Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

FASTP to replace trimmomatic, picard and fastqc. Also handles gzipped input #19

Closed
DennisSchmitz opened this issue Apr 10, 2019 · 1 comment
Labels
enhancement New feature or request

Comments

@DennisSchmitz
Copy link
Owner

@dnieuw showed fastp, a new preprocessing tool, see paper and code.

It might be able, in a single process, to eliminate the usage of trimmomatic, picard and fastqc. It handles all these functions into one process. Furthermore, it is compatible with MultiQC and it automatically accepts gzipped input files (and even outputs as gzipped files).

Should try it out, would speed up and simplify the pipeline greatly. Furthermore, it gives greater control over pre-processing and should play more nicely with Snakemake's DAG.

@DennisSchmitz DennisSchmitz added the enhancement New feature or request label Apr 10, 2019
@DennisSchmitz DennisSchmitz added this to the v0.9.2 milestone Apr 10, 2019
@florianzwagemaker florianzwagemaker removed this from the v0.9.2 milestone May 2, 2019
@DennisSchmitz DennisSchmitz moved this from Issues to To do (long term) in general enhancements May 16, 2019
@DennisSchmitz
Copy link
Owner Author

Something to keep in mind for later, but the current setup works so there is no need to replace it anymore.

general enhancements automation moved this from To do (long term) to Done Jul 3, 2019
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request
Projects
Development

No branches or pull requests

2 participants