Handle NA insert sizes in extract_fragment_size rule#195
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A hotfix for an issue that arises when absolutely nothing comes out of a barcode, and trying to convert
NAvalue to integer inextract_fragment_sizerule.Somehow in previous #191 Picard was still getting an insert size out of very few reads so this edge case was not being properly tested. In some cases it might be useful to still try to produce the bigWig files, so configuration
fragment_sizeis used when aNAis found.Related to this, I added priority for all the rules that calculate values for reports and the MultiQC reports. The rationale behind this is that it is OK if the pipeline fails because some sample had no reads, and hence it is not possible to produce the bigWig file, but in order to troubleshoot or understand what happens, MultiQC results are valuable, so we want the MultiQC report to be a preferred rule when possible, to save the user a
minute run --keep-goingin as many cases as possible.