Run versions process with nanopore medaka workflow

genomic-medicine-sweden / gms-artic

A nextflow pipeline with a GMS touch for running the ARTIC network's fieldbioinformatics tools (https://github.com/artic-network/fieldbioinformatics).

GNU Affero General Public License v3.0

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Run versions process with nanopore medaka workflow #62

Closed henningonsbring closed 1 year ago

henningonsbring commented 2 years ago

The purpose of the code changes are as follows:

I added so versions process is running with medaka
Blacked the whole project to get consistent formatting of the code

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

henningonsbring commented 2 years ago

Let me know what you think about me running black on the code @JD2112, if you do not like it I can do a new PR with only adding the version process to the medaka workflow.

henningonsbring commented 2 years ago

After testing the code here is the content of the versions.csv file when running the medaka workflow on nanopore data:

artic,1.1.3
bwa,0.7.17-r1188
constellations,0.1.10
gofasta,0.0.4
mafft,7.505
medaka,1.0.3
minimap2,2.17-r941
muscle,v3.8.1551
nanopolish,0.13.2
nextclade,1.10.2
pangolin-data,1.12
pangolin,4.1.2
porechop,0.3.2pre
python,3.6.15
samtools,1.10
scorpio,0.3.17
snakemake,5.13.0

JD2112 commented 2 years ago

@henningonsbring fine for me. Nice you checked this out.