Filtlong | quality filtering tool for long reads | Widget library

by rrwick C++ Version: v0.2.1 License: GPL-3.0

X-Ray Key Features Code Snippets Community Discussions(1)Vulnerabilities Install Support

kandi X-RAY | Filtlong Summary

Filtlong is a C++ library typically used in User Interface, Widget applications. Filtlong has no bugs, it has no vulnerabilities, it has a Strong Copyleft License and it has low support. You can download it from GitHub.

Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter.

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Quality

Security

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Support

Filtlong has a low active ecosystem.

It has 182 star(s) with 18 fork(s). There are 13 watchers for this library.

It had no major release in the last 12 months.

There are 14 open issues and 20 have been closed. On average issues are closed in 119 days. There are 1 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of Filtlong is v0.2.1

Quality

Filtlong has 0 bugs and 0 code smells.

Security

Filtlong has no vulnerabilities reported, and its dependent libraries have no vulnerabilities reported.

Filtlong code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

Filtlong is licensed under the GPL-3.0 License. This license is Strong Copyleft.

Strong Copyleft licenses enforce sharing, and you can use them when creating open source projects.

Reuse

Filtlong releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

It has 768 lines of code, 87 functions and 7 files.

It has high code complexity. Code complexity directly impacts maintainability of the code.

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Filtlong Key Features

No Key Features are available at this moment for Filtlong.

Filtlong Examples and Code Snippets

No Code Snippets are available at this moment for Filtlong.

Community Discussions

Trending Discussions on Filtlong

Snakemake shell command should only take one file at a time, but it's trying to do multiple files at once

QUESTION

Snakemake shell command should only take one file at a time, but it's trying to do multiple files at once

Asked 2019-Sep-17 at 18:59

First off, I'm sorry if I'm not explaining my problem clearly, English is not my native language.

I'm trying to make a snakemake rule that takes a fastq file and filters it with a program called Filtlong. I have multiple fastq files on which I want to run this rule and it should output a filtered file per fastq file but apparently it takes all of the fastq files as input for a single Filtlong command.

The fastq files are in separate directories and the snakemake rule should write the filtered files to separate directories aswell.

This is how my code looks right now:

...

ANSWER

Answered 2019-Sep-17 at 18:59

You shouldn't use the expand function in your input section of the filter_reads rule. What you are doing now is requiring all your samples to be the input of each filtered file: that is what you can observe in your error message.

There is another complication that you introduce out of nothing: you mix both wildcards and variables. In your example the {FILT_DIR} is just a predefined value while the {sample} is a wildcard that Snakemake uses to match the rules. Try the following (pay special attention on single/double brackets and on the formatted string (the one that has the form f"")):

Source https://stackoverflow.com/questions/57977484

Community Discussions, Code Snippets contain sources that include Stack Exchange Network

Vulnerabilities

No vulnerabilities reported

Install Filtlong

Filtlong builds into a stand-alone executable:.

Support

For any new features, suggestions and bugs create an issue on GitHub. If you have any questions check and ask questions on community page Stack Overflow .

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