Not an issue of aMeta per se but I have recently discovered that the latest version FastQC v0.12.1 (first screenshot) installed currently with aMeta can give quite a different adapter stats compared to e.g. the version FastQC v0.11.9 (second screenshot). The stats otherwise (if one looks at the numbers) are identical (as far as I can see), but the conclusions about adapter content are very different, although adapter trimming was run in both case, i.e. the different versions of FastQC were run on the same trimmed fastq-file. Needs to be inspected further.
Not an issue of aMeta per se but I have recently discovered that the latest version FastQC v0.12.1 (first screenshot) installed currently with aMeta can give quite a different adapter stats compared to e.g. the version FastQC v0.11.9 (second screenshot). The stats otherwise (if one looks at the numbers) are identical (as far as I can see), but the conclusions about adapter content are very different, although adapter trimming was run in both case, i.e. the different versions of FastQC were run on the same trimmed fastq-file. Needs to be inspected further.