tdanhorn
tdanhorn
Good point, I agree, thanks!
I second the inclusion of Picard Tools CollectHsMetrics (for WES/targeted sequencing), and there is CollectWgsMetrics for WGS. Picard is already there, so all that is needed is an option to...
I see the problem with the ORA reference genome -- you'll have to know exactly what was used and have access to it. (This is basically the same issue as...
Thank your for doing this, @MatthiasZepper. I think it follows the principle of "least surprise". Don't know how easy it would be, but if you wanted to avoid people inadvertently...
I believe this is a structural issue. The statements using MirGeneDB is in an `if` clause governed by the `--mirgenedb` parameter, but nothing seems to control the use of miRBase...
Can you confirm that this fails reproducibly with the newest version 3.16.1 that came out yesterday? It would probably also be helpful if you could post the `.nextflow.log` and any...
Since this is a stand-alone process just for `awk`, it looks to me like a very good use case for the gawk module. (If it were a line in some...
Currently the check has been modified to `if ((meta.lane || meta.lane == 0) && fastq_2) { ...`. I wonder if there is a simpler, possibly even more robust way. What...
Thanks for trying! I used the empty string (`""`) as test, because I don't know what the value of a missing lane would be (Groovy is not my native language),...
Thank you foe taking this on! I agree with all of your suggestions. A couple of additional points: * It may be worthwhile spelling out clearly that -- unlike for...