nf-core / nf-core/viralintegration
Add MetaPhlAn 3.0 module
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enhancement
- Dominant language
- Python
- Stars
- 19
- Forks
- 11
- PR merge metrics
- No merged PRs in 30d
Description
Description of feature
Last summer, @parnaljoshi came up with the idea of using MetaPhlAn to look for viral reads in tumor data. The general approach was:
- align tumor fastq to human genome with STAR
- save unmapped reads
- run unmapped reads through MetaPhlAn:
metaphlan $out_prefix"Unmapped.out.mate1",$out_prefix"Unmapped.out.mate2" --bowtie2out metagenome.bowtie2.bz2 --add_viruses --ignore_eukaryotes --nproc 16 --input_type fastq --read_min_len 30 > "analysis/star_results/"$substring.txt
First, we need to simply add the metaphlan3 module.
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