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: about 1 month ago
JSON representation
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 6 years ago)
- Default Branch: master
- Last Pushed: 2023-09-18T11:12:53.000Z (about 2 years ago)
- Last Synced: 2025-02-28T21:07:52.395Z (9 months ago)
- Language: Python
- Size: 107 KB
- Stars: 0
- Watchers: 3
- Forks: 0
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- Changelog: HISTORY.md
- License: LICENSE
Awesome Lists containing this project
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
```