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feat: Cnvkit target wrapper (#1878)
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### Description
wrappers for cnvkit target and antitarget

### 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).

---------

Co-authored-by: Filipe G. Vieira <1151762+fgvieira@users.noreply.github.com>
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Smeds and fgvieira committed Oct 19, 2023
1 parent bcd4a24 commit 07f3b16
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6 changes: 6 additions & 0 deletions bio/cnvkit/antitarget/environment.yaml
@@ -0,0 +1,6 @@
channels:
- conda-forge
- bioconda
- nodefaults
dependencies:
- cnvkit =0.9.10
14 changes: 14 additions & 0 deletions bio/cnvkit/antitarget/meta.yaml
@@ -0,0 +1,14 @@
name: "cnvkit antitarget"
url: https://cnvkit.readthedocs.io/en/stable/pipeline.html#antitarget
description: >
Given a “target” BED file that lists the chromosomal coordinates of the tiled regions used for targeted resequencing, derive
a BED file off-target/”antitarget” regions.
input:
- bed: bed file
- accessible: sequence-accessible coordinates in chromosomes from the given reference genome
output:
- bed: bed file
params:
- extra: additional parameters that will be forwarded to cnvkit antitarget
authors:
- Patrik Smeds
11 changes: 11 additions & 0 deletions bio/cnvkit/antitarget/test/Snakefile
@@ -0,0 +1,11 @@
rule cnvkit_antitarget:
input:
bed="test.bed",
output:
bed="test.antitarget.bed",
log:
"logs/test.target.log",
params:
extra = "" # optional
wrapper:
"master/bio/cnvkit/antitarget"

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