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feat: add test for datavzrd (#1755)
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### Description

There is no test for the datavzrd wrapper which is why the tests are
always passing for updates even if the updated version does not exist.

### QC
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* [x] I confirm that:

For all wrappers added by this PR, 

* there is a test case which covers any introduced changes,
* `input:` and `output:` file paths in the resulting rule can be changed
arbitrarily,
* either the wrapper can only use a single core, or the example rule
contains a `threads: x` statement with `x` being a reasonable default,
* rule names in the test case are in
[snake_case](https://en.wikipedia.org/wiki/Snake_case) and somehow tell
what the rule is about or match the tools purpose or name (e.g.,
`map_reads` for a step that maps reads),
* all `environment.yaml` specifications follow [the respective best
practices](https://stackoverflow.com/a/64594513/2352071),
* wherever possible, command line arguments are inferred and set
automatically (e.g. based on file extensions in `input:` or `output:`),
* all fields of the example rules in the `Snakefile`s and their entries
are explained via comments (`input:`/`output:`/`params:` etc.),
* `stderr` and/or `stdout` are logged correctly (`log:`), depending on
the wrapped tool,
* temporary files are either written to a unique hidden folder in the
working directory, or (better) stored where the Python function
`tempfile.gettempdir()` points to (see
[here](https://docs.python.org/3/library/tempfile.html#tempfile.gettempdir);
this also means that using any Python `tempfile` default behavior
works),
* the `meta.yaml` contains a link to the documentation of the respective
tool or command,
* `Snakefile`s pass the linting (`snakemake --lint`),
* `Snakefile`s are formatted with
[snakefmt](https://github.com/snakemake/snakefmt),
* Python wrapper scripts are formatted with
[black](https://black.readthedocs.io).
* Conda environments use a minimal amount of channels, in recommended
ordering. E.g. for bioconda, use (conda-forge, bioconda, nodefaults, as
conda-forge should have highest priority and defaults channels are
usually not needed because most packages are in conda-forge nowadays).
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FelixMoelder committed Aug 18, 2023
1 parent 1b729e1 commit 996bdcf
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Showing 2 changed files with 9 additions and 1 deletion.
8 changes: 8 additions & 0 deletions test.py
Expand Up @@ -1039,6 +1039,14 @@ def test_dada2_add_species():
)


@skip_if_not_modified
def test_datavzrd():
run(
"utils/datavzrd",
["snakemake", "--cores", "1", "--use-conda", "results/datavzrd-report/A"],
)


@skip_if_not_modified
def test_deseq2_deseqdataset():
# from HTSeqcount / Featurecount
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2 changes: 1 addition & 1 deletion utils/datavzrd/test/Snakefile
Expand Up @@ -7,7 +7,7 @@ rule datavzrd:
input:
config="resources/{sample}.datavzrd.yaml",
# optional files required for rendering the given config
table="data/A.tsv",
table="data/{sample}.tsv",
params:
extra="",
output:
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