Add chopper to supercede Nanolyse

[CJREID]

Description of feature

Filtlong and Nanolyse are very time-consuming steps in the process for long-read/hybrid datasets, mainly because neither of them can be multi-threaded. Chopper combines Nanofilt and Nanolyse and allows multi-threading.

Whilst Nanofilt performs the same function as Filtlong in principle, Filtlong is probably still preferable as its methods are more comprehensive and allow a hybrid approach with short reads. Nonetheless, Chopper could be used mainly as a multi-threaded version of Nanolyse and a config option could be added if filtering by Chopper is preferred by the user. Chopper doesn't have a containerised version as yet but it is installable via conda.

[d4straub]

Thanks! I wasnt aware though that there isnt any containerized version. Most packages that are available in bioconda have docker & singularity containers. Without at least a docker container, we wont implement the tool into pipelines. Maybe it would be worth it to make an issue in the Chopper repo asking for a docker container.

[jfy133]

Note chopper should have a biocontainer! I think it's hit the biocontainer API failing to open the quay.io container, I shall I ask on the biocontainers gitter :)

[jfy133]

Ref: https://matrix.to/#/!wNQPhGTQvTINsnORJY:gitter.im/$VGVoXXCoXFQhqnuHoPeTbGVv1sGXBabPY0rtVy39nS8?via=gitter.im&via=matrix.org

[jfy133]

https://quay.io/repository/biocontainers/chopper?tab=tags

Docker container is open, now need to wait 24h and singularity shoul dbe available :)

[d4straub]

Awesome!

[CJREID]

Thanks guys!

[jfy133]

Chopper already exists