Muscle version 3.8 to allow nanopore analysis with medaka

[henningonsbring]

The purpose of the code changes are as follows:

Running nanopore analysis with the most recent container(s?) causes articNcovNanopore:sequenceAnalysisMedaka:articMinIONMedaka to crash. When it worked we used muscle v3.8, recently an unknown update has upgraded muscle to v5.1. In 5.1 the syntax is different and the -in and -out flag has changed names to -align and -output. Further the developers refers to v5 as a "major re-write", therefore it could be risky to use this version.

Me and @talnor have failed to identify which recent dependency upgrade that causes muscle to be upgraded. I suggest we just add muscle=3.8 to the .yml file to make sure analysis wont get stuck on:

Invalid command line
Unknown option in

Standard test procedure

• [ ] The self-test mentioned in the README finished successfully
• [ ] Produced files contain expected values
• [ ] The code has been reviewed by @octocat

This version is a:

• [ ] MAJOR - when you make incompatible API changes
• [x] MINOR - when you add functionality in a backwards compatible manner
• [ ] PATCH - when you make backwards compatible bug fixes or documentation/instructions

[JD2112]

Great! Thanks for the info. :) I had the same issue on Tuesday with articNcovNanopore:sequenceAnalysisNanopolish:articMinIONNanopolish. It showed Running: muscle -in 20200311_1427_X1_FAK72834_a3787181_barcode09.muscle.in.fasta -out 20200311_1427_X1_FAK72834_a3787181_barcode09.muscle.out.fasta Command failed:muscle -in 20200311_1427_X1_FAK72834_a3787181_barcode09.muscle.in.fasta -out 20200311_1427_X1_FAK72834_a3787181_barcode09.muscle.out.fasta

I already updated muscle=3.8 in the nanopore yml file (primer-scheme branch; on reply issues #46) which is not merged yet!

Please feel free to merge whenever you have time.