Error because of large chromosomes

[MargaridaMCM]

As part of the pipeline, Bowtie alignment files are indexed using samtools' BAI index. The problem is that the BAI index can only index chromosomes smaller than 512 Mbp. For larger chromosomes, a CSI index (also from samtools) needs to be used instead (it doesn't have a hardcoded limit).

The marsupial opossum's chromosomes 1 and 2 are larger than 512 Mbp. The same is true for other marsupials and several plants.

Would it be possible to update the pipeline to use a CSI index instead of a BAI index? I realise the answer depends on the downstream tools that use the .bai file. If the .bai file is only required for samtools own use, the fix would be straightforward (using option -c when indexing the bam file with samtools).

[lpantano]

Hi @MargaridaMCM , this is interesting. I have never had to use these big chromosomes. Would you mind to make the changes and see what happens? I am not sure if all tools are compatible with this...

[MargaridaMCM]

Hi @lpantano - I ran dev forcing samtools to index using the CSI instead of the BAI index, and that solved the problem! The pipeline finished successfully, and all the expected output files were generated.

I forced indexing using the CSI index by going to ../../nf-core/modules/samtools/index/main.nf and substituting samtools index by samtools index -c. I know this is not the proper way to do this using DSL 2; it needs to be specified as a parameter somewhere. But I don't feel confident (yet) with the DSL 2 syntax.

[atrigila]

Closed via #391