Felix Lenner
Felix Lenner
I have added a suggestion in #30. One thing is to think about if you have an aligned BAM with some unaligned reads. For example, add 100 unaligned reads to...
@nf-core-bot fix linting
At the same time, the default for `--write-index` is csi. Just curious, is there any downside using csi for bam?
No, not at all. But I was thinking about adding `--write-index` to some bcftools modules as well, where it would be csi vs tbi.
I tried using csi a bit but just encountered a tool that expects and needs bai, and I'm sure there might be others like it. Maybe bai is the best...
I added a `val bam_index_extension`to the [minimap2/align](https://github.com/nf-core/modules/blob/master/modules/nf-core/minimap2/align/main.nf#L11) module, together with: https://github.com/nf-core/modules/blob/80b0d74de0fd21efe4036882dae0d05154f6cae7/modules/nf-core/minimap2/align/main.nf#L32 In the samtools modules it would feel a bit strange to specify the output type in the config and...
> > I'm leaning towards the idea of just adding another value channel which determines if the index is made, and if so what type; if empty no index is...
Sure, I'll fix it during the summer! @SPPearce
Alright, will take a closer look.
Writing to /tmp can create issues on clusters. The TmpDir _should_ be created within the working directory.