Update pangolin v4 - Githubissues

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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Update pangolin v4 #53

Closed talnor closed 2 years ago

talnor commented 2 years ago

The purpose of the code changes are as follows:

I did a thing

Standard test procedure

[ ] The self-test mentioned in the README finished successfully
[x] Produced files contain expected values
[x] 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

talnor commented 2 years ago

Fixes issue https://github.com/genomic-medicine-sweden/gms-artic/issues/52

sofstam commented 2 years ago

Tests for this PR for Stockholm region (CG)

source activate D_mutant

mutant analyse sarscov2 /home/proj/development/mutant/cases/maturejay/fastq/ --config_artic /home/proj/development/mutant/configs/artic-dev.json --config_case /home/proj/development/mutant/cases/maturejay/case_config.json --outdir /home/proj/development/mutant/cases/maturejay/results/ --profiles slurm,singularity

Results:

bcftools,1.10.2
bwa,0.7.17-r1188
constellations,0.1.4
fastqc,0.11.9
freebayes,1.3.5
gofasta,1.0.0
ivar,1.3.1
multiqc,1.11
nextclade,1.10.2
pangolin-data,1.2.133
pangolin,4.0.2
picard,2.25.2
python,3.8.12
samtools,1.10
scorpio,0.3.16
snakemake,6.4.1
trim_galore,0.6.4_dev
usher,v0.5.3

sofstam commented 2 years ago

Tests for this PR for Stockholm region (CG)

source activate D_mutant

mutant analyse sarscov2 /home/proj/development/mutant/cases/maturejay/fastq/ --config_artic /home/proj/development/mutant/configs/artic-dev.json --config_case /home/proj/development/mutant/cases/maturejay/case_config.json --outdir /home/proj/development/mutant/cases/maturejay/results/ --profiles slurm,singularity

Results:

bcftools,1.10.2
bwa,0.7.17-r1188
constellations,0.1.4
fastqc,0.11.9
freebayes,1.3.5
gofasta,1.0.0
ivar,1.3.1
multiqc,1.11
nextclade,1.10.2
pangolin-data,1.2.133
pangolin,4.0.2
picard,2.25.2
python,3.8.12
samtools,1.10
scorpio,0.3.16
snakemake,6.4.1
trim_galore,0.6.4_dev
usher,v0.5.3