Nils Homer

@angadps this seems like a completely reasonable request. You can also take a look at the auxiliary tags in the consensus BAM, that give you the number of raw reads...

@sstadick The read structure is [modified](https://github.com/fulcrumgenomics/fgbio/blob/ed906cd29a7f38c9da0583c8307dc7fbcd94880b/src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala#L780) to have the last segment be a variable #. It's then used [here](https://github.com/fulcrumgenomics/fgbio/blob/ed906cd29a7f38c9da0583c8307dc7fbcd94880b/src/main/scala/com/fulcrumgenomics/fastq/DemuxFastqs.scala#L860)

@asmlgkj I am assuming duplex sequencing below (observe both strands). In general, the `-M` option works as `-M X Y Z`, where `X` is total consensus depth, `Y` is the...

As a heads up, I’ll be slow to respond to prioritize client work. Thanks for your understanding.

@blackbeerd the input reads are both mapped to the reverse strand, so unfortunately these are not FR pairs [`ClipBam`](http://fulcrumgenomics.github.io/fgbio/tools/latest/ClipBam.html) says: > Clipping overlapping reads is only performed on FR read...

Where’s a good place to contribute documentation for my future self about these config options?

Thanks @mlin this is super helpful and thank you for your patience. I’m really enjoying using miniwdl so hopefully these questions are not seen as a criticism but a desire...

@dpark01 can you send a link to anexample Docker file? I do frequently have multiple conda environments (see https://github.com/nh13/conda-env-builder) but as long as base is activated I can switch prior...

Your example works when I use `docker run -it` but not through miniWDL, likely because miniWDL is not using a login shell. Any other thoughts?

@dpark01 I tried adding conda into the path when building my docker image too. It worked just fine with `cromwell`, so there's something different here between cromwell and miniWDL. Edit:...