https://github.com/mlin/minimap2-scatter
WIP proof-of-concept
https://github.com/mlin/minimap2-scatter
Last synced: 3 months ago
JSON representation
WIP proof-of-concept
- Host: GitHub
- URL: https://github.com/mlin/minimap2-scatter
- Owner: mlin
- License: mit
- Created: 2021-07-13T09:23:50.000Z (almost 5 years ago)
- Default Branch: main
- Last Pushed: 2021-08-06T19:38:04.000Z (almost 5 years ago)
- Last Synced: 2025-01-07T20:46:10.302Z (over 1 year ago)
- Language: wdl
- Homepage:
- Size: 5.86 KB
- Stars: 0
- Watchers: 2
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
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README
# minimap2-scatter
## WIP proof-of-concept
See also: https://github.com/mlin/minimap2/tree/distributed-mapping
How to:
```bash
git clone --recursive https://github.com/mlin/minimap2-scatter.git
cd minimap2-scatter
make # builds Docker image locally
export MINIWDL__DOWNLOAD_CACHE__PUT=true
export MINIWDL__DOWNLOAD_CACHE__GET=true
export MINIWDL__DOWNLOAD_CACHE__DIR=/tmp/miniwdl_download_cache
miniwdl run _demo.wdl \
db_fasta=s3://idseq-public-references/test/viral-alignment-indexes/viral_nt \
fastq=https://github.com/chanzuckerberg/idseq-workflows/raw/main/short-read-mngs/test/norg_13__nacc_35__uniform_weight_per_organism__hiseq_reads__v10__R1.fastq.gz \
fastq2=https://github.com/chanzuckerberg/idseq-workflows/raw/main/short-read-mngs/test/norg_13__nacc_35__uniform_weight_per_organism__hiseq_reads__v10__R2.fastq.gz \
shards=4 --verbose
```