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fix: fix freebayes parallel (#1807)
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### Description

Freebayes parallel is once again failing due to issues with some of its
dependencies. As a workaround htslib need to be pinned to v.1.16 as
already described
[here](bioconda/bioconda-recipes#42643 (comment)).

### 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
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* 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 Sep 18, 2023
1 parent f723338 commit 2aa2f62
Showing 1 changed file with 1 addition and 0 deletions.
1 change: 1 addition & 0 deletions bio/freebayes/environment.yaml
Expand Up @@ -6,6 +6,7 @@ dependencies:
- freebayes =1.3.6
- bcftools =1.15 # pinned to prevent conflicts with vcflib 1.0.3
- vcflib =1.0.3 # pinned because of bug in v1.0.9 (https://github.com/vcflib/vcflib/issues/389)
- htslib =1.16 # pinned because of bug (https://github.com/bioconda/bioconda-recipes/issues/42643#issuecomment-1692969153)
- parallel =20230722
- bedtools =2.31.0
- sed =4.8
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