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perf: bwa mem2 version update and use wrapper utils (#553)
* Version updates, added docs, code re-format * Added stdout to log
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- bioconda | ||
- nodefaults | ||
dependencies: | ||
- bwa-mem2 ==2.2.1 | ||
- bwa-mem2 =2.2 |
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name: "bwa-mem2 index" | ||
description: "Creates a bwa-mem2 index." | ||
url: https://github.com/bwa-mem2/bwa-mem2 | ||
authors: | ||
- Christopher Schröder | ||
- Patrik Smeds | ||
- Patrik Smeds | ||
input: | ||
- Reference genome (FASTA ) | ||
output: | ||
- Indexed reference genome |
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name: "bwa-mem2" | ||
description: Bwa-mem2 is the next version of the bwa-mem algorithm in bwa. It produces alignment identical to bwa and is ~1.3-3.1x faster depending on the use-case, dataset and the running machine. Optional sorting using samtools or picard. | ||
url: https://github.com/bwa-mem2/bwa-mem2 | ||
authors: | ||
- Christopher Schröder | ||
- Johannes Köster | ||
- Julian de Ruiter | ||
input: | ||
- FASTQ file(s) | ||
- reference genome | ||
output: | ||
- SAM/BAM/CRAM file | ||
notes: | | ||
* The `extra` param allows for additional arguments for bwa-mem2. | ||
* The `sorting` param allows to enable sorting, and can be either 'none', 'samtools' or 'picard'. | ||
* The `sort_extra` allows for extra arguments for samtools/picard |
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