Link checking for the GATK documentation
Dear Broad Team! I would like to thank you for providing such a good technical documentation for GATK, which in general seems to be one of the most extensive documentations in the bioinformatics community. However, and probably related to that, I repeatedly find myself taken aback by broken links.
For example, the first link in the documentation of the HaplotypeCaller will not lead to a correct article.
Similarly, the links provided in GATK error messages sometimes do not lead to the correct article, for example in the following message
A USER ERROR has occurred: Fasta dict file XXXX for reference XXX does not exist. Please see http://gatkforums.broadinstitute.org/discussion/1601/how-can-i-prepare-a-fasta-file-to-use-as-reference for help creating it.
As a humble suggestion, maybe there is the possibility to add a broken link checker (e.g. lychee) to the CI system, so that articles in the "Getting started" and "technical documentation" sections, as well as links in the source code get checked.
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Hi Mario Fasold , I completely agree with you regarding the broken links. I've relayed this post and now there's an issue on the GATK repo: https://github.com/broadinstitute/gatk/issues/8682
It probably will take some time to fix these broken links scattered across the docs due to the bandwidth of the GATK team, but I support your suggestion to use something like lychee. I'll find out if there's any reason why it shouldn't be added to the CI system.
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