Retrieve GFF3 Paths from Ensembl RR #8
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| name: Retrieve GFF3 Paths from Ensembl RR | |
| on: | |
| schedule: | |
| - cron: '0 0 * * 6' | |
| workflow_dispatch: | |
| jobs: | |
| retrieve-ensembl-rr-gff3: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| - name: Install lftp | |
| run: sudo apt-get update && sudo apt-get install -y lftp | |
| - name: Set Environment Variables | |
| run: | | |
| #ensembl ftp | |
| echo "FTP=ftp.ensembl.org" >> $GITHUB_ENV | |
| echo "FTP_URL=ftp://ftp.ensembl.org" >> $GITHUB_ENV | |
| echo "DIR=/pub/rapid-release/species/" >> $GITHUB_ENV | |
| #tmp files | |
| echo "PATHS=paths.tsv" >> $GITHUB_ENV | |
| echo "EXISTING_ACCESSIONS=existing_accessions.tsv" >> $GITHUB_ENV | |
| echo "DIRS=directories.txt" >> $GITHUB_ENV | |
| echo "SCRAPE=scrape.txt" >> $GITHUB_ENV | |
| #output | |
| echo "OUTPUT=ensembl_rapid_release.tsv" >> $GITHUB_ENV | |
| - name: Get existing Assemblies or Initialize Output File | |
| run: | | |
| output="${{env.OUTPUT}}" | |
| # Initialize the output file for FTP paths if it doesn't exist | |
| if [[ ! -f "$output" ]]; then | |
| echo -e "accession\tfull_path" > "$output" | |
| fi | |
| # Save existing accessions to a file, skipping the header | |
| awk 'NR > 1 {print $1}' "$output" | sort > "${{env.EXISTING_ACCESSIONS}}" | |
| - name: Scrape FTP directory | |
| run: | | |
| # Use lftp to connect to the server and list all files | |
| lftp -c " | |
| set net:timeout 10 | |
| set net:max-retries 3 | |
| open ${{env.FTP}} | |
| cd ${{env.DIR}} | |
| ls -R | |
| quit | |
| " > "${{env.SCRAPE}}" | |
| - name: Filter new GFF3 paths | |
| run: | | |
| # Process the raw output to get only new .gff3.gz files (excluding existing accessions) | |
| awk ' | |
| # When a directory name is printed (ends with a colon), store it | |
| /:$/ {dir=substr($0, 1, length($0)-1); next} | |
| # If the line contains .gff3.gz, print the full path (directory + filename) | |
| /\.gff3\.gz$/ {print dir "/" $NF} | |
| ' "${{env.SCRAPE}}" | grep -vFf "${{env.EXISTING_ACCESSIONS}}" > "${{env.PATHS}}" | |
| rm "${{env.SCRAPE}}" | |
| rm "${{env.EXISTING_ACCESSIONS}}" | |
| # Check if the output file is empty | |
| if [ ! -s "${{env.PATHS}}" ]; then | |
| echo "Any new path found. Exiting.." | |
| exit 0 | |
| fi | |
| - name: Map GFF3 paths to TSV file | |
| run: | | |
| # Map the filtered GFF3 paths to TSV file | |
| awk -F'/' '{ | |
| accession = $3; | |
| https_path = "https://ftp.ensembl.org/pub/rapid-release/species" substr($0, 2); | |
| print accession "\t" https_path | |
| }' "${{env.PATHS}}" >> "${{env.OUTPUT}}" | |
| rm "${{env.PATHS}}" | |
| - name: Commit & Push changes | |
| uses: actions-js/push@master | |
| with: | |
| github_token: ${{ secrets.GITHUB_TOKEN }} |