vcftools | tools written in Perl and C++ for working with VCF files | Genomics library

by vcftools C++ Version: v0.1.16 License: LGPL-3.0

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kandi X-RAY | vcftools Summary

vcftools is a C++ library typically used in Artificial Intelligence, Genomics applications. vcftools has no bugs, it has no vulnerabilities, it has a Weak Copyleft License and it has low support. You can download it from GitHub.

A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

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Quality

Security

License

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Support

vcftools has a low active ecosystem.

It has 420 star(s) with 145 fork(s). There are 32 watchers for this library.

It had no major release in the last 12 months.

There are 96 open issues and 79 have been closed. On average issues are closed in 108 days. There are 4 open pull requests and 0 closed requests.

It has a neutral sentiment in the developer community.

The latest version of vcftools is v0.1.16

Quality

vcftools has 0 bugs and 0 code smells.

Security

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

vcftools code analysis shows 0 unresolved vulnerabilities.

There are 0 security hotspots that need review.

License

vcftools is licensed under the LGPL-3.0 License. This license is Weak Copyleft.

Weak Copyleft licenses have some restrictions, but you can use them in commercial projects.

Reuse

vcftools releases are available to install and integrate.

Installation instructions, examples and code snippets are available.

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vcftools Key Features

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vcftools Examples and Code Snippets

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Community Discussions

Trending Discussions on vcftools

Problems getting two output files in Nextflow

QUESTION

Problems getting two output files in Nextflow

Asked 2021-Oct-27 at 15:08

Hello all!

I´m trying to write a small Nextflow pipeline that runs vcftools comands in 300 vcf´s. The pipe takes four inputs: vcf, pop1, pop2 and a .txt file, and would have to generate two outputs: a .log.weir.fst and a .log.log file. When i run the pipeline, it only gives the .log.weir.fst files but not the .log files.

Here´s my process definition:

...

ANSWER

Answered 2021-Oct-27 at 15:08

Note that bash .command.sh and bash .command.run do different things. The latter is basically a wrapper around the former that sets up the environment and stages the declared input files, among other things. If running the latter produces the unusual behavior, you'll need to dig deeper.

It's not completely clear to me what the problem is here. My guess is that vcftools might behave differently when run non-interactively, such that it sends it's logging to STDERR. If that's the case, the logging will be captured in a file called .command.err. To instead send that to a file, you can just redirect STDERR in the usual way, untested:

Source https://stackoverflow.com/questions/69732459

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