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fix: Lofreq indelqual (#1325)
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### Description

Fixed an error within indelqual wrapper that kept indelqual from running
properly.

### QC
<!-- Make sure that you can tick the boxes below. -->

* [ 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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tgroth97 and fgvieira committed May 4, 2023
1 parent 235c2e7 commit dabecf0
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20 changes: 17 additions & 3 deletions bio/lofreq/indelqual/test/Snakefile
@@ -1,12 +1,26 @@
rule lofreq_indelqual:
rule lofreq_uniform_indelqual:
input:
bam="data/{sample}.bam",
output:
"out/indelqual/{sample}.indel.bam"
"out/indelqual/{sample}.uindel.bam"
log:
"logs/{sample}.log"
"logs/{sample}.uindel.log"
params:
extra="-u 15"
threads: 8
wrapper:
"master/bio/lofreq/indelqual"

rule lofreq_dindel_indelqual:
input:
bam="data/{sample}.bam",
ref="data/hg38_chr21.fa"
output:
"out/indelqual/{sample}.dindel.bam"
log:
"logs/{sample}.dindel.log"
params:
extra="--dindel"
threads: 8
wrapper:
"master/bio/lofreq/indelqual"
581 changes: 69 additions & 512 deletions bio/lofreq/indelqual/test/data/a.bam

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