Chris Wright

I would install minimap2 in a distinct conda environment and trying running it in isolation. Please refer to the minimap2 documentation for how to do this. If you observe similar...

Here is the full output of running the `medaka_consensus` convenience script on a small dataset: ``` $ medaka_consensus -i fastq/barcode01/subset.fastq.gz -d ref/reference.subseq.fa.gz -o medaka -t 48 Checking program versions This...

Medaka does not support gbk files as input, only fasta. If you wish to annotate the output VCF file you will need to use a standalone program dedicated to that...

Hi @an22an, You haven't mentioned on which OS you are running. I note that you saying you are running with Docker. It is possible that your docker configuration has limited...

@yangao07 how did you build the source distribution, it appears simply to be invalid.

I believe this is still an issue, and as pointed out above due to incorrect unwanted coercion in nextflow's argument parsing.

I confirm the data is left as a string with 21.10.6: ``` $ nextflow run main.nf --badvalue 1.1234e5 N E X T F L O W ~ version 21.10.6 Launching...

I noted similar behaviour previously with other operators: https://github.com/nextflow-io/nextflow/discussions/2437#discussion-3675155 This was originally and issue then got moved to a discussion for reasons unknown.

`combine` is a weird one because it has two (I would say) unrelated behaviours as illustrated in the docs: without a join key it's a Cartesian product (all pairwise combinations),...

The example given for `transpose` is not anything I would recognise as a transpose from linear algebra. I'm hard pressed to even describe what it's doing. I can see from...