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CHANGELOG.md
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# biobox 0.3.2
## MINOR CHANGES
* Update README (PR #177).
# biobox 0.3.1
## NEW FUNCTIONALITY
* `bcl_convert`: add `force` argument (PR #171).
* `cellranger/cellranger_count`: Align fastq files using Cell Ranger count (PR #163).
## MINOR CHANGES
@@ -10,6 +17,10 @@
* Bump viash to `0.9.4` (PR #175).
## DOCUMENTATION
* Update README (PR #176).
# biobox 0.3.0
## NEW FUNCTIONALITY

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# 🌱📦 biobox
[![ViashHub](https://img.shields.io/badge/ViashHub-biobox-7a4baa.png)](https://web.viash-hub.com/packages/biobox)
[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fbiobox-blue.png)](https://github.com/viash-hub/biobox)
[![ViashHub](https://img.shields.io/badge/ViashHub-biobox-7a4baa.svg)](https://www.viash-hub.com/packages/biobox)
[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2Fbiobox-blue.svg)](https://github.com/viash-hub/biobox)
[![GitHub
License](https://img.shields.io/github/license/viash-hub/biobox.png)](https://github.com/viash-hub/biobox/blob/main/LICENSE)
License](https://img.shields.io/github/license/viash-hub/biobox.svg)](https://github.com/viash-hub/biobox/blob/main/LICENSE)
[![GitHub
Issues](https://img.shields.io/github/issues/viash-hub/biobox.png)](https://github.com/viash-hub/biobox/issues)
Issues](https://img.shields.io/github/issues/viash-hub/biobox.svg)](https://github.com/viash-hub/biobox/issues)
[![Viash
version](https://img.shields.io/badge/Viash-v0.9.0--RC6-blue)](https://viash.io)
version](https://img.shields.io/badge/Viash-v0.9.4-blue.svg)](https://viash.io)
A collection of bioinformatics tools for working with sequence data.
A curated collection of high-quality, standalone bioinformatics
components built with [Viash](https://viash.io).
## Objectives
## Introduction
- **Reusability**: Facilitating the use of components across various
projects and contexts.
- **Reproducibility**: Ensuring that components are reproducible and can
be easily shared.
- **Best Practices**: Adhering to established standards in software
development and bioinformatics.
`biobox` offers a suite of reliable bioinformatics components, similar
to [nf-core/modules](https://github.com/nf-core/modules) and
[snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),
but built using the [Viash](https://viash.io) framework.
This approach emphasizes **reusability**, **reproducibility**, and
adherence to **best practices**. Key features of `biobox` components
include:
- **Standalone & Nextflow Ready:** Run components directly via the
command line or seamlessly integrate them into Nextflow workflows.
- **High Quality Standards:**
- Comprehensive documentation for components and parameters.
- Full exposure of underlying tool arguments.
- Containerized (Docker) for dependency management and
reproducibility.
- Unit tested for verified functionality.
## Example Usage
Viash components in biobox can be run in various ways:
``` mermaid lang="mermaid"
flowchart TD
A[biobox v0.3.1] --> 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=biobox&version=v0.3.1&component=arriba&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://biobox@v0.3.1/arriba -- --help
viash run vsh://biobox@v0.3.1/arriba -- \
--bam path/to/input.bam \
--genome path/to/genome.fa \
--gene_annotation path/to/annotation.gtf \
--fusions path/to/output.txt
```
This will run the component with the specified input files and output
the results to the specified output file.
### 3. Via the Nextflow CLI or Seqera Cloud
You can run this component as a Nextflow pipeline.
``` bash
nextflow run https://packages.viash-hub.com/vsh/biobox \
-revision v0.3.1 \
-main-script target/nextflow/arriba/main.nf \
-latest -resume \
-profile docker \
--bam path/to/input.bam \
--genome path/to/genome.fa \
--gene_annotation path/to/annotation.gtf \
--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: arriba
repository: vsh://biobox@v0.3.1
```
**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
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.
## Contribution Guidelines
The contribution guidelines describes which steps you should follow to
contribute a component to this repository.
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
@@ -55,18 +140,3 @@ contribute a component to this repository.
See the
[CONTRIBUTING](https://github.com/viash-hub/biobox/blob/main/CONTRIBUTING.md)
file for more details.
## Support and Community
For support, questions, or to join our community:
- **Issues**: Submit questions or issues via the [GitHub issue
tracker](https://github.com/viash-hub/biobox/issues).
- **Discussions**: Join our discussions via [GitHub
Discussions](https://github.com/viash-hub/biobox/discussions).
## License
This repository is licensed under an MIT license. See the
[LICENSE](https://github.com/viash-hub/biobox/blob/main/LICENSE) file
for details.

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README.qmd
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format: gfm
---
```{r setup, include=FALSE}
project <- yaml::read_yaml("_viash.yaml")
license <- paste0(project$links$repository, "/blob/main/LICENSE")
contributing <- paste0(project$links$repository, "/blob/main/CONTRIBUTING.md")
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$version else "v0.3.1"
comp <- "arriba"
```
# 🌱📦 `r project$name`
# 🌱📦 `r pkg`
[![ViashHub](https://img.shields.io/badge/ViashHub-`r project$name`-7a4baa)](https://web.viash-hub.com/packages/`r project$name`)
[![GitHub](https://img.shields.io/badge/GitHub-viash--hub%2F`r project$name`-blue)](`r project$links$repository`)
[![GitHub License](https://img.shields.io/github/license/viash-hub/`r project$name`)](`r license`)
[![GitHub Issues](https://img.shields.io/github/issues/viash-hub/`r project$name`)](`r project$links$issue_tracker`)
[![Viash version](https://img.shields.io/badge/Viash-v`r gsub("-", "--", project$viash_version)`-blue)](https://viash.io)
[![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$viash_version)`-blue.svg)](https://viash.io)
`r project$description`
`r package$summary`
## Objectives
## Introduction
- **Reusability**: Facilitating the use of components across various projects and contexts.
- **Reproducibility**: Ensuring that components are reproducible and can be easily shared.
- **Best Practices**: Adhering to established standards in software development and bioinformatics.
`r package$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` -- \
--bam path/to/input.bam \
--genome path/to/genome.fa \
--gene_annotation path/to/annotation.gtf \
--fusions path/to/output.txt
```
This will run the component with the specified input files and output the results to the specified output file.
### 3. Via the Nextflow CLI or Seqera Cloud
You can run this component as a Nextflow pipeline.
```bash
nextflow run https://packages.viash-hub.com/vsh/`r pkg` \
-revision `r ver` \
-main-script target/nextflow/`r comp`/main.nf \
-latest -resume \
-profile docker \
--bam path/to/input.bam \
--genome path/to/genome.fa \
--gene_annotation path/to/annotation.gtf \
--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
We encourage contributions from the community. To contribute:
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. **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.
## Contribution Guidelines
The contribution guidelines describes which steps you should follow to contribute a component to this repository.
```{r echo=FALSE}
lines <- readr::read_lines("CONTRIBUTING.md")
@@ -49,14 +121,3 @@ knitr::asis_output(
```
See the [CONTRIBUTING](`r contributing`) file for more details.
## Support and Community
For support, questions, or to join our community:
- **Issues**: Submit questions or issues via the [GitHub issue tracker](`r project$links$issue_tracker`).
- **Discussions**: Join our discussions via [GitHub Discussions](`r project$links$repository`/discussions).
## License
This repository is licensed under an MIT license. See the [LICENSE](`r license`) file for details.

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_viash.yaml
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name: biobox
summary: |
A curated collection of high-quality, standalone bioinformatics components built with [Viash](https://viash.io).
description: |
A collection of bioinformatics tools for working with sequence data.
`biobox` offers a suite of reliable bioinformatics components, similar to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio), but built using the [Viash](https://viash.io) framework.
This approach emphasizes **reusability**, **reproducibility**, and adherence to **best practices**. Key features of `biobox` components include:
* **Standalone & Nextflow Ready:** Run components directly via the command line or seamlessly integrate them into Nextflow workflows.
* **High Quality Standards:**
* Comprehensive documentation for components and parameters.
* Full exposure of underlying tool arguments.
* Containerized (Docker) for dependency management and reproducibility.
* Unit tested for verified functionality.
license: MIT
keywords: [bioinformatics, modules, sequencing]
links:

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name: cellranger_count
namespace: cellranger
summary: Align fastq files using Cell Ranger count.
description: |
Count gene expression and/or feature barcode reads from a single sample and GEM well
keywords: [cellranger, single-cell, rna-seq, alignment, count]
links:
documentation: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count
repository: https://github.com/10XGenomics/cellranger/blob/main/bin/sc_rna/count
homepage: https://www.10xgenomics.com/support/software/cell-ranger/latest
issue_tracker: https://github.com/10XGenomics/cellranger/issues
references:
doi: 10.1038/ncomms14049
license: Proprietary
requirements:
commands: [cellranger]
authors:
- __merge__: /src/_authors/emma_rousseau.yaml
roles: [author]
- __merge__: /src/_authors/robrecht_cannoodt.yaml
roles: [author]
argument_groups:
- name: FASTQ inputs
arguments:
- name: --fastqs
type: file
required: true
multiple: true
example:
["sample_S1_L001_R1_001.fastq.gz", "sample_S1_L001_R2_001.fastq.gz"]
description: The fastq.gz files to align. Can also be a single directory containing fastq.gz files.
# name: --project
# -> not included because it would conflict with our symlink processing of the input files
- name: --description
type: string
description: Sample description to embed in output files
- name: --sample
type: string
description: Prefix of the filenames of FASTQs to select
example: sample_S1
- name: --lanes
type: integer
description: Only use FASTQs from selected lanes.
example: [1, 2, 3]
multiple: true
- name: --libraries
type: file
description: CSV file declaring input library data sources
example: libraries.csv
- name: Reference inputs
arguments:
- name: --transcriptome
type: file
required: true
description: Path of folder containing 10x-compatible transcriptome reference. Can also be a `.tar.gz` file.
example: transcriptome.tar.gz
- name: --feature_ref
type: file
description: Feature reference CSV file, declaring Feature Barcode constructs and associated barcodes
example: feature_ref.csv
- name: Analysis settings
arguments:
- name: --expect_cells
type: integer
description: Expected number of recovered cells, used as input to cell calling algorithm.
- name: --force_cells
type: integer
description: |
Force pipeline to use this number of cells, bypassing cell calling algorithm. Minimum: 10.
- name: --r1_length
type: integer
description: Hard trim the input Read 1 to this length before analysis
- name: --r2_length
type: integer
description: Hard trim the input Read 2 to this length before analysis
- name: --include_introns
type: boolean_true
description: "Include intronic reads in count. Default: true."
- name: --chemistry
type: string
example: "auto"
description: |
Assay configuration.
NOTE: by default the assay configuration is detected automatically, which is the recommended mode. You usually will not need to specify a chemistry.
Options are:
- `'auto'` for autodetection
- `'threeprime'` for Single Cell 3'
- `'fiveprime'` for Single Cell 5'
- `'SC3Pv1'` or `'SC3Pv2'` or `'SC3Pv3'` or `'SC3Pv4'` for
Single Cell 3' v1/v2/v3/v4
- `'SC3Pv3LT'` for Single Cell 3' v3 LT
- `'SC3Pv3HT'` for Single Cell 3' v3 HT
- `'SC5P-PE'` or `'SC5P-PE-v3'` or `'SC5P-R2'` or `'SC5P-R2-v3'` for Single Cell 5', paired-end/R2-only
- `'SC-FB'` for Single Cell Antibody-only 3' v2 or 5'
To analyze the GEX portion of multiome data, chemistry must be set to `'ARC-v1'`.
See the [10x Genomics FAQ](https://kb.10xgenomics.com/hc/en-us/articles/115003764132-How-does-Cell-Ranger-auto-detect-chemistry-) for more information on how chemistry is detected.
- name: --cell_annotation_model
type: string
description: |
Cell annotation model to use. Valid model names can be viewed by
running `cellranger cloud annotation models` or on the
[10x Genomics Support site](https://www.10xgenomics.com/support).
If "auto", uses the default model for the species.
If not provided, does not run cell annotation.
- name: --min_crispr_umi
type: integer
description: |
Minimum CRISPR UMI threshold. Default: 3.
- name: Outputs
arguments:
- name: --output
type: file
direction: output
description: The folder to store the alignment results.
required: true
- name: --create_bam
type: boolean_true
description: |
Enable or disable BAM file generation. Setting this to false
reduces the total computation time and the size of the output
directory (BAM file not generated). We recommend setting
it to true if unsure. See https://10xgen.com/create-bam for
additional guidance.
- name: "--no_secondary"
type: boolean_true
description: Disable secondary analysis, e.g. clustering.
- name: Additional arguments
arguments:
- name: --no_libraries
type: boolean_true
description: |
Proceed with processing using a `--feature_ref` but no Feature Barcode libraries specified with the 'libraries' flag.
- name: --check_library_compatibility
type: boolean_true
description: |
Whether to check for barcode compatibility between libraries.
- name: --tenx_cloud_token
type: file
description: |
The path to the 10x Cloud Analysis user token used to enable cell
annotation. If not provided, will default to the location stored
through cellranger cloud auth setup.
- name: --dry
type: boolean_true
description: |
Do not execute the pipeline. Generate a pipeline invocation (.mro) file and stop.
resources:
- type: bash_script
path: script.sh
test_resources:
- type: bash_script
path: test.sh
engines:
- type: docker
image: quay.io/nf-core/cellranger:8.0.0
setup:
- type: docker
run: |
DEBIAN_FRONTEND=noninteractive apt update && \
apt upgrade -y && apt install -y procps && rm -rf /var/lib/apt/lists/*
- type: docker
run: |
cellranger --version | sed 's/ cellranger-/: /' > /var/software_versions.txt
runners:
- type: executable
- type: nextflow

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```
docker run --rm -it quay.io/nf-core/cellranger:9.0.1 \
cellranger count --help
```
Count gene expression and/or feature barcode reads from a single sample and GEM
well
Usage: cellranger count [OPTIONS] --id <ID> --create-bam <true|false>
Options:
--id <ID>
A unique run id and output folder name [a-zA-Z0-9_-]+
--description <TEXT>
Sample description to embed in output files [default: ]
--transcriptome <PATH>
Path of folder containing 10x-compatible transcriptome reference
--fastqs <PATH>
Path to input FASTQ data
--project <TEXT>
Name of the project folder within a mkfastq or bcl2fastq-generated
folder from which to pick FASTQs
--sample <PREFIX>
Prefix of the filenames of FASTQs to select
--lanes <NUMS>
Only use FASTQs from selected lanes
--libraries <CSV>
CSV file declaring input library data sources
--feature-ref <CSV>
Feature reference CSV file, declaring Feature Barcode constructs and
associated barcodes
--expect-cells <NUM>
Expected number of recovered cells, used as input to cell calling
algorithm
--force-cells <NUM>
Force pipeline to use this number of cells, bypassing cell calling
algorithm. [MINIMUM: 10]
--create-bam <true|false>
Enable or disable BAM file generation. Setting --create-bam=false
reduces the total computation time and the size of the output
directory (BAM file not generated). We recommend setting
--create-bam=true if unsure. See https://10xgen.com/create-bam for
additional guidance [possible values: true, false]
--nosecondary
Disable secondary analysis, e.g. clustering. Optional
--r1-length <NUM>
Hard trim the input Read 1 to this length before analysis
--r2-length <NUM>
Hard trim the input Read 2 to this length before analysis
--include-introns <true|false>
Include intronic reads in count [default: true] [possible values:
true, false]
--chemistry <CHEM>
Assay configuration. NOTE: by default the assay configuration is
detected automatically, which is the recommended mode. You usually
will not need to specify a chemistry. Options are: 'auto' for
autodetection, 'threeprime' for Single Cell 3', 'fiveprime' for
Single Cell 5', 'SC3Pv1' or 'SC3Pv2' or 'SC3Pv3' or 'SC3Pv4' for
Single Cell 3' v1/v2/v3/v4, 'SC3Pv3LT' for Single Cell 3' v3 LT,
'SC3Pv3HT' for Single Cell 3' v3 HT, 'SC5P-PE' or 'SC5P-PE-v3' or
'SC5P-R2' or 'SC5P-R2-v3' for Single Cell 5', paired-end/R2-only,
'SC-FB' for Single Cell Antibody-only 3' v2 or 5'. To analyze the GEX
portion of multiome data, chemistry must be set to 'ARC-v1' [default:
auto]
--no-libraries
Proceed with processing using a --feature-ref but no Feature Barcode
libraries specified with the 'libraries' flag
--check-library-compatibility <true|false>
Whether to check for barcode compatibility between libraries.
[default: true] [possible values: true, false]
--tenx-cloud-token-path <PATH>
The path to the 10x Cloud Analysis user token used to enable cell
annotation. If not provided, will default to the location stored
through cellranger cloud auth setup
--cell-annotation-model <MODEL>
Cell annotation model to use. Valid model names can be viewed by
running `cellranger cloud annotation models` or on the 10x Genomics
Support site (https://www.10xgenomics.com/support). If "auto", uses
the default model for the species. If not provided, does not run cell
annotation
--min-crispr-umi <NUM>
Minimum CRISPR UMI threshold [default: 3]
--dry
Do not execute the pipeline. Generate a pipeline invocation (.mro)
file and stop
--jobmode <MODE>
Job manager to use. Valid options: local (default), sge, lsf, slurm or
path to a .template file. Search for help on "Cluster Mode" at
support.10xgenomics.com for more details on configuring the pipeline
to use a compute cluster
--localcores <NUM>
Set max cores the pipeline may request at one time. Only applies to
local jobs
--localmem <NUM>
Set max GB the pipeline may request at one time. Only applies to local
jobs
--localvmem <NUM>
Set max virtual address space in GB for the pipeline. Only applies to
local jobs
--mempercore <NUM>
Reserve enough threads for each job to ensure enough memory will be
available, assuming each core on your cluster has at least this much
memory available. Only applies to cluster jobmodes
--maxjobs <NUM>
Set max jobs submitted to cluster at one time. Only applies to cluster
jobmodes
--jobinterval <NUM>
Set delay between submitting jobs to cluster, in ms. Only applies to
cluster jobmodes
--overrides <PATH>
The path to a JSON file that specifies stage-level overrides for cores
and memory. Finer-grained than --localcores, --mempercore and
--localmem. Consult https://10xgen.com/resource-override for an
example override file
--output-dir <PATH>
Output the results to this directory
--uiport <PORT>
Serve web UI at http://localhost:PORT
--disable-ui
Do not serve the web UI
--noexit
Keep web UI running after pipestance completes or fails
--nopreflight
Skip preflight checks
-h, --help
Print help

111
src/cellranger/cellranger_count/script.sh Normal file
View File

@@ -0,0 +1,111 @@
#!/bin/bash
set -eo pipefail
## VIASH START
par_fastqs='/opt/cellranger-8.0.0/lib/python/cellranger-tiny-fastq'
par_transcriptome='/opt/cellranger-8.0.0/lib/python/cellranger-tiny-ref'
par_output='test_data/bam'
par_chemistry="auto"
par_expect_cells="3000"
par_secondary_analysis="false"
## VIASH END
## PROCESS INPUT FILES
# We change into the tempdir later, so we need absolute paths.
par_transcriptome=$(realpath $par_transcriptome)
par_output=$(realpath $par_output)
# create temporary directory
tmp_dir=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXXXX")
function clean_up {
rm -rf "$tmp_dir"
}
trap clean_up EXIT
# process inputs
# for every fastq file found, make a symlink into the tempdir
fastq_dir="$tmp_dir/fastqs"
mkdir -p "$fastq_dir"
IFS=";"
for var in $par_fastqs; do
unset IFS
abs_path=$(realpath $var)
if [ -d "$abs_path" ]; then
find "$abs_path" -name *.fastq.gz -exec ln -s {} "$fastq_dir" \;
else
ln -s "$abs_path" "$fastq_dir"
fi
done
# process reference
# Note: should we do this?
if file "${par_transcriptome}" | grep -q 'gzip compressed data'; then
echo "> Untarring transcriptome"
ref_dir="${tmp_dir}/reference"
mkdir -p "${ref_dir}"
tar -xvf "${par_transcriptome}" -C "${ref_dir}"
par_transcriptome="${ref_dir}"
fi
## PROCESS PARAMETERS
# unset flags
[[ "$par_no_secondary" == "false" ]] && unset par_no_secondary
[[ "$par_no_libraries" == "false" ]] && unset par_no_libraries
[[ "$par_dry" == "false" ]] && unset par_dry
# change ifs from ; to ,
par_lanes=${par_lanes//;/,}
# if memory is defined, subtract 2GB from memory
if [[ "$meta_memory_gb" != "" ]]; then
# if memory is less than 2gb, unset it
if [[ "$meta_memory_gb" -lt 2 ]]; then
echo "WARNING: Memory is less than 2GB, unsetting memory requirements"
unset meta_memory_gb
else
meta_memory_gb=$((meta_memory_gb-2))
fi
fi
## RUN CELLRANGER COUNT
echo "> Running cellranger count"
cd "$tmp_dir"
id=run
cellranger count \
--id="$id" \
--fastqs="${fastq_dir}" \
--transcriptome="${par_transcriptome}" \
--disable-ui \
${meta_cpus:+"--localcores=${meta_cpus}"} \
${meta_memory_gb:+"--localmem=${meta_memory_gb}"} \
${par_description:+"--description=${par_description}"} \
${par_sample:+"--sample=${par_sample}"} \
${par_lanes:+"--lanes=${par_lanes}"} \
${par_libraries:+"--libraries=${par_libraries}"} \
${par_feature_ref:+"--feature-ref=${par_feature_ref}"} \
${par_expect_cells:+"--expect-cells=${par_expect_cells}"} \
${par_force_cells:+"--force-cells=${par_force_cells}"} \
${par_create_bam:+"--create-bam=${par_create_bam}"} \
${par_no_secondary:+--nosecondary} \
${par_r1_length:+"--r1-length=${par_r1_length}"} \
${par_r2_length:+"--r2-length=${par_r2_length}"} \
${par_include_introns:+--include-introns=${par_include_introns}} \
${par_chemistry:+"--chemistry=${par_chemistry}"} \
${par_no_libraries:+--no-libraries} \
${par_check_library_compatibility:+"--check-library-compatibility=${par_check_library_compatibility}"} \
${par_cell_annotation_model:+"--cell-annotation-model=${par_cell_annotation_model}"} \
${par_min_cripser_umi:+"--min-cripser-umi=${par_min_cripser_umi}"} \
${par_tenx_cloud_token:+"--tenx-cloud-token-path=${par_tenx_cloud_token}"} \
${par_dry:+--dry-run}
echo "> Copying output"
if [ -d "$id/outs/" ]; then
if [ ! -d "${par_output}" ]; then
mkdir -p "${par_output}"
fi
mv "$id/outs/"* "${par_output}"
fi
exit 0

56
src/cellranger/cellranger_count/test.sh Normal file
View File

@@ -0,0 +1,56 @@
#!/bin/bash
set -e
## VIASH START
## VIASH END
# create temporary directory
tmp_dir=$(mktemp -d "${meta_temp_dir}/${meta_name}-XXXXXXXX")
function clean_up {
rm -rf "${tmp_dir}"
}
trap clean_up EXIT
echo "Copy test data from Cell Ranger installation directory"
mkdir -p "${tmp_dir}/test_data/"
cp -r "/opt/cellranger-8.0.0/external/cellranger_tiny_fastq/" "${tmp_dir}/test_data"
cp -r "/opt/cellranger-8.0.0/external/cellranger_tiny_ref/" "${tmp_dir}/test_data"
input_dir="${tmp_dir}/test_data/cellranger_tiny_fastq"
reference_dir="${tmp_dir}/test_data/cellranger_tiny_ref"
## TEST 1: run with folder input
echo "Running ${meta_name} with folder input"
output_dir="${tmp_dir}/test1/"
mkdir -p "${output_dir}"
"${meta_executable}" \
--fastqs "${input_dir}" \
--transcriptome "${reference_dir}" \
--output "${output_dir}" \
--lanes 1
[[ $? != 0 ]] && echo "Non zero exit code: $?" && exit 1
[[ ! -f "${output_dir}/filtered_feature_bc_matrix.h5" ]] && echo "Output file could not be found!" && exit 1
[[ -f "${output_dir}/possorted_genome_bam.bam" ]] && echo "Output file should not be found!" && exit 1
[[ ! -d "${output_dir}/analysis" ]] && echo "Analysis output directory should exist!" && exit 1
## TEST 2: run with individual file input
echo "Running ${meta_name} with individual file input"
output_dir="${tmp_dir}/test2/"
mkdir -p "${output_dir}"
"${meta_executable}" \
--fastqs "${input_dir}/tinygex_S1_L001_R1_001.fastq.gz" \
--fastqs "${input_dir}/tinygex_S1_L001_R2_001.fastq.gz" \
--transcriptome "${reference_dir}" \
--output "${output_dir}" \
--no_secondary \
--create_bam
[[ $? != 0 ]] && echo "Non zero exit code: $?" && exit 1
[[ ! -f "${output_dir}/filtered_feature_bc_matrix.h5" ]] && echo "Output file could not be found!" && exit 1
[[ ! -f "${output_dir}/possorted_genome_bam.bam" ]] && echo "Output file could not be found!" && exit 1
[[ -d "${output_dir}/analysis" ]] && echo "Analysis output directory should not exist!" && exit 1
echo "All tests succeeded!"

26
src/cellranger/cellranger_mkref/script.sh
View File

@@ -9,9 +9,9 @@ par_output="output.tar.gz"
## VIASH END
# create temporary directory
tmpdir=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXXXX")
tmp_dir=$(mktemp -d "$meta_temp_dir/$meta_name-XXXXXXXX")
function clean_up {
rm -rf "$tmpdir"
rm -rf "$tmp_dir"
}
trap clean_up EXIT
@@ -20,19 +20,31 @@ par_genome_fasta=$(realpath $par_genome_fasta)
par_transcriptome_gtf=$(realpath $par_transcriptome_gtf)
par_output=$(realpath $par_output)
# if memory is defined, subtract 2GB from memory
if [[ "$meta_memory_gb" != "" ]]; then
# if memory is less than 2gb, unset it
if [[ "$meta_memory_gb" -lt 2 ]]; then
echo "WARNING: Memory is less than 2GB, unsetting memory requirements"
unset meta_memory_gb
else
meta_memory_gb=$((meta_memory_gb-2))
fi
fi
echo "> Unzipping input files"
unpigz -c "$par_genome_fasta" > "$tmpdir/genome.fa"
unpigz -c "$par_genome_fasta" > "$tmp_dir/genome.fa"
echo "> Building star index"
cd "$tmpdir"
cd "$tmp_dir"
cellranger mkref \
--fasta "$tmpdir/genome.fa" \
--fasta "$tmp_dir/genome.fa" \
--genes "$par_transcriptome_gtf" \
--genome output \
${par_reference_version:+--ref-version $par_reference_version} \
${meta_cpus:+--nthreads $meta_cpus} \
${meta_memory_gb:+--memgb $(($meta_memory_gb-2))} # always keep 2 gb for the OS itself
${meta_memory_gb:+--memgb ${meta_memory_gb}}
echo "> Creating archive"
tar --use-compress-program="pigz -k " -cf "$par_output" -C "$tmpdir/output" .
tar --use-compress-program="pigz -k " -cf "$par_output" -C "$tmp_dir/output" .
exit 0

17
target/executable/agat/agat_convert_bed2gff/.config.vsh.yaml
View File

@@ -238,13 +238,24 @@ build_info:
output: "target/executable/agat/agat_convert_bed2gff"
executable: "target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_convert_bed2gff/agat_convert_bed2gff
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_bed2gff"
LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_convert_embl2gff/.config.vsh.yaml
View File

@@ -228,13 +228,24 @@ build_info:
output: "target/executable/agat/agat_convert_embl2gff"
executable: "target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_convert_embl2gff/agat_convert_embl2gff
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_embl2gff"
LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_convert_genscan2gff/.config.vsh.yaml
View File

@@ -233,13 +233,24 @@ build_info:
output: "target/executable/agat/agat_convert_genscan2gff"
executable: "target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_convert_genscan2gff/agat_convert_genscan2gff
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_genscan2gff"
LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_convert_mfannot2gff/.config.vsh.yaml
View File

@@ -189,13 +189,24 @@ build_info:
output: "target/executable/agat/agat_convert_mfannot2gff"
executable: "target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_convert_mfannot2gff/agat_convert_mfannot2gff
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_mfannot2gff"
LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_convert_sp_gff2gtf/.config.vsh.yaml
View File

@@ -231,13 +231,24 @@ build_info:
output: "target/executable/agat/agat_convert_sp_gff2gtf"
executable: "target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_convert_sp_gff2gtf/agat_convert_sp_gff2gtf
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2gtf"
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_convert_sp_gff2tsv/.config.vsh.yaml
View File

@@ -191,13 +191,24 @@ build_info:
output: "target/executable/agat/agat_convert_sp_gff2tsv"
executable: "target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_convert_sp_gff2tsv/agat_convert_sp_gff2tsv
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gff2tsv"
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_convert_sp_gxf2gxf/.config.vsh.yaml
View File

@@ -198,13 +198,24 @@ build_info:
output: "target/executable/agat/agat_convert_sp_gxf2gxf"
executable: "target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_convert_sp_gxf2gxf/agat_convert_sp_gxf2gxf
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_convert_sp_gxf2gxf"
LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_sp_add_introns/.config.vsh.yaml
View File

@@ -189,13 +189,24 @@ build_info:
output: "target/executable/agat/agat_sp_add_introns"
executable: "target/executable/agat/agat_sp_add_introns/agat_sp_add_introns"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_sp_add_introns/agat_sp_add_introns
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_add_introns"
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_sp_filter_feature_from_kill_list/.config.vsh.yaml
View File

@@ -239,13 +239,24 @@ build_info:
output: "target/executable/agat/agat_sp_filter_feature_from_kill_list"
executable: "target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_sp_filter_feature_from_kill_list/agat_sp_filter_feature_from_kill_list
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_filter_feature_from_kill_list"
LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_sp_merge_annotations/.config.vsh.yaml
View File

@@ -187,13 +187,24 @@ build_info:
output: "target/executable/agat/agat_sp_merge_annotations"
executable: "target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_sp_merge_annotations/agat_sp_merge_annotations
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_merge_annotations"
LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_sp_statistics/.config.vsh.yaml
View File

@@ -234,13 +234,24 @@ build_info:
output: "target/executable/agat/agat_sp_statistics"
executable: "target/executable/agat/agat_sp_statistics/agat_sp_statistics"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_sp_statistics/agat_sp_statistics
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/.*v\.//; s/\s.*//' | sed 's/^/AGAT: /' > /var/softwa
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_sp_statistics"
LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/agat/agat_sq_stat_basic/.config.vsh.yaml
View File

@@ -230,13 +230,24 @@ build_info:
output: "target/executable/agat/agat_sq_stat_basic"
executable: "target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/agat/agat_sq_stat_basic/agat_sq_stat_basic
View File

@@ -452,9 +452,9 @@ RUN agat --version | sed 's/AGAT\s\(.*\)/agat: "\1"/' > /var/software_versions.t
LABEL org.opencontainers.image.authors="Leïla Paquay"
LABEL org.opencontainers.image.description="Companion container for running component agat agat_sq_stat_basic"
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z"
LABEL org.opencontainers.image.source="https://github.com/NBISweden/AGAT"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/arriba/.config.vsh.yaml
View File

@@ -709,13 +709,24 @@ build_info:
output: "target/executable/arriba"
executable: "target/executable/arriba/arriba"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/arriba/arriba
View File

@@ -452,9 +452,9 @@ RUN arriba -h | grep 'Version:' 2>&1 | sed 's/Version:\s\(.*\)/arriba: "\1"/' >
LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
LABEL org.opencontainers.image.description="Companion container for running component arriba"
LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z"
LABEL org.opencontainers.image.source="https://github.com/suhrig/arriba"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bases2fastq/.config.vsh.yaml
View File

@@ -397,13 +397,24 @@ build_info:
output: "target/executable/bases2fastq"
executable: "target/executable/bases2fastq/bases2fastq"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bases2fastq/bases2fastq
View File

@@ -456,9 +456,9 @@ RUN echo "bases2fastq: $(bases2fastq --version | cut -d' ' -f3)" > /var/software
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component bases2fastq"
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bbmap/bbmap_bbsplit/.config.vsh.yaml
View File

@@ -371,13 +371,24 @@ build_info:
output: "target/executable/bbmap/bbmap_bbsplit"
executable: "target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bbmap/bbmap_bbsplit/bbmap_bbsplit
View File

@@ -454,9 +454,9 @@ cp -r bbmap/* /usr/local/bin
RUN bbsplit.sh --version 2>&1 | awk '/BBMap version/{print "BBMAP:", $NF}' > /var/software_versions.txt
LABEL org.opencontainers.image.description="Companion container for running component bbmap bbmap_bbsplit"
LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z"
LABEL org.opencontainers.image.source="https://github.com/BioInfoTools/BBMap/blob/master/sh/bbsplit.sh"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bcftools/bcftools_annotate/.config.vsh.yaml
View File

@@ -472,13 +472,24 @@ build_info:
output: "target/executable/bcftools/bcftools_annotate"
executable: "target/executable/bcftools/bcftools_annotate/bcftools_annotate"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bcftools/bcftools_annotate/bcftools_annotate
View File

@@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_annotate"
LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bcftools/bcftools_concat/.config.vsh.yaml
View File

@@ -338,13 +338,24 @@ build_info:
output: "target/executable/bcftools/bcftools_concat"
executable: "target/executable/bcftools/bcftools_concat/bcftools_concat"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bcftools/bcftools_concat/bcftools_concat
View File

@@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_concat"
LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bcftools/bcftools_norm/.config.vsh.yaml
View File

@@ -419,13 +419,24 @@ build_info:
output: "target/executable/bcftools/bcftools_norm"
executable: "target/executable/bcftools/bcftools_norm/bcftools_norm"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bcftools/bcftools_norm/bcftools_norm
View File

@@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_norm"
LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bcftools/bcftools_sort/.config.vsh.yaml
View File

@@ -188,13 +188,24 @@ build_info:
output: "target/executable/bcftools/bcftools_sort"
executable: "target/executable/bcftools/bcftools_sort/bcftools_sort"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bcftools/bcftools_sort/bcftools_sort
View File

@@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_sort"
LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bcftools/bcftools_stats/.config.vsh.yaml
View File

@@ -461,13 +461,24 @@ build_info:
output: "target/executable/bcftools/bcftools_stats"
executable: "target/executable/bcftools/bcftools_stats/bcftools_stats"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bcftools/bcftools_stats/bcftools_stats
View File

@@ -456,9 +456,9 @@ RUN echo "bcftools: \"$(bcftools --version | grep 'bcftools' | sed -n 's/^bcftoo
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bcftools bcftools_stats"
LABEL org.opencontainers.image.created="2025-04-29T10:54:42Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:33Z"
LABEL org.opencontainers.image.source="https://github.com/samtools/bcftools"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bcl_convert/.config.vsh.yaml
View File

@@ -431,13 +431,24 @@ build_info:
output: "target/executable/bcl_convert"
executable: "target/executable/bcl_convert/bcl_convert"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bcl_convert/bcl_convert
View File

@@ -462,9 +462,9 @@ RUN echo "bcl-convert: \"$(bcl-convert -V 2>&1 >/dev/null | sed -n '/Version/ s/
LABEL org.opencontainers.image.authors="Toni Verbeiren, Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component bcl_convert"
LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z"
LABEL org.opencontainers.image.source="https://github.com/viash-hub/biobox"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bd_rhapsody/bd_rhapsody_make_reference/.config.vsh.yaml
View File

@@ -277,13 +277,24 @@ build_info:
output: "target/executable/bd_rhapsody/bd_rhapsody_make_reference"
executable: "target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bd_rhapsody/bd_rhapsody_make_reference/bd_rhapsody_make_reference
View File

@@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_make_reference"
LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:35Z"
LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1/Extra_Utilities/"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/.config.vsh.yaml
View File

@@ -1118,13 +1118,24 @@ build_info:
output: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis"
executable: "target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bd_rhapsody/bd_rhapsody_sequence_analysis/bd_rhapsody_sequence_analysis
View File

@@ -465,9 +465,9 @@ RUN VERSION=$(ls -v /var/bd_rhapsody_cwl | grep '^v' | sed 's#v##' | tail -1)
RUN echo "bdgenomics/rhapsody: \"$VERSION\"" > /var/software_versions.txt
LABEL org.opencontainers.image.authors="Robrecht Cannoodt, Weiwei Schultz"
LABEL org.opencontainers.image.description="Companion container for running component bd_rhapsody bd_rhapsody_sequence_analysis"
LABEL org.opencontainers.image.created="2025-04-29T10:54:44Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z"
LABEL org.opencontainers.image.source="https://bitbucket.org/CRSwDev/cwl/src/master/v2.2.1"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_bamtobed/.config.vsh.yaml
View File

@@ -238,13 +238,24 @@ build_info:
output: "target/executable/bedtools/bedtools_bamtobed"
executable: "target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_bamtobed/bedtools_bamtobed
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtobed"
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_bamtofastq/.config.vsh.yaml
View File

@@ -190,13 +190,24 @@ build_info:
output: "target/executable/bedtools/bedtools_bamtofastq"
executable: "target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_bamtofastq/bedtools_bamtofastq
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bamtofastq"
LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_bed12tobed6/.config.vsh.yaml
View File

@@ -179,13 +179,24 @@ build_info:
output: "target/executable/bedtools/bedtools_bed12tobed6"
executable: "target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_bed12tobed6/bedtools_bed12tobed6
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bed12tobed6"
LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_bedtobam/.config.vsh.yaml
View File

@@ -217,13 +217,24 @@ build_info:
output: "target/executable/bedtools/bedtools_bedtobam"
executable: "target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_bedtobam/bedtools_bedtobam
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_bedtobam"
LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_genomecov/.config.vsh.yaml
View File

@@ -340,13 +340,24 @@ build_info:
output: "target/executable/bedtools/bedtools_genomecov"
executable: "target/executable/bedtools/bedtools_genomecov/bedtools_genomecov"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_genomecov/bedtools_genomecov
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_genomecov"
LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_getfasta/.config.vsh.yaml
View File

@@ -235,13 +235,24 @@ build_info:
output: "target/executable/bedtools/bedtools_getfasta"
executable: "target/executable/bedtools/bedtools_getfasta/bedtools_getfasta"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_getfasta/bedtools_getfasta
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Dries Schaumont"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_getfasta"
LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:38Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_groupby/.config.vsh.yaml
View File

@@ -276,13 +276,24 @@ build_info:
output: "target/executable/bedtools/bedtools_groupby"
executable: "target/executable/bedtools/bedtools_groupby/bedtools_groupby"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_groupby/bedtools_groupby
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_groupby"
LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_intersect/.config.vsh.yaml
View File

@@ -413,13 +413,24 @@ build_info:
output: "target/executable/bedtools/bedtools_intersect"
executable: "target/executable/bedtools/bedtools_intersect/bedtools_intersect"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_intersect/bedtools_intersect
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_intersect"
LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_links/.config.vsh.yaml
View File

@@ -213,13 +213,24 @@ build_info:
output: "target/executable/bedtools/bedtools_links"
executable: "target/executable/bedtools/bedtools_links/bedtools_links"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_links/bedtools_links
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_links"
LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:40Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_merge/.config.vsh.yaml
View File

@@ -282,13 +282,24 @@ build_info:
output: "target/executable/bedtools/bedtools_merge"
executable: "target/executable/bedtools/bedtools_merge/bedtools_merge"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_merge/bedtools_merge
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_merge"
LABEL org.opencontainers.image.created="2025-04-29T10:54:48Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/bedtools/bedtools_sort/.config.vsh.yaml
View File

@@ -225,13 +225,24 @@ build_info:
output: "target/executable/bedtools/bedtools_sort"
executable: "target/executable/bedtools/bedtools_sort/bedtools_sort"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/bedtools/bedtools_sort/bedtools_sort
View File

@@ -456,9 +456,9 @@ RUN echo "bedtools: \"$(bedtools --version | sed -n 's/^bedtools //p')\"" > /var
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component bedtools bedtools_sort"
LABEL org.opencontainers.image.created="2025-04-29T10:54:47Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:39Z"
LABEL org.opencontainers.image.source="https://github.com/arq5x/bedtools2"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/busco/busco_download_datasets/.config.vsh.yaml
View File

@@ -161,13 +161,24 @@ build_info:
output: "target/executable/busco/busco_download_datasets"
executable: "target/executable/busco/busco_download_datasets/busco_download_datasets"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/busco/busco_download_datasets/busco_download_datasets
View File

@@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component busco busco_download_datasets"
LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/busco/busco_list_datasets/.config.vsh.yaml
View File

@@ -148,13 +148,24 @@ build_info:
output: "target/executable/busco/busco_list_datasets"
executable: "target/executable/busco/busco_list_datasets/busco_list_datasets"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/busco/busco_list_datasets/busco_list_datasets
View File

@@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component busco busco_list_datasets"
LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/busco/busco_run/.config.vsh.yaml
View File

@@ -426,13 +426,24 @@ build_info:
output: "target/executable/busco/busco_run"
executable: "target/executable/busco/busco_run/busco_run"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/busco/busco_run/busco_run
View File

@@ -452,9 +452,9 @@ RUN busco --version | sed 's/BUSCO\s\(.*\)/busco: "\1"/' > /var/software_version
LABEL org.opencontainers.image.authors="Dorien Roosen"
LABEL org.opencontainers.image.description="Companion container for running component busco busco_run"
LABEL org.opencontainers.image.created="2025-04-29T10:54:45Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:36Z"
LABEL org.opencontainers.image.source="https://gitlab.com/ezlab/busco"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

416
target/executable/cellranger/cellranger_count/.config.vsh.yaml Normal file
View File

@@ -0,0 +1,416 @@
name: "cellranger_count"
namespace: "cellranger"
version: "main"
authors:
- name: "Emma Rousseau"
roles:
- "author"
info:
links:
email: "emma@data-intuitive.com"
github: "emmarousseau"
linkedin: "emmarousseau1"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Bioinformatician"
- name: "Robrecht Cannoodt"
roles:
- "author"
info:
links:
email: "robrecht@data-intuitive.com"
github: "rcannood"
orcid: "0000-0003-3641-729X"
linkedin: "robrechtcannoodt"
organizations:
- name: "Data Intuitive"
href: "https://www.data-intuitive.com"
role: "Data Science Engineer"
- name: "Open Problems"
href: "https://openproblems.bio"
role: "Core Member"
argument_groups:
- name: "FASTQ inputs"
arguments:
- type: "file"
name: "--fastqs"
description: "The fastq.gz files to align. Can also be a single directory containing\
\ fastq.gz files."
info: null
example:
- "sample_S1_L001_R1_001.fastq.gz"
- "sample_S1_L001_R2_001.fastq.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: true
multiple_sep: ";"
- type: "string"
name: "--description"
description: "Sample description to embed in output files"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--sample"
description: "Prefix of the filenames of FASTQs to select"
info: null
example:
- "sample_S1"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--lanes"
description: "Only use FASTQs from selected lanes."
info: null
example:
- 1
- 2
- 3
required: false
direction: "input"
multiple: true
multiple_sep: ";"
- type: "file"
name: "--libraries"
description: "CSV file declaring input library data sources"
info: null
example:
- "libraries.csv"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Reference inputs"
arguments:
- type: "file"
name: "--transcriptome"
description: "Path of folder containing 10x-compatible transcriptome reference.\
\ Can also be a `.tar.gz` file."
info: null
example:
- "transcriptome.tar.gz"
must_exist: true
create_parent: true
required: true
direction: "input"
multiple: false
multiple_sep: ";"
- type: "file"
name: "--feature_ref"
description: "Feature reference CSV file, declaring Feature Barcode constructs\
\ and associated barcodes"
info: null
example:
- "feature_ref.csv"
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Analysis settings"
arguments:
- type: "integer"
name: "--expect_cells"
description: "Expected number of recovered cells, used as input to cell calling\
\ algorithm."
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--force_cells"
description: "Force pipeline to use this number of cells, bypassing cell calling\
\ algorithm. Minimum: 10.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--r1_length"
description: "Hard trim the input Read 1 to this length before analysis"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--r2_length"
description: "Hard trim the input Read 2 to this length before analysis"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--include_introns"
description: "Include intronic reads in count. Default: true."
info: null
direction: "input"
- type: "string"
name: "--chemistry"
description: "Assay configuration.\n\nNOTE: by default the assay configuration\
\ is detected automatically, which is the recommended mode. You usually will\
\ not need to specify a chemistry. \n\nOptions are:\n\n- `'auto'` for autodetection\n\
- `'threeprime'` for Single Cell 3'\n- `'fiveprime'` for Single Cell 5'\n- `'SC3Pv1'`\
\ or `'SC3Pv2'` or `'SC3Pv3'` or `'SC3Pv4'` for\nSingle Cell 3' v1/v2/v3/v4\n\
- `'SC3Pv3LT'` for Single Cell 3' v3 LT\n- `'SC3Pv3HT'` for Single Cell 3' v3\
\ HT\n- `'SC5P-PE'` or `'SC5P-PE-v3'` or `'SC5P-R2'` or `'SC5P-R2-v3'` for Single\
\ Cell 5', paired-end/R2-only\n- `'SC-FB'` for Single Cell Antibody-only 3'\
\ v2 or 5'\n\nTo analyze the GEX portion of multiome data, chemistry must be\
\ set to `'ARC-v1'`.\n\nSee the [10x Genomics FAQ](https://kb.10xgenomics.com/hc/en-us/articles/115003764132-How-does-Cell-Ranger-auto-detect-chemistry-)\
\ for more information on how chemistry is detected.\n"
info: null
example:
- "auto"
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "string"
name: "--cell_annotation_model"
description: "Cell annotation model to use. Valid model names can be viewed by\n\
running `cellranger cloud annotation models` or on the\n[10x Genomics Support\
\ site](https://www.10xgenomics.com/support).\n\nIf \"auto\", uses the default\
\ model for the species.\nIf not provided, does not run cell annotation.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "integer"
name: "--min_crispr_umi"
description: "Minimum CRISPR UMI threshold. Default: 3.\n"
info: null
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- name: "Outputs"
arguments:
- type: "file"
name: "--output"
description: "The folder to store the alignment results."
info: null
must_exist: true
create_parent: true
required: true
direction: "output"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--create_bam"
description: "Enable or disable BAM file generation. Setting this to false\nreduces\
\ the total computation time and the size of the output\ndirectory (BAM file\
\ not generated). We recommend setting\nit to true if unsure. See https://10xgen.com/create-bam\
\ for\nadditional guidance.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--no_secondary"
description: "Disable secondary analysis, e.g. clustering."
info: null
direction: "input"
- name: "Additional arguments"
arguments:
- type: "boolean_true"
name: "--no_libraries"
description: "Proceed with processing using a `--feature_ref` but no Feature Barcode\
\ libraries specified with the 'libraries' flag.\n"
info: null
direction: "input"
- type: "boolean_true"
name: "--check_library_compatibility"
description: "Whether to check for barcode compatibility between libraries.\n"
info: null
direction: "input"
- type: "file"
name: "--tenx_cloud_token"
description: "The path to the 10x Cloud Analysis user token used to enable cell\n\
annotation. If not provided, will default to the location stored\nthrough cellranger\
\ cloud auth setup.\n"
info: null
must_exist: true
create_parent: true
required: false
direction: "input"
multiple: false
multiple_sep: ";"
- type: "boolean_true"
name: "--dry"
description: "Do not execute the pipeline. Generate a pipeline invocation (.mro)\
\ file and stop.\n"
info: null
direction: "input"
resources:
- type: "bash_script"
path: "script.sh"
is_executable: true
summary: "Align fastq files using Cell Ranger count."
description: "Count gene expression and/or feature barcode reads from a single sample\
\ and GEM well\n"
test_resources:
- type: "bash_script"
path: "test.sh"
is_executable: true
info: null
status: "enabled"
scope:
image: "public"
target: "public"
requirements:
commands:
- "ps"
keywords:
- "cellranger"
- "single-cell"
- "rna-seq"
- "alignment"
- "count"
license: "Proprietary"
references:
doi:
- "10.1038/ncomms14049"
links:
repository: "https://github.com/10XGenomics/cellranger/blob/main/bin/sc_rna/count"
homepage: "https://www.10xgenomics.com/support/software/cell-ranger/latest"
documentation: "https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/using/count"
issue_tracker: "https://github.com/10XGenomics/cellranger/issues"
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/nf-core/cellranger:8.0.0"
target_registry: "images.viash-hub.com"
target_tag: "main"
namespace_separator: "/"
setup:
- type: "docker"
run:
- "DEBIAN_FRONTEND=noninteractive apt update && \\\napt upgrade -y && apt install\
\ -y procps && rm -rf /var/lib/apt/lists/*\n"
- type: "docker"
run:
- "cellranger --version | sed 's/ cellranger-/: /' > /var/software_versions.txt\n"
entrypoint: []
cmd: null
- type: "native"
id: "native"
build_info:
config: "src/cellranger/cellranger_count/config.vsh.yaml"
runner: "executable"
engine: "docker|native"
output: "target/executable/cellranger/cellranger_count"
executable: "target/executable/cellranger/cellranger_count/cellranger_count"
viash_version: "0.9.4"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\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 := 'main'"
keywords:
- "bioinformatics"
- "modules"
- "sequencing"
license: "MIT"
organization: "vsh"
links:
repository: "https://github.com/viash-hub/biobox"
issue_tracker: "https://github.com/viash-hub/biobox/issues"

1724
target/executable/cellranger/cellranger_count/cellranger_count Executable file
View File

File diff suppressed because it is too large Load Diff

17
target/executable/cellranger/cellranger_mkref/.config.vsh.yaml
View File

@@ -198,13 +198,24 @@ build_info:
output: "target/executable/cellranger/cellranger_mkref"
executable: "target/executable/cellranger/cellranger_mkref/cellranger_mkref"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

30
target/executable/cellranger/cellranger_mkref/cellranger_mkref
View File

@@ -454,9 +454,9 @@ RUN apt-get update && \
LABEL org.opencontainers.image.authors="Emma Rousseau"
LABEL org.opencontainers.image.description="Companion container for running component cellranger cellranger_mkref"
LABEL org.opencontainers.image.created="2025-04-29T10:54:49Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:41Z"
LABEL org.opencontainers.image.source="https://github.com/10XGenomics/cellranger/blob/main/lib/python/cellranger/reference_builder.py"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER
@@ -1115,9 +1115,9 @@ $( if [ ! -z ${VIASH_META_MEMORY_PIB+x} ]; then echo "${VIASH_META_MEMORY_PIB}"
## VIASH END
# create temporary directory
tmpdir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")
tmp_dir=\$(mktemp -d "\$meta_temp_dir/\$meta_name-XXXXXXXX")
function clean_up {
rm -rf "\$tmpdir"
rm -rf "\$tmp_dir"
}
trap clean_up EXIT
@@ -1126,22 +1126,34 @@ par_genome_fasta=\$(realpath \$par_genome_fasta)
par_transcriptome_gtf=\$(realpath \$par_transcriptome_gtf)
par_output=\$(realpath \$par_output)
# if memory is defined, subtract 2GB from memory
if [[ "\$meta_memory_gb" != "" ]]; then
# if memory is less than 2gb, unset it
if [[ "\$meta_memory_gb" -lt 2 ]]; then
echo "WARNING: Memory is less than 2GB, unsetting memory requirements"
unset meta_memory_gb
else
meta_memory_gb=\$((meta_memory_gb-2))
fi
fi
echo "> Unzipping input files"
unpigz -c "\$par_genome_fasta" > "\$tmpdir/genome.fa"
unpigz -c "\$par_genome_fasta" > "\$tmp_dir/genome.fa"
echo "> Building star index"
cd "\$tmpdir"
cd "\$tmp_dir"
cellranger mkref \\
--fasta "\$tmpdir/genome.fa" \\
--fasta "\$tmp_dir/genome.fa" \\
--genes "\$par_transcriptome_gtf" \\
--genome output \\
\${par_reference_version:+--ref-version \$par_reference_version} \\
\${meta_cpus:+--nthreads \$meta_cpus} \\
\${meta_memory_gb:+--memgb \$((\$meta_memory_gb-2))} # always keep 2 gb for the OS itself
\${meta_memory_gb:+--memgb \${meta_memory_gb}}
echo "> Creating archive"
tar --use-compress-program="pigz -k " -cf "\$par_output" -C "\$tmpdir/output" .
tar --use-compress-program="pigz -k " -cf "\$par_output" -C "\$tmp_dir/output" .
exit 0
VIASHMAIN
bash "\$tempscript" &
wait "\$!"

17
target/executable/cutadapt/.config.vsh.yaml
View File

@@ -743,13 +743,24 @@ build_info:
output: "target/executable/cutadapt"
executable: "target/executable/cutadapt/cutadapt"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/cutadapt/cutadapt
View File

@@ -455,9 +455,9 @@ RUN cutadapt --version | sed 's/\(.*\)/cutadapt: "\1"/' > /var/software_versions
LABEL org.opencontainers.image.authors="Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component cutadapt"
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z"
LABEL org.opencontainers.image.source="https://github.com/marcelm/cutadapt"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/falco/.config.vsh.yaml
View File

@@ -320,13 +320,24 @@ build_info:
output: "target/executable/falco"
executable: "target/executable/falco/falco"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/falco/falco
View File

@@ -464,9 +464,9 @@ RUN echo "falco: \"$(falco -v | sed -n 's/^falco //p')\"" > /var/software_versio
LABEL org.opencontainers.image.authors="Toni Verbeiren"
LABEL org.opencontainers.image.description="Companion container for running component falco"
LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:43Z"
LABEL org.opencontainers.image.source="https://github.com/smithlabcode/falco"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/fastp/.config.vsh.yaml
View File

@@ -1086,13 +1086,24 @@ build_info:
output: "target/executable/fastp"
executable: "target/executable/fastp/fastp"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/fastp/fastp
View File

@@ -452,9 +452,9 @@ RUN fastp --version 2>&1 | sed 's# #: "#;s#$#"#' > /var/software_versions.txt
LABEL org.opencontainers.image.authors="Robrecht Cannoodt"
LABEL org.opencontainers.image.description="Companion container for running component fastp"
LABEL org.opencontainers.image.created="2025-04-29T10:54:43Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:34Z"
LABEL org.opencontainers.image.source="https://github.com/OpenGene/fastp"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/fastqc/.config.vsh.yaml
View File

@@ -343,13 +343,24 @@ build_info:
output: "target/executable/fastqc"
executable: "target/executable/fastqc/fastqc"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/fastqc/fastqc
View File

@@ -452,9 +452,9 @@ RUN echo "fastqc: $(fastqc --version | sed -n 's/^FastQC //p')" > /var/software_
LABEL org.opencontainers.image.authors="Theodoro Gasperin Terra Camargo"
LABEL org.opencontainers.image.description="Companion container for running component fastqc"
LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:43Z"
LABEL org.opencontainers.image.source="https://github.com/s-andrews/FastQC"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/featurecounts/.config.vsh.yaml
View File

@@ -648,13 +648,24 @@ build_info:
output: "target/executable/featurecounts"
executable: "target/executable/featurecounts/featurecounts"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/featurecounts/featurecounts
View File

@@ -452,9 +452,9 @@ RUN featureCounts -v 2>&1 | sed 's/featureCounts v\([0-9.]*\)/featureCounts: \1/
LABEL org.opencontainers.image.authors="Sai Nirmayi Yasa"
LABEL org.opencontainers.image.description="Companion container for running component featurecounts"
LABEL org.opencontainers.image.created="2025-04-29T10:54:46Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:37Z"
LABEL org.opencontainers.image.source="https://github.com/ShiLab-Bioinformatics/subread"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

17
target/executable/fq_subsample/.config.vsh.yaml
View File

@@ -193,13 +193,24 @@ build_info:
output: "target/executable/fq_subsample"
executable: "target/executable/fq_subsample/fq_subsample"
viash_version: "0.9.4"
git_commit: "c733de2e4cc21eccb241060f82bce0b332f79d81"
git_commit: "b0db228825f3441b4651527e8775e8fc87d06e60"
git_remote: "https://github.com/viash-hub/biobox"
git_tag: "v0.2.0-32-gc733de2"
git_tag: "v0.2.0-35-gb0db228"
package_config:
name: "biobox"
version: "main"
description: "A collection of bioinformatics tools for working with sequence data.\n"
summary: "A curated collection of high-quality, standalone bioinformatics components\
\ built with [Viash](https://viash.io).\n"
description: "`biobox` offers a suite of reliable bioinformatics components, similar\
\ to [nf-core/modules](https://github.com/nf-core/modules) and [snakemake-wrappers/bio](https://github.com/snakemake/snakemake-wrappers/tree/master/bio),\
\ but built using the [Viash](https://viash.io) framework.\n\nThis approach emphasizes\
\ **reusability**, **reproducibility**, and adherence to **best practices**. Key\
\ features of `biobox` components include:\n\n* **Standalone & Nextflow Ready:**\
\ Run components directly via the command line or seamlessly integrate them into\
\ Nextflow workflows.\n* **High Quality Standards:**\n * Comprehensive documentation\
\ for components and parameters.\n * Full exposure of underlying tool arguments.\n\
\ * Containerized (Docker) for dependency management and reproducibility.\n\
\ * Unit tested for verified functionality.\n"
info: null
viash_version: "0.9.4"
source: "src"

4
target/executable/fq_subsample/fq_subsample
View File

@@ -453,9 +453,9 @@ mv target/release/fq /usr/local/bin/ && \
cd / && rm -rf /fq
LABEL org.opencontainers.image.description="Companion container for running component fq_subsample"
LABEL org.opencontainers.image.created="2025-04-29T10:54:51Z"
LABEL org.opencontainers.image.created="2025-05-06T20:11:43Z"
LABEL org.opencontainers.image.source="https://github.com/stjude-rust-labs/fq"
LABEL org.opencontainers.image.revision="c733de2e4cc21eccb241060f82bce0b332f79d81"
LABEL org.opencontainers.image.revision="b0db228825f3441b4651527e8775e8fc87d06e60"
LABEL org.opencontainers.image.version="main"
VIASHDOCKER

Some files were not shown because too many files have changed in this diff Show More