Muscle needs to be downgraded for nanopore analyses

[henningonsbring]

Today I downloaded the latest nanopore and pangolin containers from dockerhub to run an analysis of nanopore data. When running gms-artic the analysis crashed. To problem is that muscle is upgraded (and I don't understand how that happened). See error for the step where I get stuck:

singularity exec artic-ncov2019-nanopore.sif muscle -in kindcorgi_220410-154114_barcode15.muscle.in.fasta -out kindcorgi_220410-154114_barcode15.muscle.out.fasta

Invalid command line
Unknown option in

I tried to fix this error with this PR, but it did not work. In PR linked in last sentence the problem is also described in more detail.

What needs to be done: Downgrade muscle to 3.8

What are the arguments for getting it done: Needed to run analysis of nanopore data with medaka

Task is considered finished when: It is possible to run analysis of nanopore data with medaka

[sofstam]

I tried to replicate this issue with:

singularity pull artic-ncov2019-nanopore.sif docker://genomicmedicinesweden/gms-artic-nanopore:latest

and then I ran:

singularity exec artic-ncov2019-nanopore.sif muscle

I get the following:

[sofstam]

This seems to be solved. I am closing this issue.

[henningonsbring]

yes, it is solved