Test datasets #7
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Test datasets | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '30 4 * * TUE' | |
| jobs: | |
| check: | |
| runs-on: ubuntu-20.04 | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| - name: download datasets | |
| run: | | |
| grep -h container modules/datasets.nf | |
| grep -h container modules/datasets.nf | sort | uniq | |
| grep -h container modules/datasets.nf | sort | uniq | awk '{print $2}' | |
| grep -h container modules/datasets.nf | sort | uniq | head -n 1 | awk '{print $2}' | cut -f 2 -d ":" | |
| DATASETS_VER=$(grep -h container modules/datasets.nf \ | |
| | grep datasets \ | |
| | sort \ | |
| | uniq \ | |
| | head -n 1 \ | |
| | awk '{print $2}' \ | |
| | cut -f 2 -d ":" \ | |
| | sed 's/'\''//g') | |
| echo "The datasets version is $DATASETS_VER" | |
| wget https://github.com/ncbi/datasets/releases/download/v${DATASETS_VER}/linux-amd64.cli.package.zip && \ | |
| unzip linux-amd64.cli.package.zip && \ | |
| rm linux-amd64.cli.package.zip && \ | |
| chmod +x dataformat datasets | |
| - name: get accessions | |
| run: | | |
| taxons=("Acinetobacter baumannii", | |
| "Burkholderia cenocepacia", | |
| "Campylobacter jejuni", | |
| "Citrobacter sp", | |
| "Elizabethkingia meningoseptica", | |
| "Escherichia coli", | |
| "Klebsiella oxytoca", | |
| "Legionella pneumophila", | |
| "Pseudomonas sp", | |
| "Raoultella ornithinolytica", | |
| "Salmonella enterica") | |
| for taxon in ${taxons[@]} | |
| do | |
| echo "the taxon is now $taxon" | |
| organism=$(echo $taxon | sed 's/ /_/g') | |
| echo "Getting the representative genome" | |
| ./datasets summary genome taxon "$taxon" --reference --limit 5 --as-json-lines | \ | |
| dataformat tsv genome --fields accession,assminfo-refseq-category,assminfo-level,organism-name,assmstats-total-ungapped-len | \ | |
| grep -v Homo | \ | |
| tr '\\t' ',' \ | |
| | tee ${organism}_genomes.csv | |
| echo "Getting additional genomes" | |
| ./datasets summary genome taxon "$taxon" --limit 5 --as-json-lines | \ | |
| dataformat tsv genome --fields accession,assminfo-refseq-category,assminfo-level,organism-name,assmstats-total-ungapped-len | \ | |
| grep -v Homo | \ | |
| grep -v "Assembly Accession" | \ | |
| tr '\\t' ',' \ | |
| | tee -a ${organism}_genomes.csv | |
| done | |
| head *genomes.csv |