snakemake-wrappers
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fix: name of bamqc
Description
The subcommand name was wrong in the description. Additionally add a region param fro target analyse.
QC
- [x] I confirm that:
For all wrappers added by this PR,
- there is a test case which covers any introduced changes,
-
input:
andoutput:
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 withx
being a reasonable default, - rule names in the test case are in 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, - wherever possible, command line arguments are inferred and set automatically (e.g. based on file extensions in
input:
oroutput:
), - all fields of the example rules in the
Snakefile
s and their entries are explained via comments (input:
/output:
/params:
etc.), -
stderr
and/orstdout
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; this also means that using any Pythontempfile
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, - Python wrapper scripts are formatted with black.
- 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).