"
+  id: "nextflow"
+  directives:
+    tag: "$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: "v0.1.1"
+  namespace_separator: "/"
+  setup:
+  - type: "apk"
+    packages:
+    - "bash"
+    - "yq-go"
+  - type: "docker"
+    run:
+    - "/usr/bin/yq --version | sed 's/.*version\\sv\\(.*\\)/yq: \"\\1\"/' > /var/software_versions.txt\n"
+  entrypoint: []
+  cmd: null
+- type: "native"
+  id: "native"
+build_info:
+  config: "src/yq/config.vsh.yaml"
+  runner: "nextflow"
+  engine: "docker|native"
+  output: "target/nextflow/yq"
+  executable: "target/nextflow/yq/main.nf"
+  viash_version: "0.9.4"
+  git_commit: "2c079795592b75ecd0db2bacaf0b748fa84e1293"
+  git_remote: "https://github.com/viash-hub/toolbox"
+  git_tag: "v0.1.0-13-g2c07979"
+package_config:
+  name: "toolbox"
+  version: "v0.1.1"
+  summary: "A collection of curated command-line tools for general IT tasks, built\
+    \ with Viash.\n"
+  description: "`toolbox` provides a versatile suite of IT components, following the\
+    \ robust Viash (https://viash.io) framework.\nThis package focuses on delivering\
+    \ reliable, standalone tools that can be easily integrated into larger computational\
+    \ workflows.\n\nThe core philosophy emphasizes **reusability**, **reproducibility**,\
+    \ and adherence to **best practices** in component creation. Key features of `toolbox`\
+    \ components include:\n\n* **Standalone & Nextflow Ready:** Execute components\
+    \ directly from the command line or seamlessly incorporate them into Nextflow\
+    \ workflows.\n* **High Quality Standards:**\n    * Comprehensive documentation\
+    \ for each component and its parameters.\n    * Full exposure of the underlying\
+    \ tool's arguments for maximum flexibility.\n    * Containerized (Docker) to ensure\
+    \ consistent environments and manage dependencies, leading to enhanced reproducibility.\n\
+    \    * Unit tested to verify functionality and ensure reliability.\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 := 'v0.1.1'"
+  keywords:
+  - "toolbox"
+  - "command-line"
+  - "tools"
+  license: "MIT"
+  organization: "vsh"
+  links:
+    repository: "https://github.com/viash-hub/toolbox"
+    issue_tracker: "https://github.com/viash-hub/toolbox/issues"
--- a/target/nextflow/yq/main.nf
+++ b/target/nextflow/yq/main.nf
--- a/target/nextflow/yq/nextflow.config
+++ b/target/nextflow/yq/nextflow.config
@@ -0,0 +1,125 @@
+manifest {
+  name = 'yq'
+  mainScript = 'main.nf'
+  nextflowVersion = '!>=20.12.1-edge'
+  version = 'v0.1.1'
+  description = 'A portable YAML, JSON, XML, CSV, TOML and properties processor'
+}
+
+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 }
+}
+
+
--- a/target/nextflow/yq/nextflow_schema.json
+++ b/target/nextflow/yq/nextflow_schema.json
@@ -0,0 +1,164 @@
+{
+"$schema": "http://json-schema.org/draft-07/schema",
+"title": "yq",
+"description": "A portable YAML, JSON, XML, CSV, TOML and properties processor",
+"type": "object",
+"definitions": {
+
+    
+    
+    "inputs" : {
+    "title": "Inputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "input": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, example: `input.yaml`. files to be processed",
+                "help_text": "Type: `file`, required, example: `input.yaml`. files to be processed"
+            
+            }
+    
+
+}
+},
+    
+    
+    "outputs" : {
+    "title": "Outputs",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "output": {
+                "type":
+                "string",
+                "description": "Type: `file`, required, default: `$id.$key.output.yaml`, example: `output.yaml`. output file",
+                "help_text": "Type: `file`, required, default: `$id.$key.output.yaml`, example: `output.yaml`. output file"
+            ,
+                "default":"$id.$key.output.yaml"
+            }
+    
+
+}
+},
+    
+    
+    "arguments" : {
+    "title": "Arguments",
+    "type": "object",
+    "description": "No description",
+    "properties": {
+    
+        
+                "eval": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `.name = \"foo\"`. expression to evaluate",
+                "help_text": "Type: `string`, required, example: `.name = \"foo\"`. expression to evaluate"
+            
+            }
+    
+
+        ,
+                "indent": {
+                "type":
+                "integer",
+                "description": "Type: `integer`. sets indent level for output (default 2)",
+                "help_text": "Type: `integer`. sets indent level for output (default 2)"
+            
+            }
+    
+
+        ,
+                "input_format": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``auto`, `a`, `yaml`, `y`, `json`, `j`, `props`, `p`, `csv`, `c`, `tsv`, `t`, `xml`, `x`, `base64`, `uri`, `toml`, `shell`, `s`, `lua`, `l``. parse format for input",
+                "help_text": "Type: `string`, choices: ``auto`, `a`, `yaml`, `y`, `json`, `j`, `props`, `p`, `csv`, `c`, `tsv`, `t`, `xml`, `x`, `base64`, `uri`, `toml`, `shell`, `s`, `lua`, `l``. parse format for input. (default \"auto\")",
+                "enum": ["auto", "a", "yaml", "y", "json", "j", "props", "p", "csv", "c", "tsv", "t", "xml", "x", "base64", "uri", "toml", "shell", "s", "lua", "l"]
+            
+            
+            }
+    
+
+        ,
+                "output_format": {
+                "type":
+                "string",
+                "description": "Type: `string`, choices: ``auto`, `a`, `yaml`, `y`, `json`, `j`, `props`, `p`, `csv`, `c`, `tsv`, `t`, `xml`, `x`, `base64`, `uri`, `toml`, `shell`, `s`, `lua`, `l``. output format type",
+                "help_text": "Type: `string`, choices: ``auto`, `a`, `yaml`, `y`, `json`, `j`, `props`, `p`, `csv`, `c`, `tsv`, `t`, `xml`, `x`, `base64`, `uri`, `toml`, `shell`, `s`, `lua`, `l``. output format type. (default \"auto\")",
+                "enum": ["auto", "a", "yaml", "y", "json", "j", "props", "p", "csv", "c", "tsv", "t", "xml", "x", "base64", "uri", "toml", "shell", "s", "lua", "l"]
+            
+            
+            }
+    
+
+        ,
+                "pretty_print": {
+                "type":
+                "boolean",
+                "description": "Type: `boolean_true`, default: `false`. pretty print, shorthand for \u0027",
+                "help_text": "Type: `boolean_true`, default: `false`. pretty print, shorthand for \u0027... style = \"\"\u0027"
+            ,
+                "default":false
+            }
+    
+
+}
+},
+    
+    
+    "nextflow input-output arguments" : {
+    "title": "Nextflow input-output arguments",
+    "type": "object",
+    "description": "Input/output parameters for Nextflow itself. Please note that both publishDir and publish_dir are supported but at least one has to be configured.",
+    "properties": {
+    
+        
+                "publish_dir": {
+                "type":
+                "string",
+                "description": "Type: `string`, required, example: `output/`. Path to an output directory",
+                "help_text": "Type: `string`, required, example: `output/`. Path to an output directory."
+            
+            }
+    
+
+        ,
+                "param_list": {
+                "type":
+                "string",
+                "description": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel",
+                "help_text": "Type: `string`, example: `my_params.yaml`. Allows inputting multiple parameter sets to initialise a Nextflow channel. A `param_list` can either be a list of maps, a csv file, a json file, a yaml file, or simply a yaml blob.\n\n* A list of maps (as-is) where the keys of each map corresponds to the arguments of the pipeline. Example: in a `nextflow.config` file: `param_list: [ [\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027], [\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027] ]`.\n* A csv file should have column names which correspond to the different arguments of this pipeline. Example: `--param_list data.csv` with columns `id,input`.\n* A json or a yaml file should be a list of maps, each of which has keys corresponding to the arguments of the pipeline. Example: `--param_list data.json` with contents `[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]`.\n* A yaml blob can also be passed directly as a string. Example: `--param_list \"[ {\u0027id\u0027: \u0027foo\u0027, \u0027input\u0027: \u0027foo.txt\u0027}, {\u0027id\u0027: \u0027bar\u0027, \u0027input\u0027: \u0027bar.txt\u0027} ]\"`.\n\nWhen passing a csv, json or yaml file, relative path names are relativized to the location of the parameter file. No relativation is performed when `param_list` is a list of maps (as-is) or a yaml blob.",
+                "hidden": true
+            
+            }
+    
+
+}
+}
+},
+"allOf": [
+
+    {
+    "$ref": "#/definitions/inputs"
+    },
+
+    {
+    "$ref": "#/definitions/outputs"
+    },
+
+    {
+    "$ref": "#/definitions/arguments"
+    },
+
+    {
+    "$ref": "#/definitions/nextflow input-output arguments"
+    }
+]
+}