Nils Homer

Improve the help message, remove duplicate option descriptions, and get clarify options with the same flag

2

Four suggestions based off of 8c24fb15335825bc54d3548db23009c1ca479711: 1. The "-h" or "--help" options get a strange error. If they aren't implemented, then shouldn't the tool complain "no such option exist" versus...

Support interleaved paired end FASTQs

1

In many cases, I get a single FASTQ with pared end reads "interleaved", namely reads for a pair are consecutive, have the same name except for a trailing `/1` or...

No assembly reported for 100 reads with the same sequence

8

@lh3 I was playing around with this tool but I couldn't get it to work on a "simple" case. I duplicated a read 100 times and would expect it to...

expose min_elen as a command line option

2

https://github.com/lh3/fermi-lite/issues/7

due to low qualities. I have found that in some cases, I want to ignore filtering by low base qualitiy.

Using custom objects with paths

27

Now that we can [pass around custom (value/metadata) classes](https://github.com/nextflow-io/nextflow/issues/1934#issuecomment-821574865) and have them cached, it would be wonderful if Nextflow could recognize `Path` members/properties so they are localized and available for...

Cromwell fails to find the docker image when the digest is none (<none>)

2

I am trying to run Cromwell with docker images that were loaded with `docker load`. This means that the digests are unavailable (i.e. ``). Unforutnately, this means that when looking...

Appetite for looking up samples by Sample_ID

1

I wanted to gauge your appetite for being able to lookup samples by `Sample_ID`. 1. `get_sample(id: str) -> Optional[Sample]` In the simple case where no lane is defined, it will...