feat: remove existing run directory option for strelka #1297
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christopher-schroeder
changed the title
|
Wouldn't it be better to output to a temp folder and then copy relevant results to their final destination? |
Yes, ok - why not. |
fgvieira
reviewed
Apr 27, 2023
johanneskoester
requested changes
May 4, 2023
bio/strelka/germline/test/Snakefile
Outdated
| @@ -7,13 +7,13 @@ rule strelka_germline: | |||
| fasta_index="genome.fasta.fai" | |||
| output: | |||
| # Strelka results - either use directory or complete file path | |||
| directory("strelka/{sample}") | |||
| variants="strelka/{sample}.vcf.gz" | |||
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Can you please add the other possibilities (indices etc.) so that the people have a comprehensive example of what can be given here?
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yes, the wrapper is not done yet
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I unresolved this just so that I don't forget the request until it is done.
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
johanneskoester
approved these changes
Jun 12, 2023
johanneskoester
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Jun 13, 2023
🤖 I have created a release \*beep\* \*boop\* --- ## [2.0.0](https://www.github.com/snakemake/snakemake-wrappers/compare/v1.32.1...v2.0.0) (2023-06-13) ### ⚠ BREAKING CHANGES * replace individual seqkit wrappers with a single wrapper for all seqkit commands (#1426) ### Features * remove existing run directory option for strelka ([#1297](https://www.github.com/snakemake/snakemake-wrappers/issues/1297)) ([6f384dd](https://www.github.com/snakemake/snakemake-wrappers/commit/6f384ddc857293ec799526b75d355f5015191f70)) * replace individual seqkit wrappers with a single wrapper for all seqkit commands ([#1426](https://www.github.com/snakemake/snakemake-wrappers/issues/1426)) ([c7a4d96](https://www.github.com/snakemake/snakemake-wrappers/commit/c7a4d960044888825f2b9475d4df7b8f09cec0a0)) --- This PR was generated with [Release Please](https://github.com/googleapis/release-please). See [documentation](https://github.com/googleapis/release-please#release-please). Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
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Description
When strelka reruns it doesn't like if the run directory exists. Add an option to delete it before.
QC
For all wrappers added by this PR,
input:andoutput:file paths in the resulting rule can be changed arbitrarily,threads: xstatement withxbeing a reasonable default,map_readsfor a step that maps reads),environment.yamlspecifications follow the respective best practices,input:oroutput:),Snakefiles and their entries are explained via comments (input:/output:/params:etc.),stderrand/orstdoutare logged correctly (log:), depending on the wrapped tool,tempfile.gettempdir()points to (see here; this also means that using any Pythontempfiledefault behavior works),meta.yamlcontains a link to the documentation of the respective tool or command,Snakefiles pass the linting (snakemake --lint),Snakefiles are formatted with snakefmt,