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bwa and bwa-mem2 index could infer prefix from output #228

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fgvieira opened this issue Oct 15, 2020 · 1 comment
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bwa and bwa-mem2 index could infer prefix from output #228

fgvieira opened this issue Oct 15, 2020 · 1 comment
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enhancement New feature or request

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@fgvieira
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Is your feature request related to a problem? Please describe.
At least in bwa and bwa-mem2 index, the destination (prefix) could be directly inferred from the output, being unnecessary to specify the prefix param.

Describe the solution you'd like
The wrapper would infer the prefix from snakemake.output[0]

@Smeds do you think it makes sense?
@fgvieira fgvieira added the enhancement New feature or request label Oct 15, 2020
tdayris pushed a commit to tdayris/snakemake-wrappers that referenced this issue Oct 19, 2020
[dev] (bwa): Automatic prefix detection (snakemake#228)
0d2b20f
tdayris pushed a commit to tdayris/snakemake-wrappers that referenced this issue Oct 19, 2020
[dev] (bwa): Automatix prefix detection (snakemake#228)
661f288
@tdayris tdayris mentioned this issue Oct 19, 2020
Merged
johanneskoester added a commit that referenced this issue Jan 26, 2022
@tdayris @johanneskoester @dlaehnemann
feat: explicitly specify bwa index in bwa wrappers (#232)
0e323b1 
* [fix] (template): Missing code in wrappers' doc. Error #187

* [dev] (bwa): Automatic prefix detection (#228)

* [dev] (bwa): Automatix prefix detection (#228)

* [doc] (bwa): Snakefiles updated

* [dev] (bwa): Aln was forgotten at first

* [dev] (black): Reformatting

* Update Snakefile_samtools

* minimal formatting commit to trigger tests

test logs are not available any more

* revert test trigger change

* feat!: remove tmp dir parameter in bwa mem wrapper as this is now handled automatically by snakemake

* fix: fixed index adressing

* fmt

* fixes

* fixes

* fixed failing lint, fixed syntax

* add missing logfile

Co-authored-by: tdayris <[email protected]>
Co-authored-by: Johannes Köster <[email protected]>
Co-authored-by: David Laehnemann <[email protected]>
Co-authored-by: Johannes Köster <[email protected]>
@fgvieira
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fgvieira commented Mar 2, 2022

Fixed in #232. Closing.

@fgvieira fgvieira closed this as completed Mar 2, 2022
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@fgvieira