We encourage contributions from the community. To contribute:
- Fork the Repository: Start by forking this repository to your account.
- Develop Your Component: Create your Viash component, ensuring it aligns with our best practices (detailed below).
- Submit a Pull Request: After testing your component, submit a pull request for review.
-
Find a tool to contribute to this repo.
-
Check whether it is already in the Project board.
-
Check whether there is a corresponding Snakemake wrapper or nf-core module which we can use as inspiration.
-
Create an issue to show that you are working on this component.
Change all occurrences of xxx
to the name of the component.
Create a file at src/xxx/config.vsh.yaml
with contents:
name: xxx
description: xxx
keywords: [tag1, tag2]
links:
homepage: yyy
documentation: yyy
issue_tracker: yyy
repository: yyy
references:
doi: 12345/12345678.yz
license: MIT/Apache-2.0/GPL-3.0/...
argument_groups:
- name: Inputs
arguments: <...>
- name: Outputs
arguments: <...>
- name: Arguments
arguments: <...>
resources:
- type: bash_script
path: script.sh
test_resources:
- type: bash_script
path: test.sh
- type: file
path: test_data
engines:
- <...>
runners:
- type: executable
- type: nextflow
Fill in the relevant metadata fields in the config. Here is an example of the metadata of an existing component.
name: arriba
description: Detect gene fusions from RNA-Seq data
keywords: [Gene fusion, RNA-Seq]
links:
homepage: https://arriba.readthedocs.io/en/latest/
documentation: https://arriba.readthedocs.io/en/latest/
repository: https://github.com/suhrig/arriba
issue_tracker: https://github.com/suhrig/arriba/issues
references:
doi: 10.1101/gr.257246.119
bibtex: |
@article{
... a bibtex entry in case the doi is not available ...
}
license: MIT
Google biocontainer <name of component>
and find the container that is most suitable. Typically the link will be https://quay.io/repository/biocontainers/xxx?tab=tags
.
If no such container is found, you can create a custom container in the next step.
To help develop the component, we store the --help
output of the tool in a file at src/xxx/help.txt
.
cat <<EOF > src/xxx/help.txt
```sh
xxx --help
```
EOF
docker run quay.io/biocontainers/xxx:tag xxx --help >> src/xxx/help.txt
Notes:
-
This help file has no functional purpose, but it is useful for the developer to see the help output of the tool.
-
Some tools might not have a
--help
argument but instead have a-h
argument. For example, forarriba
, the help message is obtained by runningarriba -h
:docker run quay.io/biocontainers/arriba:2.4.0--h0033a41_2 arriba -h
To help develop the component, it's interesting to have some test data available. In most cases, we can use the test data from the Snakemake wrappers.
To make sure we can reproduce the test data in the future, we store the command to fetch the test data in a file at src/xxx/test_data/script.sh
.
cat <<EOF > src/xxx/test_data/script.sh
# clone repo
if [ ! -d /tmp/snakemake-wrappers ]; then
git clone --depth 1 --single-branch --branch master https://github.com/snakemake/snakemake-wrappers /tmp/snakemake-wrappers
fi
# copy test data
cp -r /tmp/snakemake-wrappers/bio/xxx/test/* src/xxx/test_data
EOF
The test data should be suitable for testing this component. Ensure that the test data is small enough: ideally <1KB, preferably <10KB, if need be <100KB.
By looking at the help file, we add the input arguments to the config file. Here is an example of the input arguments of an existing component.
For instance, in the arriba help file, we see the following:
Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
-g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
[-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
-o fusions.tsv [-O fusions.discarded.tsv] \
[OPTIONS]
-x FILE File in SAM/BAM/CRAM format with main alignments as generated by STAR
(Aligned.out.sam). Arriba extracts candidate reads from this file.
Based on this information, we can add the following input arguments to the config file.
argument_groups:
- name: Inputs
arguments:
- name: --bam
alternatives: -x
type: file
description: |
File in SAM/BAM/CRAM format with main alignments as generated by STAR
(`Aligned.out.sam`). Arriba extracts candidate reads from this file.
required: true
example: Aligned.out.bam
Check the documentation for more information on the format of input arguments.
Several notes:
-
Argument names should be formatted in
--snake_case
. This means arguments like--foo-bar
should be formatted as--foo_bar
, and short arguments like-f
should receive a longer name like--foo
. -
Input arguments can have
multiple: true
to allow the user to specify multiple files. -
The description should be formatted in markdown.
By looking at the help file, we now also add output arguments to the config file.
For example, in the arriba help file, we see the following:
Usage: arriba [-c Chimeric.out.sam] -x Aligned.out.bam \
-g annotation.gtf -a assembly.fa [-b blacklists.tsv] [-k known_fusions.tsv] \
[-t tags.tsv] [-p protein_domains.gff3] [-d structural_variants_from_WGS.tsv] \
-o fusions.tsv [-O fusions.discarded.tsv] \
[OPTIONS]
-o FILE Output file with fusions that have passed all filters.
-O FILE Output file with fusions that were discarded due to filtering.
Based on this information, we can add the following output arguments to the config file.
argument_groups:
- name: Outputs
arguments:
- name: --fusions
alternatives: -o
type: file
direction: output
description: |
Output file with fusions that have passed all filters.
required: true
example: fusions.tsv
- name: --fusions_discarded
alternatives: -O
type: file
direction: output
description: |
Output file with fusions that were discarded due to filtering.
required: false
example: fusions.discarded.tsv
Note:
- Preferably, these outputs should not be directories but files. For example, if a tool outputs a directory
foo/
containing filesfoo/bar.txt
andfoo/baz.txt
, there should be two output arguments--bar
and--baz
(as opposed to one output argument which outputs the wholefoo/
directory).
Finally, add all other arguments to the config file. There are a few exceptions:
-
Arguments related to specifying CPU and memory requirements are handled separately and should not be added to the config file.
-
Arguments related to printing the information such as printing the version (
-v
,--version
) or printing the help (-h
,--help
) should not be added to the config file. -
If the help lists defaults, do not add them as defaults but to the description. Example:
description: <Explanation of parameter>. Default: 10.
Note:
- Prefer using
boolean_true
overboolean_false
. This avoids confusion when specifying values for this argument in a Nextflow workflow. For example, consider the CLI option--no-indels
forcutadapt
. If the config forcutadapt
would specify an argumentno_indels
of typeboolean_false
, the script of the component must pass a--no-indels
argument tocutadapt
whenpar_no_indels
is set tofalse
. This becomes problematic setting a value for this argument usingfromState
in a nextflow workflow: withfromState: ["no_indels": true]
, the value that gets passed to the script istrue
and the--no-indels
flag would not be added to the options forcutadapt
. This is inconsitent to what one might expect when interpreting["no_indels": true]
. When usingboolean_true
, the reasoning becomes simpler because its value no longer represents the effect of the argument, but wether or not the flag is set.
To ensure reproducibility of components, we require that all components are run in a Docker container.
engines:
- type: docker
image: quay.io/biocontainers/xxx:0.1.0--py_0
The container should have your tool installed, as well as ps
.
If you didn't find a suitable container in the previous step, you can create a custom container. For example:
engines:
- type: docker
image: python:3.10
setup:
- type: python
packages: numpy
For more information on how to do this, see the documentation.
Here is a list of base containers we can recommend:
- Bash:
bash
,ubuntu
- C#:
ghcr.io/data-intuitive/dotnet-script
- JavaScript:
node
- Python:
python
,nvcr.io/nvidia/pytorch
- R:
eddelbuettel/r2u
,rocker/tidyverse
- Scala:
sbtscala/scala-sbt
Next, we need to write a runner script that runs the tool with the input arguments. Create a Bash script named src/xxx/script.sh
which runs the tool with the input arguments.
#!/bin/bash
## VIASH START
## VIASH END
# unset flags
[[ "$par_option" == "false" ]] && unset par_option
xxx \
--input "$par_input" \
--output "$par_output" \
${par_option:+--option}
When building a Viash component, Viash will automatically replace the ## VIASH START
and ## VIASH END
lines (and anything in between) with environment variables based on the arguments specified in the config.
As an example, this is what the Bash script for the arriba
component looks like:
#!/bin/bash
## VIASH START
## VIASH END
# unset flags
[[ "$par_skip_duplicate_marking" == "false" ]] && unset par_skip_duplicate_marking
[[ "$par_extra_information" == "false" ]] && unset par_extra_information
[[ "$par_fill_gaps" == "false" ]] && unset par_fill_gaps
arriba \
-x "$par_bam" \
-a "$par_genome" \
-g "$par_gene_annotation" \
-o "$par_fusions" \
${par_known_fusions:+-k "${par_known_fusions}"} \
${par_blacklist:+-b "${par_blacklist}"} \
# ...
${par_extra_information:+-X} \
${par_fill_gaps:+-I}
Notes:
-
If your arguments can contain special variables (e.g.
$
), you can use quoting (need to find a documentation page for this) to make sure you can use the string as input. Example:-x ${par_bam@Q}
. -
Optional arguments can be passed to the command conditionally using Bash parameter expansion. For example:
${par_known_fusions:+-k ${par_known_fusions@Q}}
-
If your tool allows for multiple inputs using a separator other than
;
(which is the default Viash multiple separator), you can substitute these values with a command like:par_disable_filters=$(echo $par_disable_filters | tr ';' ',')
. -
If you have a lot of boolean variables that you would like to unset when the value is
false
, you can avoid duplicate code by using the following syntax:
unset_if_false=(
par_argument_1
par_argument_2
par_argument_3
par_argument_4
)
for par in ${unset_if_false[@]}; do
test_val="${!par}"
[[ "$test_val" == "false" ]] && unset $par
done
this code is equivalent to
[[ "$par_argument_1" == "false" ]] && unset par_argument_1
[[ "$par_argument_2" == "false" ]] && unset par_argument_2
[[ "$par_argument_3" == "false" ]] && unset par_argument_3
[[ "$par_argument_4" == "false" ]] && unset par_argument_4
If the unit test requires test resources, these should be provided in the test_resources
section of the component.
test_resources:
- type: bash_script
path: test.sh
- type: file
path: test_data
Create a test script at src/xxx/test.sh
that runs the component with the test data. This script should run the component (available with $meta_executable
) with the test data and check if the output is as expected. The script should exit with a non-zero exit code if the output is not as expected. For example:
#!/bin/bash
set -e
## VIASH START
## VIASH END
#############################################
# helper functions
assert_file_exists() {
[ -f "$1" ] || { echo "File '$1' does not exist" && exit 1; }
}
assert_file_doesnt_exist() {
[ ! -f "$1" ] || { echo "File '$1' exists but shouldn't" && exit 1; }
}
assert_file_empty() {
[ ! -s "$1" ] || { echo "File '$1' is not empty but should be" && exit 1; }
}
assert_file_not_empty() {
[ -s "$1" ] || { echo "File '$1' is empty but shouldn't be" && exit 1; }
}
assert_file_contains() {
grep -q "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
}
assert_file_not_contains() {
grep -q "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
}
assert_file_contains_regex() {
grep -q -E "$2" "$1" || { echo "File '$1' does not contain '$2'" && exit 1; }
}
assert_file_not_contains_regex() {
grep -q -E "$2" "$1" && { echo "File '$1' contains '$2' but shouldn't" && exit 1; }
}
#############################################
echo "> Run $meta_name with test data"
"$meta_executable" \
--input "$meta_resources_dir/test_data/reads_R1.fastq" \
--output "output.txt" \
--option
echo ">> Check if output exists"
assert_file_exists "output.txt"
echo ">> Check if output is empty"
assert_file_not_empty "output.txt"
echo ">> Check if output is correct"
assert_file_contains "output.txt" "some expected output"
echo "> All tests succeeded!"
Notes:
-
Do always check the contents of the output file. If the output is not deterministic, you can use regular expressions to check the output.
-
If possible, generate your own test data instead of copying it from an external resource.
For the sake of transparency and reproducibility, we require that the versions of the software used in the component are documented.
For now, this is managed by creating a file /var/software_versions.txt
in the setup
section of the Docker engine.
engines:
- type: docker
image: quay.io/biocontainers/xxx:0.1.0--py_0
setup:
- type: docker
# note: /var/software_versions.txt should contain:
# arriba: "2.4.0"
run: |
echo "xxx: \"0.1.0\"" > /var/software_versions.txt