`qc_plot(modules='all')` does not check whether the FastQC report has data for that module.
JohnMMa opened this issue · 0 comments
After FastQC version 0.11.6, kmer content is no longer being reported, see https://github.com/s-andrews/FastQC/releases/tag/v0.11.6. However, when we run qc_plot with modules='all', the results from .valid_fastqc_modules(modules='all') will still contain ("Kmer Content", despite qc$summary no longer having an entry for it. This means, the plot.func(qc, status = status) step will throw an error when modules reach "kmer_content", owing to status = NA.
qc_plot should including checking for the output .valid_fastqc_modules(modules='all') on whether qc has data for the module(s) selected. A PR is nearly ready and will be submitted within today.
The attached 5k_pbmc_protein_v3_nextgem_gex_S1_L001_R1_001_fastqc.zip is an example from this; it's generated by running fastqc version 0.12.1 with default parameters on one of the FASTQ files from the 10X Genomics 5k_pbmc_protein_v3_nextgem data set.