https://github.com/ssi-dk/bifrost_min_read_check

Bifrost Component: Min Read Check - Checks that provided read files have a minimum number of reads for analysis
https://github.com/ssi-dk/bifrost_min_read_check

Last synced: 3 days ago
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Bifrost Component: Min Read Check - Checks that provided read files have a minimum number of reads for analysis

• Host: GitHub
• URL: https://github.com/ssi-dk/bifrost_min_read_check
• Owner: ssi-dk
• License: mit
• Created: 2019-10-18T07:46:36.000Z (about 5 years ago)
• Default Branch: master
• Last Pushed: 2023-09-18T11:12:53.000Z (about 1 year ago)
• Last Synced: 2023-09-18T13:00:32.812Z (about 1 year ago)
• Language: Python
• Size: 107 KB
• Stars: 0
• Watchers: 3
• Forks: 1
• Open Issues: 0
• Metadata Files:
  • Readme: README.md
  • Changelog: HISTORY.md
  • License: LICENSE

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README

        
# bifrost_min_read_check

This component is run given a sample id already added into the bifrostDB.From this it'll pull the paired_reads and run a check to ensure that the raw data has a minimum set of reads as to allow other programs in the workflow to work. The output of this is a simple boolean on if it 'has_min_num_of_reads'

## Programs: (see Dockerfile) 

```

snakemake-minimal==5.7.1; \

bbmap==38.58; 

```

## Summary of c run: (see pipeline.smk and config.yaml)

```

java -ea -cp /opt/conda/opt/bbmap-38.58-0/current/ jgi.BBDuk in={input.reads[0]} in2={input.reads[1]} ref={params.adapters} ktrim=r k=23 mink=11 hdist=1 tbo qtrim=r minlength=30 1> {log.out_file} 2> {output.stats_file}

rule__greater_than_min_reads_check.py

```