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Update 241105

Update 241105 #90

Workflow file for this run

name: Test Grandeur workflow with salmonella
on: [pull_request, workflow_dispatch]
jobs:
test:
runs-on: ubuntu-20.04
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Install Nextflow
run: |
wget -qO- get.nextflow.io | bash
sudo mv nextflow /usr/local/bin/
nextflow -version
- name: Run Grandeur
run: |
docker --version
mkdir fastas
for accession in GCA_019710395.3_ASM1971039v3 GCA_001652385.2_ASM165238v2 GCA_013344545.1_ASM1334454v1
do
all=$(echo $accession | cut -f 2 -d "_")
fir=$(echo $all | cut -c 1-3)
mid=$(echo $all | cut -c 4-6)
end=$(echo $all | cut -c 7-9)
wget https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/$fir/$mid/$end/$accession/${accession}_genomic.fna.gz
gzip -d ${accession}_genomic.fna.gz
mv ${accession}_genomic.fna fastas/.
done
ls fastas/* > fastas.txt
nextflow run . -profile docker -c .github/workflows/github_actions.config --fasta_list fastas.txt
cat grandeur/grandeur_summary.tsv
cat grandeur/summary/software_versions.yml
ls grandeur/multiqc/multiqc_report.html
- name: Check Salmonella file
run: |
for file in grandeur/seqsero2/seqsero2_results.txt
do
head $file
wc -l $file
done