lumc/hutspot

Multisample DNAseq variant calling pipeline for use in diagnostics

hutspot's Issues

fastq-count fails when input files are not gzipped

This is due to the merge_r1 and merge_r2 steps producing a file ending in the .gz extension, regardless of whether their input was actually gzipped or not.

Update bwa to post-january 2019 version

There's a CVE for BWA that allows an attacker to execute arbitrary code by providing a malicious .alt file: https://nvd.nist.gov/vuln/detail/CVE-2019-10269#vulnCurrentDescriptionTitle

This has been fixed in BWA in lh3/bwa#232

However, there is no official BWA release since October 2017. Bioconda, and therefore biocontainers, also use the latest official release.

@rhpvorderman @Redmar-van-den-Berg Thoughts? Probably make our own container based off most recent BWA master branch?