- Nextflow
- Singularity
The file run.sh
indicates commands to run.
First, modify the gofasta.config
file, especially the following attributes to adapt to the local hpc environment
fastqueue = 'common,dedicated'
fastqos= '--qos=fast'
normalqueue = 'cnrvir'
normalqos = '-A cnrvir'
longqueue = 'cnrvir'
longqos = '-A cnrvir'
bigmemqueue = 'common'
executor
Then run nextflow:
nextflow run gofasta.nf -c gofasta.config
It will produce the output files in the results
folder, in particular:
- context.aligned.fasta_masked.fasta.gz: The masked sequences of the global contextual samples
- gisaid_pangolin.tsv: Pangolin annotation of all the sequences
- bootaligns/*: Bootstrap alignments
- boottrees/*: Bootstrap trees
- align.treefile: Phylogenetic tree
- align_fbp.treefile: Phylogenetic tree with bootstrap supports
- ba286.aligned.fasta_closest.txt: The name of the closest sequences to BA.2.86 queries
- ba286.aligned.fasta_closest_unique_sequences.fasta.gz: The sequences of the closest sequences to BA.2.86 queries
- ba286.aligned.fasta_closest_unique_sequences.fasta_masked.fasta.gz: The masked sequences of the closest sequences to BA.2.86 queries
R (v4.3.0)
> source("figures/lineageStats.R")
> source("figures/plot_mutations.R")